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3D structural models and function annotation for all proteins encoded by the genome of SARS-CoV-2

Table I: Structure prediction and structure-based function annotation of SARS-CoV-2 genome.



Protein sequence translated from SARS-CoV-2 genome


1 C-I-TASSER structure model and estimated accuracyProtein name and function (based on UniProt curation of SARS-CoV-2 proteome)Solved experimental structure



1>QHD43415_1 (L=180)

MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLS

EARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRSDARTAP

HGHVMVELVAELEGIQYGRSGETLGVLVPHVGEIPVAYRK

VLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQEN

WNTKHSSGVTRELMRELNGG


Estimate TM-score=0.55 Host translation inhibitor nsp1.

Inhibits host translation by interacting with the 40S ribosomal subunit. The nsp1-40S ribosome complex further induces an endonucleolytic cleavage near the 5'UTR of host mRNAs, targeting them for degradation. Viral mRNAs are not susceptible to nsp1-mediated endonucleolytic RNA cleavage thanks to the presence of a 5'-end leader sequence and are therefore protected from degradation. By suppressing host gene expression, nsp1 facilitates efficient viral gene expression in infected cells and evasion from host immune response.

[GO term predictions] [Ligand binding site predictions] NA(range:NA);




2> QHD43415_2 (L=638)

AYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLD

FIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLA

KKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRI

RSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKAT

CEFCGTENLTKEGATTCGYLPQNAVVKIYCPACHNSEVGP

EHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKC

AYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVN

INIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFK

QIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEA

ARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRL

IDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTV

YEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIV

GGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKL

KALNLGETFVTHSKGLYRKCVKSREETGLLMPLKAPKEII

FLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVG

TPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG








[QHD43415_2.pdb]

Estimate TM-score=0.40 Non-structural protein 2 (nsp2).

May play a role in the modulation of host cell survival signaling pathway by interacting with host PHB and PHB2. Indeed, these two proteins play a role in maintaining the functional integrity of the mitochondria and protecting cells from various stresses.

[GO term predictions] [Ligand binding site predictions] NA(range:NA);




3>QHD43415_3 (L=1945)

APTKVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCS

AYTVELGTEVNEFACVVADAVIKTLQPVSELLTPLGIDLD

EWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEE

EEFEPSTQYEYGTEDDYQGKPLEFGATSAALQPEEEQEED

WLDDDSQQTVGQQDGSEDNQTTTIQTIVEVQPQLEMELTP

VVQTIEVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVV

NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLK

VGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENF

NQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF

DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITES

KPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYID

INGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA

VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYT

VEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREM

LAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY

GARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLN

LEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPE

EHFIETISLAGSYKDWSYSGQSTQLGIEFLKRGDKSVYYT

SNPTTFHLDGEVITFDNLKTLLSLREVRTIKVFTTVDNIN

LHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTF

YVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKY

PQVNGLTSIKWADNNCYLATALLTLQQIELKFNPPALQDA

YYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQH

ANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ

FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKH

GTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSE

YKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEIDPKLDN

YYKKDNSYFTEQPIDLVPNQPYPNASFDNFKFVCDNIKFA

DDLNQLTGYKKPASRELKVTFFPDLNGDVVAIDYKHYTPS

FKKGAKLLHKPIVWHVNNATNKATYKPNTWCIRCLWSTKP

VETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQ

KDVLECNVKTTEVVGDIILKPANNSLKITEEVGHTDLMAA

YVDNSSLTIKKPNELSRVLGLKTLATHGLAAVNSVPWDTI

ANYAKPFLNKVVSTTTNIVTRCLNRVCTNYMPYFFTLLLQ

LCTFTRSTNSRIKASMPTTIAKNTVKSVGKFCLEASFNYL

KSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSNLG

MPSYCTGYREGYLNSTNVTIATYCTGSIPCSVCLSGLDSL

DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFF

YVLGLAAIMQLFFSYFAVHFISNSWLMWLIINLVQMAPIS

AMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRA

TRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTF

CAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKN

GSIHLYFDKAGQKTYERHSLSHFVNLDNLRANNTKGSLPI

NVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVS

DVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEA

ELAKNVSLDNVLSTFISAARQGFVDSDVETKDVVECLKLS

HQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARH

INAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNL

PFKLTCATTRQVVNVVTTKIALKGG






[QHD43415_3.pdb]

Estimate TM-score=0.58 Papain-like proteinase.

Responsible for the cleavages located at the N-terminus of the replicase polyprotein. In addition, PL-PRO possesses a deubiquitinating/deISGylating activity and processes both 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains from cellular substrates. Participates together with nsp4 in the assembly of virally-induced cytoplasmic double-membrane vesicles necessary for viral replication. Antagonizes innate immune induction of type I interferon by blocking the phosphorylation, dimerization and subsequent nuclear translocation of host IRF3. Prevents also host NF-kappa-B signaling.

[GO term predictions] [Ligand binding site predictions] 6W6Y(range:207-379);

6W9C(range:748-1060);


4>QHD43415_4 (L=500)

KIVNNWLKQLIKVTLVFLFVAAIFYLITPVHVMSKHTDFS

SEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQRGG

SYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLH

FLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFK

DASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSIIQ

FPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGR

WVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDI

SASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTL

LFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFL

AHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKR

RVVFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQ

YNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSN

SGSDVLYQPPQTSITSAVLQ






[QHD43415_4.pdb]

Estimate TM-score=0.53 Non-structural protein 4 (nsp4).

Participates in the assembly of virally-induced cytoplasmic double-membrane vesicles necessary for viral replication.

[GO term predictions] [Ligand binding site predictions] NA(range:NA);




5>QHD43415_5 (L=306)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPR

HVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGH

SMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG

SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFC

YMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI

TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE

PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRT

ILGSALLEDEFTPFDVVRQCSGVTFQ




[QHD43415_5.pdb]

Estimate TM-score=0.96 Proteinase 3CL-PRO.

Cleaves the C-terminus of replicase polyprotein at 11 sites. Recognizes substrates containing the core sequence [ILMVF]-Q-|-[SGACN]. Also able to bind an ADP-ribose-1''-phosphate (ADRP).

[GO term predictions] [Ligand binding site predictions] 6LU7(range:1-306);




6>QHD43415_6 (L=290)

SAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYEN

AFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAY

FNMVYMPASWVMRIMTWLDMVDTSLSGFKLKDCVMYASAV

VLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYGNALDQ

AISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIF

FITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLG

VYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKLLGVGG

KPCIKVATVQ






[QHD43415_6.pdb]

Estimate TM-score=0.37 Non-structural protein 6 (nsp6).

Plays a role in the initial induction of autophagosomes from host reticulum endoplasmic. Later, limits the expansion of these phagosomes that are no longer able to deliver viral components to lysosomes.

[GO term predictions] [Ligand binding site predictions] NA(range:NA);






7>QHD43415_7 (L=83)

SKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDIL

LAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRA

TLQ





[QHD43415_7.pdb]

Estimate TM-score=0.63 Non-structural protein 7 (nsp7).

Forms a hexadecamer with nsp8 (8 subunits of each) that may participate in viral replication by acting as a primase. Alternatively, may synthesize substantially longer products than oligonucleotide primers.

[GO term predictions] [Ligand binding site predictions] 6M71(range:1-83);





8>QHD43415_8 (L=198)

AIASEFSSLPSYAAFATAQEAYEQAVANGDSEVVLKKLKK

SLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKR

AKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNII

PLTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVV

DADSKIVQLSEISMDNSPNLAWPLIVTALRANSAVKLQ



[QHD43415_8.pdb]

Estimate TM-score=0.88 Non-structural protein 8 (nsp8).

Forms a hexadecamer with nsp7 (8 subunits of each) that may participate in viral replication by acting as a primase. Alternatively, may synthesize substantially longer products than oligonucleotide primers.

[GO term predictions] [Ligand binding site predictions] 6M71(range:84-132);






9>QHD43415_9 (L=113)

NNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRF

VLALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTP

KGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQ



[QHD43415_9.pdb]

Estimate TM-score=0.93 Non-structural protein 9 (nsp9).

May participate in viral replication by acting as a ssRNA-binding protein.

[GO term predictions] [Ligand binding site predictions] 6W4B(range:1-113);




10>QHD43415_10 (L=139)

AGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITN

CVKMLCTHTGTGQAITVTPEANMDQESFGGASCCLYCRCH

IDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVC

GMWKGYGCSCDQLREPMLQ




[QHD43415_10.pdb]

Estimate TM-score=0.90 Non-structural protein 10 (nsp10).

Plays a pivotal role in viral transcription by stimulating both nsp14 3'-5' exoribonuclease and nsp16 2'-O-methyltransferase activities. Therefore plays an essential role in viral mRNAs cap methylation.

[GO term predictions] [Ligand binding site predictions] 6W75(range:1-139);




11>QHD43415_11 (L=932)

SADAQSFLNRVCGVSAARLTPCGTGTSTDVVYRAFDIYND

KVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNY

QHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLT

KYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKK

DWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAG

IVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSL

LMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERL

KLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTV

FPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVN

LHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAA

LTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHF

FFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYF

DCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMS

YEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGV

SICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHN

MLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLAR

KHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGT

SSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYV

RNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSD

DAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCW

TETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGA

GCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADV

FHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEF

YEAMYTPHTVLQ


[QHD43415_11.pdb]

Estimate TM-score=0.80 RNA-directed RNA polymerase (RdRp).

Responsible for replication and transcription of the viral RNA genome.

[GO term predictions] [Ligand binding site predictions] 6M71(range:1-932);




12>QHD43415_12 (L=601)

AVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHK

LVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSHKPPIS

FPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDY

ILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSD

RELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQIGEYTF

EKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTL

VPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTL

QGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVDALCEK

ALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTV

NALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIG

DPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPDMFLGT

CRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVI

THDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNA

VASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHSCNVNR

FNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQ





[QHD43415_12.pdb]

Estimate TM-score=0.99 Helicase (Hel).

Multi-functional protein with a zinc-binding domain in N-terminus displaying RNA and DNA duplex-unwinding activities with 5' to 3' polarity. Activity of helicase is dependent on magnesium.

[GO term predictions] [Ligand binding site predictions] NA(range:NA);




13>QHD43415_13 (L=527)

AENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCV

DIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFITREEAI

RHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAV

PTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWN

VVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTSMKYFVK

IGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPF

MIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCL

AVHECFVKRVDWTIEYPIIGDELKINAACRKVQHMVVKAA

LLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKA

YKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCR

FDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKSAFVNLK

QLPFFYYSDSPCESHGKQVVSDIDYVPLKSATCITRCNLG

GAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLW

NTFTRLQ




[QHD43415_13.pdb]

Estimate TM-score=0.99 Proofreading exoribonuclease / Guanine-N7 methyltransferase (ExoN).

Enzyme possessing two different activities: an exoribonuclease activity acting on both ssRNA and dsRNA in a 3' to 5' direction and a N7-guanine methyltransferase activity. Acts as a proofreading exoribonuclease for RNA replication, thereby lowering the sensitivity of the virus to RNA mutagens.

[GO term predictions] [Ligand binding site predictions] NA(range:NA);






14>QHD43415_14 (L=346)

SLENVAFNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDV

ELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIA

ANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLT

VFFDGRVDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQA

SLNGVTLIGEAVKTQFNYYKKVDGVVQQLPETYFTQSRNL

QEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDF

SHSQLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFI

TDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKV

TIDYTEISFMLWCKDGHVETFYPKLQ





[QHD43415_14.pdb]

Estimate TM-score=0.99 Uridylate-specific endoribonuclease (NendoU).

Mn(2+)-dependent, uridylate-specific enzyme, which leaves 2'-3'-cyclic phosphates 5' to the cleaved bond.

[GO term predictions] [Ligand binding site predictions] 6VWW(range:1-346);






15>QHD43415_15 (L=298)

SSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLPKGI

MMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAP

GTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHT

ANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFIQQK

LALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNAS

SSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLS

SYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSKGRL

IIRENNRVVISSDVLVNN




[QHD43415_15.pdb]

Estimate TM-score=0.99 2'-O-methyltransferase (2'-O-MT).

Methyltransferase that mediates mRNA cap 2'-O-ribose methylation to the 5'-cap structure of viral mRNAs. N7-methyl guanosine cap is a prerequisite for binding of nsp16. Therefore plays an essential role in viral mRNAs cap methylation which is essential to evade immune system.

[GO term predictions] [Ligand binding site predictions] 6W75(range:1-298);






16>QHD43416 (L=1273)

MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPD

KVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFD

NPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIV

NNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVY

SSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGY

FKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQT

LLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYN

ENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRV

QPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISN

CVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSF

VIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNN

LDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPC

NGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHA

PATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFL

PFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITP

GTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGS

NVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNS

PRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTI

SVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFC

TQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGF

NFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDC

LGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAG

TITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQ

KLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALN

TLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGR

LQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRV

DFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPA

ICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNT

FVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHT

SPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDL

QELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSC

CSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT







[QHD43416.pdb]

Estimate TM-score=0.84 Spike glycoprotein (S).

  • Spike protein S1 (residue 13-685): attaches the virion to the cell membrane by interacting with host receptor, initiating the infection. Binding to human ACE2 receptor and internalization of the virus into the endosomes of the host cell induces conformational changes in the Spike glycoprotein (PubMed:32142651, PubMed:32075877, PubMed:32155444). Uses also human TMPRSS2 for priming in human lung cells which is an essential step for viral entry (PubMed:32142651). Proteolysis by cathepsin CTSL may unmask the fusion peptide of S2 and activate membranes fusion within endosomes

  • Spike protein S2 (residue 686-1273): mediates fusion of the virion and cellular membranes by acting as a class I viral fusion protein. Under the current model, the protein has at least three conformational states: pre-fusion native state, pre-hairpin intermediate state, and post-fusion hairpin state. During viral and target cell membrane fusion, the coiled coil regions (heptad repeats) assume a trimer-of-hairpins structure, positioning the fusion peptide in close proximity to the C-terminal region of the ectodomain. The formation of this structure appears to drive apposition and subsequent fusion of viral and target cell membranes.

  • Spike protein S2' (residue 816-1273): acts as a viral fusion peptide which is unmasked following S2 cleavage occurring upon virus endocytosis.


[GO term predictions] [Ligand binding site predictions] 6VYB (open state)(range:1-1273);

6VXX (closed state)(range:1-1273);

6LXT(range:912-988,1164-1202);





17>QHD43417 (L=275)

MDLFMRIFTIGTVTLKQGEIKDATPSDFVRATATIPIQAS

LPFGWLIVGVALLAVFQSASKIITLKKRWQLALSKGVHFV

CNLLLLFVTVYSHLLLVAAGLEAPFLYLYALVYFLQSINF

VRIIMRLWLCWKCRSKNPLLYDANYFLCWHTNCYDYCIPY

NSVTSSIVITSGDGTTSPISEHDYQIGGYTEKWESGVKDC

VVLHSYFTSDYYQLYSTQLSTDTGVEHVTFFIYNKIVDEP

EEHVQIHTIDGSSGVVNPVMEPIYDEPTTTTSVPL





[QHD43417.pdb]

Estimate TM-score=0.28 ORF3a.

Forms homotetrameric potassium sensitive ion channels (viroporin) and may modulate virus release. Up-regulates expression of fibrinogen subunits FGA, FGB and FGG in host lung epithelial cells. Induces apoptosis in cell culture. Downregulates the type 1 interferon receptor by inducing serine phosphorylation within the IFN alpha-receptor subunit 1 (IFNAR1) degradation motif and increasing IFNAR1 ubiquitination

[GO term predictions] [Ligand binding site predictions] NA(range:NA);





18>QHD43418 (L=75)

MYSFVSEETGTLIVNSVLLFLAFVVFLLVTLAILTALRLC

AYCCNIVNVSLVKPSFYVYSRVKNLNSSRVPDLLV




[QHD43418.pdb]

Estimate TM-score=0.60 E.

Plays a central role in virus morphogenesis and assembly. Acts as a viroporin and self-assembles in host membranes forming pentameric protein-lipid pores that allow ion transport. Also plays a role in the induction of apoptosis. Activates the host NLRP3 inflammasome, leading to IL-1beta overproduction.

[GO term predictions] [Ligand binding site predictions] NA(range:NA);






19>QHD43419 (L=222)

MADSNGTITVEELKKLLEQWNLVIGFLFLTWICLLQFAYA

NRNRFLYIIKLIFLWLLWPVTLACFVLAAVYRINWITGGI

AIAMACLVGLMWLSYFIASFRLFARTRSMWSFNPETNILL

NVPLHGTILTRPLLESELVIGAVILRGHLRIAGHHLGRCD

IKDLPKEITVATSRTLSYYKLGASQRVAGDSGFAAYSRYR

IGNYKLNTDHSSSSDNIALLVQ





[QHD43419.pdb]

Estimate TM-score=0.37 M.

Component of the viral envelope that plays a central role in virus morphogenesis and assembly via its interactions with other viral proteins.

[GO term predictions] [Ligand binding site predictions] NA(range:NA);





20>QHD43420 (L=61)

MFHLVDFQVTIAEILLIIMRTFKVSIWNLDYIINLIIKNL

SKSLTENKYSQLDEEQPMEID



[QHD43420.pdb]

Estimate TM-score=0.54 ORF6.

Disrupts cell nuclear import complex formation by tethering karyopherin alpha 2 and karyopherin beta 1 to the membrane. Retention of import factors at the ER/Golgi membrane leads to a loss of transport into the nucleus. Thereby prevents STAT1 nuclear translocation in response to interferon signaling, thus blocking the expression of interferon stimulated genes (ISGs) that display multiple antiviral activities.

[GO term predictions] [Ligand binding site predictions] NA(range:NA);

21>QHD43421 (L=121)

MKIILFLALITLATCELYHYQECVRGTTVLLKEPCSSGTY

EGNSPFHPLADNKFALTCFSTQFAFACPDGVKHVYQLRAR

SVSPKLFIRQEEVQELYSPIFLIVAAIVFITLCFTLKRKTE



[QHD43421.pdb]

Estimate TM-score=0.72 ORF7a.

Non-structural protein which is dispensable for virus replication in cell culture.

[GO term predictions] [Ligand binding site predictions] NA(range:NA);





22>QHD43422 (L=121)

MKFLVFLGIITTVAAFHQECSLQSCTQHQPYVVDDPCPIH

FYSKWYIRVGARKSAPLIELCVDEAGSKSPIQYIDIGNYT

VSCLPFTINCQEPKLGSLVVRCSFYEDFLEYHDVRVVLDFI



[QHD43422.pdb]

Estimate TM-score=0.45 ORF8.

May play a role in host-virus interaction. Similar to some Bat coronavirus ns8 genes, but is entirely different from SARS ns8a or ns8b.

[GO term predictions] [Ligand binding site predictions] NA(range:NA);





23>QHD43423 (L=419)

MSDNGPQNQRNAPRITFGGPSDSTGSNQNGERSGARSKQR

RPQGLPNNTASWFTALTQHGKEDLKFPRGQGVPINTNSSP

DDQIGYYRRATRRIRGGDGKMKDLSPRWYFYYLGTGPEAG

LPYGANKDGIIWVATEGALNTPKDHIGTRNPANNAAIVLQ

LPQGTTLPKGFYAEGSRGGSQASSRSSSRSRNSSRNSTPG

SSRGTSPARMAGNGGDAALALLLLDRLNQLESKMSGKGQQ

QQGQTVTKKSAAEASKKPRQKRTATKAYNVTQAFGRRGPE

QTQGNFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSRI

GMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAY

KTFPPTEPKKDKKKKADETQALPQRQKKQQTVTLLPAADL

DDFSKQLQQSMSSADSTQA




[QHD43423.pdb]

Estimate TM-score=0.67 N.

Packages the positive strand viral genome RNA into a helical ribonucleocapsid (RNP) and plays a fundamental role during virion assembly through its interactions with the viral genome and membrane protein M. Plays an important role in enhancing the efficiency of subgenomic viral RNA transcription as well as viral replication.

[GO term predictions] [Ligand binding site predictions] 6M3M(range:50-174);





24>QHI42199 (L=38)

MGYINVFAFPFTIYSLLLCRMNSRNYIAQVDVVNFNLT




[QHI42199.pdb]

Estimate TM-score=0.49 ORF10.

Dubious/uncertain protein. It is currently unclear whether this region translates into a functional protein. The respective region in related beta-coronaviruses, such as SARS-CoV, does not correspond to translated peptide.

[GO term predictions] [Ligand binding site predictions] NA(range:NA);







Ref Credit and Source of Information : University of Michigan

Reference:

  • Chengxin Zhang, Wei Zheng, Xiaoqiang Huang, Eric W. Bell, Xiaogen Zhou, Yang Zhang (2020) Protein structure and sequence re-analysis of 2019-nCoV genome refutes snakes as its intermediate host and the unique similarity between its spike protein insertions and HIV-1. Journal of Proteome Research. 19: 1351-1360, 2020 [SI] [Manis-CoV sequence]

  • Xiaoqiang Huang, Robin Pearcs, Yang Zhang. Computational Design of Peptides to Block Binding of the SARS-CoV-2 Spike Protein to Human ACE2. BioRxiv Prinprint doi: https://doi.org/10.1101/2020.03.28.013607


For more details Study

https://zhanglab.ccmb.med.umich.edu/COVID-19/

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