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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