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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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