9FYX
Influenza a/h7n9 polymerase pre-cleavage cap-snatching complex
PDB DOI: 10.2210/pdb9fyx/pdb
Classification: VIRUS Organism(s): Homo Sapiens , Influenza A Virus (A/Zhejiang/Dtid-Zju01/2013(H7N9)) , Sus Scrofa Domesticus , Synthetic Construct
Deposited: 2024-07-04 Deposition Author(s): Cramer, P. , Cusack, S. , Dienemann, C. , Li, D. , Rotsch, A.H.
Experimental Data Snapshot
Method: ELECTRON MICROSCOPY Resolution: 3.3 Å
Influenza a/h7n9 polymerase pre-cleavage cap-snatching complex
Cramer, P. , Cusack, S. , Dienemann, C. , Li, D. , Rotsch, A.H.
Primary Citation of Related Structures: 9FYX
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| RNA polymerase II subunit D | D | 184 | Homo Sapiens , Influenza A Virus (A/Zhejiang/Dtid-Zju01/2013(H7N9)) , Sus Scrofa Domesticus , Synthetic Construct | MWGPAQPYSDSALSPKPRPFRAVFRGSALPFPAVRVEVRGRSMAAGGSDPRAGDVEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFMKTLNYTARFSRFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGRFEDEELQQILDDIQTKRSFQY |
| Transcription elongation factor SPT4 | Y | 117 | Homo Sapiens , Influenza A Virus (A/Zhejiang/Dtid-Zju01/2013(H7N9)) , Sus Scrofa Domesticus , Synthetic Construct | MALETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGIIAMMSPEDSWVSKWQRVSNFKPGVYAVSVTGRLPQGIVRELKSRGVAYKSRDTAIKT |
| Transcription elongation factor SPT5 | Z | 1087 | Homo Sapiens , Influenza A Virus (A/Zhejiang/Dtid-Zju01/2013(H7N9)) , Sus Scrofa Domesticus , Synthetic Construct | MSDSEDSNFSEEEDSERSSDGEEAEVDEERRSAAGSEKEEEPEDEEEEEEEEEYDEEEEEEDDDRPPKKPRHGGFILDEADVDDEYEDEDQWEDGAEDILEKEEIEASNIDNVVLDEDRSGARRLQNLWRDQREEELGEYYMKKYAKSSVGETVYGGSDELSDDITQQQLLPGVKDPNLWTVKCKIGEERATAISLMRKFIAYQFTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNLRLGYWNQQMVPIKEMTDVLKVVKEVANLKPKSWVRLKRGIYKDDIAQVDYVEPSQNTISLKMIPRIDYDRIKARMSLKDWFAKRKKFKRPPQRLFDAEKIRSLGGDVASDGDFLIFEGNRYSRKGFLFKSFAMSAVITEGVKPTLSELEKFEDQPEGIDLEVVTESTGKEREHNFQPGDNVEVCEGELINLQGKILSVDGNKITIMPKHEDLKDMLEFPAQELRKYFKMGDHVKVIAGRFEGDTGLIVRVEENFVILFSDLTMHELKVLPRDLQLCSETASGVDVGGQHEWGELVQLDPQTVGVIVRLERETFQVLNMYGKVVTVRHQAVTRKKDNRFAVALDSEQNNIHVKDIVKVIDGPHSGREGEIRHLFRSFAFLHCKKLVENGGMFVCKTRHLVLAGGSKPRDVTNFTVGGFAPMSPRISSPMHPSAGGQRGGFGSPGGGSGGMSRGRGRRDNELIGQTVRISQGPYKGYIGVVKDATESTARVELHSTCQTISVDRQRLTTVGSRRPGGMTSTYGRTPMYGSQTPMYGSGSRTPMYGSQTPLQDGSRTPHYGSQTPLHDGSRTPAQSGAWDPNNPNTPSRAEEEYEYAFDDEPTPSPQAYGGTPNPQTPGYPDPSSPQVNPQYNPQTPGTPAMYNTDQFSPYAAPSPQGSYQPSPSPQSYHQVAPSPAGYQNTHSPASYHPTPSPMAYQASPSPSPVGYSPMTPGAPSPGGYNPHTPGSGIEQNSSDWVTTDIQVKVRDTYLDTQVVGQTGVIRSVTGGMCSVYLKDSEKVVSISSEHLEPITPTKNNKVKVILGEDREATGVLLSIDGEDGIVRMDLDEQLKILNLRFLGKLLEA |
| Polymerase acidic protein | A | 717 | Homo Sapiens , Influenza A Virus (A/Zhejiang/Dtid-Zju01/2013(H7N9)) , Sus Scrofa Domesticus , Synthetic Construct | GMEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFASICTHLEVCFMYSDFHFIDERGESTIIESGDPNVLLKHRFEIIEGRDRTMAWTVVNSICNTTGVEKPKFLPDLYDYKENRFIDIGVTRREVHIYYLEKANKIKSEKTHIHIFSFTGEEMATKADYTLDEESRARIKTRLFTIRQEMASRGLWDSFRQSERGEETIEERFEITGTMRRLADQSLPPNFSSLENFRAYVDGFEPNGCIEGKLSQMSKEVNARIEPFLRTTPRPLRLPDGPPCSQRSKFLLMDALKLSIEDPSHEGEGIPLYDAIKCMKTFFGWKEPNIIKPHEKGINPNYLLTWKQVLAELQDIENEEKIPRTKNMKKTSQLKWALGENMAPEKVDFEDCKDVNDLKQYDSDEPEPRSLACWIQSEFNKACELTDSSWVELDEIGEDVAPIEHIASMRRNYFTAEVSHCRATEYIMKGVYINTALLNASCAAMDDFQLIPMISKCRTKEGRRKTNLYGFIIKGRSHLRNDTDVVNFVSMEFSLTDPRLEPHKWEKYCVLEIGDMLLRTAVGQVSRPMFLYVRTNGTSKIKMKWGMEMRRCLLQSLQQIESMIEAESSVKEKDLTKEFFENKSETWPIGESPKGVEEGSIGKVCRTLLAKSVFNSLYASPQLEGFSAESRKLLLIVQALRDNLEPGTFDLEGLYEAIEECLINDPWVLLNASWFNSFLTHALR |
| RNA-directed RNA polymerase catalytic subunit | B | 757 | Homo Sapiens , Influenza A Virus (A/Zhejiang/Dtid-Zju01/2013(H7N9)) , Sus Scrofa Domesticus , Synthetic Construct | MDVNPTLLFLKVPVQNAISTTFPYTGDPPYSHGTGTGYTMDTVNRTHKYSEKGKWTTNTETGAPQLNPIDGPLPEDNEPSGYAQTDCVLEAMAFLEESHPGIFENSCLETMEIVQQTRVDKLTQGRQTYDWTLNRNQPAATALANTIEVFRSNGLTANESGRLIDFLKDVMDSMDKEEMEITTHFQRKRRVRDNMTKKMVTQRTIGKKKQRLNKRSYLIRALTLNTMTKDAERGKLKRRAIATPGMQIRGFVYFVEALARSICEKLEQSGLPVGGNEKKAKLANVVRKMMTNSQDTELSFTITGDNTKWNENQNPRMFLAMITYITRNQPEWFRNVLSIAPIMFSNKMARLGKGYMFESKSMKLRTQVPAEMLANIDLKYFNKSTREKIEKIRPLLIDGTASLSPGMMMGMFNMLSTVLGVSILNLGQKKYTKTTYWWDGLQSSDDFALIVNAPNHEGIQAGVDRFYRTCKLVGINMSKKKSYINRTGTFEFTSFFYRYGFVANFSMELPSFGVSGINESADMSVGVTVIKNNMINNDLGPATAQMALQLFIKDYRYTYRCHRGDTQIQTRRAFELKKLWEQTRSKAGLLVSDGGPNLYNIRNLHIPEVCLKWELMDEDYQGRLCNPMNPFVSHKEIDSVNNAVVMPAHGPAKSMEYDAVATTHSWIPKRNRSILNTSQRGILEDEQMYQKCCNLFEKFFPSSSYRRPVGISSMVEAMVSRARIDARIDFESGRIKKEEFAEIMKICSTIEELRRQK |
| Polymerase basic protein 2 | C | 759 | Homo Sapiens , Influenza A Virus (A/Zhejiang/Dtid-Zju01/2013(H7N9)) , Sus Scrofa Domesticus , Synthetic Construct | MERIKELRDLMSQSRTREILTKTTVDHMAIIKKYTSGRQEKNPALRMKWMMAMKYPITADKRIMEMIPERNEQGQTLWSKTNDAGSDRVMVSPLAVTWWNRNGPTTSTVHYPKVYKTYFEKVERLKHGTFGPVHFRNQVKIRRRVDINPGHADLSAKEAQDVIMEVVFPNEVGARILTSESQLTITKEKKKELQDCKIAPLMVAYMLERELVRKTRFLPVAGGTSSVYIEVLHLTQGTCWEQMYTPGGEVRNDDVDQSLIIAARNIVRRATVSADPLASLLEMCHSTQIGGVRMVDILRQNPTEEQAVDICKAAMGLRISSSFSFGGFTFKRTSGSSVKREEEVLTGNLQTLKIRVHEGYEEFTMVGRRATAILRKATRRLIQLIVSGKDEQSIAEAIIVAMVFSQEDCMIKAVRGDLNFVNRANQRLNPMHQLLRHFQKDAKVLFQNWGIEPIDNVMGMIGILPDMTPSTEMSLRGVRVSKMGVDEYSSTERVVVSIDRFLRVRDQRGNVLLSPEEVSETQGTEKLTITYSSSMMWEINGPESVLVNTYQWIIRNWENVKIQWSQDPTMLYNKMEFEPFQSLVPKAARGQYSGFVRVLFQQMRDVLGTFDTVQIIKLLPFAAAPPEQSRMQFSSLTVNVRGSGMRIVVRGNSPVFNYNKATKRLTVLGKDAGALMEDPDEGTAGVESAVLRGFLILGKENKRYGPALSINELSNLAKGEKANVLIGQGDVVLVMKRKRDSSILTDSQTATKRIRMAIN |
| DNA-directed RNA polymerase II subunit E | E | 210 | Homo Sapiens , Influenza A Virus (A/Zhejiang/Dtid-Zju01/2013(H7N9)) , Sus Scrofa Domesticus , Synthetic Construct | MDDEEETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTVLVAHNDDPTDQMFVFFPEEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAPKYILEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRENQLPRIQAGDPVARYFGIKRGQVVKIIRPSETAGRYITYRLVQ |
| Likely SPT5 KOWx4-KOW5 linker, register unclear | X | 17 | Homo Sapiens , Influenza A Virus (A/Zhejiang/Dtid-Zju01/2013(H7N9)) , Sus Scrofa Domesticus , Synthetic Construct | AAAAAFAAAGAAAAAAA |
| DNA-directed RNA polymerases I, II, and III subunit RPABC2 | F | 127 | Homo Sapiens , Influenza A Virus (A/Zhejiang/Dtid-Zju01/2013(H7N9)) , Sus Scrofa Domesticus , Synthetic Construct | MSDNEDNFDGDDFDDVEEDEGLDDLENAEEEGQENVEILPSGERPQANQKRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGVDELIISD |
| DNA-directed RNA polymerase subunit | G | 171 | Homo Sapiens , Influenza A Virus (A/Zhejiang/Dtid-Zju01/2013(H7N9)) , Sus Scrofa Domesticus , Synthetic Construct | MFYHISLEHEILLHPRYFGPNLLNTVKQKLFTEVEGTCTGKYGFVIAVTTIDNIGAGVIQPGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKNDIFAIGSLMDDYLGLV |
| DNA-directed RNA polymerases I, II, and III subunit RPABC3 | H | 150 | Homo Sapiens , Influenza A Virus (A/Zhejiang/Dtid-Zju01/2013(H7N9)) , Sus Scrofa Domesticus , Synthetic Construct | MAGILFEDIFDVKDIDPEGKKFDRVSRLHCESESFKMDLILDVNIQIYPVDLGDKFRLVIASTLYEDGTLDDGEYNPTDDRPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAYVSYGGLLMRLQGDANNLHGFEVDSRVYLLMKKLAF |
| DNA-directed RNA polymerase II subunit RPB9 | I | 125 | Homo Sapiens , Influenza A Virus (A/Zhejiang/Dtid-Zju01/2013(H7N9)) , Sus Scrofa Domesticus , Synthetic Construct | MEPDGTYEPGFVGIRFCQECNNMLYPKEDKENRILLYACRNCDYQQEADNSCIYVNKITHEVDELTQIIADVSQDPTLPRTEDHPCQKCGHKEAVFFQSHSARAEDAMRLYYVCTAPHCGHRWTE |
| DNA-directed RNA polymerases I, II, and III subunit RPABC5 | J | 67 | Homo Sapiens , Influenza A Virus (A/Zhejiang/Dtid-Zju01/2013(H7N9)) , Sus Scrofa Domesticus , Synthetic Construct | MIIPVRCFTCGKIVGNKWEAYLGLLQAEYTEGDALDALGLKRYCCRRMLLAHVDLIEKLLNYAPLEK |
| DNA-directed RNA polymerase II subunit RPB11-a | K | 117 | Homo Sapiens , Influenza A Virus (A/Zhejiang/Dtid-Zju01/2013(H7N9)) , Sus Scrofa Domesticus , Synthetic Construct | MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAGYKVPHPLEHKIIIRVQTTPDYSPQEAFTNAITDLISELSLLEERFRVAIKDKQEGIE |
| RNA polymerase II, I and III subunit K | L | 58 | Homo Sapiens , Influenza A Virus (A/Zhejiang/Dtid-Zju01/2013(H7N9)) , Sus Scrofa Domesticus , Synthetic Construct | MDTQKDVQPPKQQPMIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR |
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| non-template DNA (43-mer) | n | 43 | NA | GGCAGTACTAGTATTCTAGTATTGAAAGTACTTGAGCTTGATC |
| cap(1)-RNA (35-MER) | p | 35 | NA | GAAGCGAGAAGAACACAGACAGCAGAAGACCAGGC |
| Template DNA (43-MER) | t | 43 | NA | GATCAAGCTCAAGTACTTAAGCCTGGTCTATACTAGTACTGCC |
| 3' vRNA | r | 13 | NA | CUCUGCUUCUGCU |
| 5'-vRNA | v | 14 | NA | AGUAGUAACAAGAG |
Experimental Data
Method: ELECTRON MICROSCOPY
Deposited Date: 2024-07-04 Deposition Author(s): Cramer, P. , Cusack, S. , Dienemann, C. , Li, D. , Rotsch, A.H.