9FYX | pdb_00009fyx

Influenza A/H7N9 polymerase pre-cleavage cap-snatching complex

PDB DOI: https://doi.org/10.2210/pdb9FYX/pdb
NAKB: 9FYX
EM Map EMD-50892: EMDB EMDataResource

Classification: VIRUS
Organism(s): Sus scrofa domesticus, synthetic construct, Influenza B virus, Homo sapiens, Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))
Expression System: Escherichia coli, Trichoplusia ni
Mutation(s): Yes

Deposited: 2024-07-04 Released: 2025-07-16
Deposition Author(s): Rotsch, A.H., Li, D., Dienemann, C., Cusack, S., Cramer, P.
Funding Organization(s): German Research Foundation (DFG), European Research Council (ERC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Mechanism of Co-Transcriptional Cap-Snatching by Influenza Polymerase

Rotsch, A.H., Li, D., Dupont, M., Krischuns, T., Oberthuer, C., Stelfox, A., Lukarska, M., Fianu, I., Lidschreiber, M., Naffakh, N., Dienemann, C., Cusack, S., Cramer, P.

To be published.

Macromolecule Content

Total Structure Weight: 925.2 kDa
Atom Count: 56,176
Modeled Residue Count: 6,812
Deposited Residue Count: 7,887
Unique protein chains: 18
Unique nucleic acid chains: 5

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase II subunit D	A [auth D]	184	Sus scrofa domesticus	Mutation(s): 0
UniProt
Find proteins for A0A287ADR4 (Sus scrofa) Explore A0A287ADR4 Go to UniProtKB: A0A287ADR4
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A287ADR4
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit E	B [auth E]	210	Sus scrofa domesticus	Mutation(s): 0
UniProt
Find proteins for I3LSI7 (Sus scrofa) Explore I3LSI7 Go to UniProtKB: I3LSI7
Entity Groups
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UniProt Group	I3LSI7
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC2	C [auth F]	127	Sus scrofa domesticus	Mutation(s): 0
UniProt
Find proteins for A0A4X1VEK9 (Sus scrofa) Explore A0A4X1VEK9 Go to UniProtKB: A0A4X1VEK9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A4X1VEK9
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit	D [auth G]	171	Sus scrofa domesticus	Mutation(s): 0
UniProt
Find proteins for A0A4X1VKG7 (Sus scrofa) Explore A0A4X1VKG7 Go to UniProtKB: A0A4X1VKG7
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UniProt Group	A0A4X1VKG7
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC3	E [auth H]	150	Sus scrofa domesticus	Mutation(s): 0
UniProt
Find proteins for I3LCB2 (Sus scrofa) Explore I3LCB2 Go to UniProtKB: I3LCB2
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UniProt Group	I3LCB2
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB9	F [auth I]	125	Sus scrofa domesticus	Mutation(s): 0
UniProt
Find proteins for P60899 (Sus scrofa) Explore P60899 Go to UniProtKB: P60899
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UniProt Group	P60899
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC5	G [auth J]	67	Sus scrofa domesticus	Mutation(s): 0
UniProt
Find proteins for A0A4X1VYD0 (Sus scrofa) Explore A0A4X1VYD0 Go to UniProtKB: A0A4X1VYD0
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UniProt Group	A0A4X1VYD0
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB11-a	H [auth K]	117	Sus scrofa domesticus	Mutation(s): 0
UniProt
Find proteins for F1RKE4 (Sus scrofa) Explore F1RKE4 Go to UniProtKB: F1RKE4
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UniProt Group	F1RKE4
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase II, I and III subunit K	I [auth L]	58	Sus scrofa domesticus	Mutation(s): 0
UniProt
Find proteins for A0A4X1TRS6 (Sus scrofa) Explore A0A4X1TRS6 Go to UniProtKB: A0A4X1TRS6
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UniProt Group	A0A4X1TRS6
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription elongation factor SPT4	M [auth Y]	117	Homo sapiens	Mutation(s): 0 Gene Names: SUPT4H1, SPT4H, SUPT4H
UniProt & NIH Common Fund Data Resources
Find proteins for P63272 (Homo sapiens) Explore P63272 Go to UniProtKB: P63272
PHAROS: P63272 GTEx: ENSG00000213246
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UniProt Group	P63272
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription elongation factor SPT5	N [auth Z]	1,087	Homo sapiens	Mutation(s): 0 Gene Names: SUPT5H, SPT5, SPT5H
UniProt & NIH Common Fund Data Resources
Find proteins for O00267 (Homo sapiens) Explore O00267 Go to UniProtKB: O00267
PHAROS: O00267 GTEx: ENSG00000196235
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UniProt Group	O00267
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Reference Sequence

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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit	O [auth A]	1,641	Sus scrofa domesticus	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for I3LJR4 (Sus scrofa) Explore I3LJR4 Go to UniProtKB: I3LJR4
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UniProt Group	I3LJR4
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Reference Sequence

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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta	P [auth B]	1,160	Sus scrofa domesticus	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for A0A0B8RVL1 (Sus scrofa domesticus) Explore A0A0B8RVL1 Go to UniProtKB: A0A0B8RVL1
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UniProt Group	A0A0B8RVL1
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Reference Sequence

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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB3	Q [auth C]	275	Sus scrofa domesticus	Mutation(s): 0
UniProt
Find proteins for I3LCH3 (Sus scrofa) Explore I3LCH3 Go to UniProtKB: I3LCH3
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UniProt Group	I3LCH3
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Reference Sequence

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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Polymerase acidic protein	R [auth a]	717	Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))	Mutation(s): 1 Gene Names: PA EC: 3.1
UniProt
Find proteins for M9TI86 (Influenza A virus) Explore M9TI86 Go to UniProtKB: M9TI86
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UniProt Group	M9TI86
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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-directed RNA polymerase catalytic subunit	S [auth b]	757	Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))	Mutation(s): 0 Gene Names: PB1 EC: 2.7.7.48
UniProt
Find proteins for M9TLW3 (Influenza A virus) Explore M9TLW3 Go to UniProtKB: M9TLW3
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UniProt Group	M9TLW3
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Reference Sequence

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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Polymerase basic protein 2	T [auth c]	759	Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))	Mutation(s): 0 Gene Names: PB2
UniProt
Find proteins for X5F427 (Influenza A virus) Explore X5F427 Go to UniProtKB: X5F427
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UniProt Group	X5F427
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Reference Sequence

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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
Likely SPT5 KOWx4-KOW5 linker, register unclear	W [auth X]	17	Homo sapiens	Mutation(s): 0
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Length	Organism	Image
non-template DNA (43-mer)	J [auth N]	43	synthetic construct
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Entity ID: 11
Molecule	Chains	Length	Organism	Image
cap(1)-RNA (35-MER)	K [auth P]	35	Influenza B virus
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Entity ID: 12
Molecule	Chains	Length	Organism	Image
Template DNA (43-MER)	L [auth T]	43	synthetic construct
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Entity ID: 21
Molecule	Chains	Length	Organism	Image
3' vRNA	U [auth r]	13	Influenza B virus
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Entity ID: 22
Molecule	Chains	Length	Organism	Image
5'-vRNA	V [auth v]	14	Influenza B virus
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Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
G1G (Subject of Investigation/LOI) Query on G1G Download Ideal Coordinates CCD File SDF format, chain BA [auth P] MOL2 format, chain BA [auth P] mmCIF format, chain BA [auth P]	BA [auth P]	7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-(2'-O-METHYL)-GUANOSINE C₂₂ H₃₂ N₁₀ O₁₈ P₃ CUWKXCJRSKNYSN-XPWFQUROSA-O		Interactions Focus chain BA [auth P] Interactions & Density Focus chain BA [auth P]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain JA [auth a] SDF format, chain KA [auth c] MOL2 format, chain JA [auth a] MOL2 format, chain KA [auth c] mmCIF format, chain JA [auth a] mmCIF format, chain KA [auth c]	JA [auth a], KA [auth c]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain JA [auth a] Focus chain KA [auth c] Interactions & Density Focus chain JA [auth a] Focus chain KA [auth c]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain AA [auth L] SDF format, chain CA [auth Y] SDF format, chain DA [auth A] SDF format, chain Z [auth J] SDF format, chain Y [auth I] SDF format, chain X [auth I] SDF format, chain HA [auth C] SDF format, chain GA [auth B] SDF format, chain EA [auth A] MOL2 format, chain AA [auth L] MOL2 format, chain CA [auth Y] MOL2 format, chain DA [auth A] MOL2 format, chain Z [auth J] MOL2 format, chain Y [auth I] MOL2 format, chain X [auth I] MOL2 format, chain HA [auth C] MOL2 format, chain GA [auth B] MOL2 format, chain EA [auth A] mmCIF format, chain AA [auth L] mmCIF format, chain CA [auth Y] mmCIF format, chain DA [auth A] mmCIF format, chain Z [auth J] mmCIF format, chain Y [auth I] mmCIF format, chain X [auth I] mmCIF format, chain HA [auth C] mmCIF format, chain GA [auth B] mmCIF format, chain EA [auth A]	AA [auth L] CA [auth Y] DA [auth A] EA [auth A] GA [auth B] AA [auth L], CA [auth Y], DA [auth A], EA [auth A], GA [auth B], HA [auth C], X [auth I], Y [auth I], Z [auth J]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth L] Focus chain CA [auth Y] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain GA [auth B] Focus chain HA [auth C] Focus chain X [auth I] Focus chain Y [auth I] Focus chain Z [auth J] Interactions & Density Focus chain AA [auth L] Focus chain CA [auth Y] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain GA [auth B] Focus chain HA [auth C] Focus chain X [auth I] Focus chain Y [auth I] Focus chain Z [auth J]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain IA [auth a] SDF format, chain FA [auth A] MOL2 format, chain IA [auth a] MOL2 format, chain FA [auth A] mmCIF format, chain IA [auth a] mmCIF format, chain FA [auth A]	FA [auth A], IA [auth a]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain FA [auth A] Focus chain IA [auth a] Interactions & Density Focus chain FA [auth A] Focus chain IA [auth a]