9rag

Influenza A/H7N9 polymerase in complex with a 70-mer RNA template, in stalled elongation.

Method: ELECTRON MICROSCOPY D_max: 123.8 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Polymerase acidic protein

Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–RNA Heteromer Protein × 4 RNA 2 PDB declaration: hexameric（6） Consistent with all polymer counts	Chain A； UniProt 1–716	Mutation：E349K; R490I	Polymerase basic protein 2 × 1 （A0A024E1J5） RNA Pol II CTD 6 repeats (site 1A/2A) × 1 RNA product × 1 RNA-directed RNA polymerase catalytic subunit × 1 （S5ME50） RNA template (70-mer) × 1 MG MAGNESIUM ION × 3 POP PYROPHOSPHATE 2- × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 1.99 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9RAG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6TU5 Influenza A/H7N9 polymerase core (apo) Deposited 2020-01-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain AAA 201–716（516 aa） Chain DDD 201–716（516 aa）	Not recorded	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；281 K；Protein at about 9 mg/ml 0.1 M Tris pH 7.0, 8-13% PEG 8K, 0.2 M MgCl2, 0.1 M guanidine hydrochloride	Resolution 3.33 Å R-free 0.268
7QTL Influenza A/H7N9 polymerase elongation complex Deposited 2022-01-14	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: hexameric	Chain A 1–716（716 aa）	Not recorded	2TM 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine × 1 MG MAGNESIUM ION × 2 GTA P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.48 Å
7R0E Early transcription elongation state of influenza A/H7N9 polymerase backtracked due to double incoproation of nucleotide analogue T1106 and with singly incoporated T1106 at the +1 position Deposited 2022-02-01	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: hexameric	Chain A 1–716（716 aa）	Not recorded	MG MAGNESIUM ION × 2 GTA P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.51 Å
7Z4O Influenza A/H7N9 polymerase core dimer with Pol II pSer5 CTD peptide mimic bound in site 2A Deposited 2022-03-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: pentameric	Chain AAA 201–716（516 aa）	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1 M Tris pH 7.0, 13 % PEG 8K, 0.2 M MgCl2, 0.1 M guanidine hydrochloride	Resolution 3.41 Å R-free 0.273
7Z4O Influenza A/H7N9 polymerase core dimer with Pol II pSer5 CTD peptide mimic bound in site 2A Deposited 2022-03-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 4 PDB declaration: pentameric	Chain DDD 201–716（516 aa）	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1 M Tris pH 7.0, 13 % PEG 8K, 0.2 M MgCl2, 0.1 M guanidine hydrochloride	Resolution 3.41 Å R-free 0.273
7ZPL Symmetric dimer of influenza A/H7N9 polymerase bound to 5' vRNA hook Deposited 2022-04-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 6 PDB declaration: octameric	Chain A 1–716（716 aa） Chain D 1–716（716 aa）	Not recorded	MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.12 Å
7ZPM Influenza A/H7N9 polymerase apo-protein dimer complex Deposited 2022-04-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–716（716 aa） Chain D 1–716（716 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.81 Å
8BEK Early transcription elongation state of influenza A/H7N9 backtracked polymerase with singly incoporated T1106 at the U +1 position Deposited 2022-10-21	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: hexameric	Chain A 1–716（716 aa）	Not recorded	MG MAGNESIUM ION × 2 GTA P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.86 Å
8PM0 Influenza A/H7N9 polymerase in replicase-like conformation in pre-initiation state with Pol II pS5 CTD peptide mimic bound in site 1A/2A Deposited 2023-06-27	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 5 PDB declaration: hexameric	Chain A 1–716（716 aa）	Mutation：E349K; R490I	MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
8PNP Influenza A/H7N9 polymerase in pre-initiation state with continuous Pol II pS5 CTD peptide mimic bound in site 1A/2A Deposited 2023-06-30	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: pentameric	Chain A 1–716（716 aa）	Mutation：E349K; R490I	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.49 Å
8PNQ Influenza A/H7N9 polymerase in elongation state with continuous Pol II pS5 CTD peptide mimic bound in site 1A/2A Deposited 2023-06-30	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain A 1–716（716 aa）	Mutation：E349K; R490I	2KH 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine × 1 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.88 Å
8POH Influenza A/H7N9 polymerase symmetric dimer bound to the promoter (PA K289A/C489R) Deposited 2023-07-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 6 PDB declaration: decameric	Chain A 1–716（716 aa） Chain E 1–716（716 aa）	Mutation：K289A; C489R Mutation：K289A; C489R	MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8R3K Influenza A/H7N9 polymerase in self-stalled pre-termination state, with Pol II pS5 CTD peptide mimic bound in site 1A/2A. Deposited 2023-11-09	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain A 1–716（716 aa）	Mutation：E349K; R490I	POP PYROPHOSPHATE 2- × 1 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.43 Å
8R3L Influenza A/H7N9 polymerase in pre-initiation state, intermediate conformation (I) with PB2-C(I), ENDO(T), and Pol II pS5 CTD peptide mimic bound in site 1A/2A Deposited 2023-11-09	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain A 1–716（716 aa）	Mutation：E349K; R490I	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.25 Å
8RMP Influenza polymerase A/H7N9-4M (ENDO(R) \| Core1) Deposited 2024-01-08	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–716（716 aa）	Mutation：E349K; R490I	MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.77 Å
8RMQ Influenza polymerase A/H7N9-4M (ENDO(R) \| Core2) Deposited 2024-01-08	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–716（716 aa）	Mutation：E349K; R490I	MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.54 Å
8RMR Influenza polymerase A/H7N9-4M replication complex, an asymmetric polymerase dimer bound to human ANP32A Deposited 2024-01-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 1–716（716 aa） Chain D 1–716（716 aa）	Mutation：E349K; R490I Mutation：E349K; R490I	MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.25 Å
8RMS Influenza polymerase A/H7N9-4M replicase minus 627(R) (from "Influenza polymerase A/H7N9-4M replication complex" \| Local refinement) Deposited 2024-01-08	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–716（716 aa）	Mutation：E349K; R490I	MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.21 Å
8RN0 Influenza polymerase A/H7N9-4M encapsidase plus 627(R) / human ANP32A (from "Influenza polymerase A/H7N9-4M replication complex" \| Local refinement) Deposited 2024-01-09	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 1–716（716 aa）	Mutation：E349K; R490I	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.13 Å
9FYX Influenza A/H7N9 polymerase pre-cleavage cap-snatching complex Deposited 2024-07-04	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 23-meric	Chain a 1–716（716 aa）	Mutation：E119D	ZN ZINC ION × 9 G1G 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-(2'-O-METHYL)-GUANOSINE × 1 MG MAGNESIUM ION × 2 PO4 PHOSPHATE ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20 mM BICINE pH 8.0 150 mM NaCl 0.1 mM MgCl2 4% glycerol cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9G0A Influenza A/H7N9 polymerase post-cleavage cap-snatching complex Deposited 2024-07-07	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 23-meric	Chain a 1–716（716 aa）	Mutation：E119D	ZN ZINC ION × 8 MG MAGNESIUM ION × 2 G1G 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-(2'-O-METHYL)-GUANOSINE × 1 PO4 PHOSPHATE ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20 mM BICINE pH 8.0 150 mM NaCl 3 mM MgCl2 4% glycerol cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9RAF Influenza A/H7N9 polymerase in complex with a 70-mer template in stalled elongation with backtracking and stem. Deposited 2025-05-20	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain A 1–716（716 aa）	Mutation：E349K; R490I	MG MAGNESIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.15 Å

21 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	M9TI86_9INFA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–716； UniProt 1–716

Polymerase basic protein 2

Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))

UniProt A0A024E1J5

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–RNA Heteromer Protein × 4 RNA 2 PDB declaration: hexameric（6） Consistent with all polymer counts	Chain C； UniProt 1–759	Mutation：G74R; K627; D701	Polymerase acidic protein × 1 （M9TI86） RNA Pol II CTD 6 repeats (site 1A/2A) × 1 RNA product × 1 RNA-directed RNA polymerase catalytic subunit × 1 （S5ME50） RNA template (70-mer) × 1 MG MAGNESIUM ION × 3 POP PYROPHOSPHATE 2- × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 1.99 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9RAG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9RAF Influenza A/H7N9 polymerase in complex with a 70-mer template in stalled elongation with backtracking and stem. Deposited 2025-05-20	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain C 1–759（759 aa）	Mutation：G74R; K627; D701	MG MAGNESIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.15 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A024E1J5_9INFA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–759； UniProt 1–759

RNA-directed RNA polymerase catalytic subunit

Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))

UniProt S5ME50

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–RNA Heteromer Protein × 4 RNA 2 PDB declaration: hexameric（6） Consistent with all polymer counts	Chain B； UniProt 1–757	Mutation：K577G	Polymerase acidic protein × 1 （M9TI86） Polymerase basic protein 2 × 1 （A0A024E1J5） RNA Pol II CTD 6 repeats (site 1A/2A) × 1 RNA product × 1 RNA template (70-mer) × 1 MG MAGNESIUM ION × 3 POP PYROPHOSPHATE 2- × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 1.99 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9RAG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8PNP Influenza A/H7N9 polymerase in pre-initiation state with continuous Pol II pS5 CTD peptide mimic bound in site 1A/2A Deposited 2023-06-30	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: pentameric	Chain B 1–757（757 aa）	Mutation：K577G	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.49 Å
8PNQ Influenza A/H7N9 polymerase in elongation state with continuous Pol II pS5 CTD peptide mimic bound in site 1A/2A Deposited 2023-06-30	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain B 1–757（757 aa）	Mutation：K577G	2KH 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine × 1 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.88 Å
8R3K Influenza A/H7N9 polymerase in self-stalled pre-termination state, with Pol II pS5 CTD peptide mimic bound in site 1A/2A. Deposited 2023-11-09	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain B 1–757（757 aa）	Mutation：K577G	POP PYROPHOSPHATE 2- × 1 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.43 Å
8R3L Influenza A/H7N9 polymerase in pre-initiation state, intermediate conformation (I) with PB2-C(I), ENDO(T), and Pol II pS5 CTD peptide mimic bound in site 1A/2A Deposited 2023-11-09	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain B 1–757（757 aa）	Mutation：K577G	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.25 Å
8RMP Influenza polymerase A/H7N9-4M (ENDO(R) \| Core1) Deposited 2024-01-08	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–757（757 aa）	Mutation：K577G	MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.77 Å
8RMQ Influenza polymerase A/H7N9-4M (ENDO(R) \| Core2) Deposited 2024-01-08	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–757（757 aa）	Mutation：K577G	MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.54 Å
8RMR Influenza polymerase A/H7N9-4M replication complex, an asymmetric polymerase dimer bound to human ANP32A Deposited 2024-01-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain B 1–757（757 aa） Chain E 1–757（757 aa）	Mutation：K577G Mutation：K577G	MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.25 Å
8RMS Influenza polymerase A/H7N9-4M replicase minus 627(R) (from "Influenza polymerase A/H7N9-4M replication complex" \| Local refinement) Deposited 2024-01-08	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–757（757 aa）	Mutation：K577G	MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.21 Å
8RN0 Influenza polymerase A/H7N9-4M encapsidase plus 627(R) / human ANP32A (from "Influenza polymerase A/H7N9-4M replication complex" \| Local refinement) Deposited 2024-01-09	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 1–757（757 aa）	Mutation：K577G	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.13 Å
9RAF Influenza A/H7N9 polymerase in complex with a 70-mer template in stalled elongation with backtracking and stem. Deposited 2025-05-20	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain B 1–757（757 aa）	Mutation：K577G	MG MAGNESIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.15 Å

10 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	S5ME50_9INFA
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain B； PDBConstruct 1–757； UniProt 1–757

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9rag
Deposition date deposition_date	2025-05-20
Structure title title	Influenza A/H7N9 polymerase in complex with a 70-mer RNA template, in stalled elongation.
Keywords keywords	Influenza polymerase, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	37.21 Å
Radius of gyration Rg (electron density) rg_electron	37.14 Å
Forward intensity I(0) i0	758461000.00
Molecular weight molecular_weight	211800.0 kDa
Excluded volume excluded_volume	259600 Å³
Envelope volume envelope_volume	326280 Å³
Hydration-shell volume shell_volume	69990 Å³
Envelope diameter envelope_diameter	133.4 Å
Shell Rg shell_rg	45.33 Å
Envelope Rg envelope_rg	37.09 Å
Shape Rg shape_rg	37.17 Å
Total Rg total_rg	37.45 Å
Total atoms total_atoms	29018
Residues n_residues	1756
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	123.8 Å
Rg (real space) rg_real	37.10 Å
Rg uncertainty (real space) rg_real_error	0.81 Å
I(0) (real space) i0_real	7.5850e+08
I(0) uncertainty (real space) i0_real_error	1.2350e+07
Rg (reciprocal space) rg_reciprocal	37.17 Å
I(0) (reciprocal space) i0_reciprocal	758500000.0000
Solution quality estimate total_estimate	0.8724
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	44.2 Å
Skewness Skewness skewness	0.324
Kurtosis Kurtosis kurtosis	-0.193
Angular range angular_range	— – 0.2100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	218400000.0000
Real-space data points n_real_points	43
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.810; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.919

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	Polymerase acidic protein
Molecular weight formula_weight	82829.6 kDa
Mutation mutation	E349K; R490I
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	29875

MEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFASICTHLEVCFMYSDFHFIDERGESTIIESGDPNVLLKHRFEIIEGRDRTMAWTVVNSICNTTGVEKPKFLPDLYDYKENRFIEIGVTRREVHIYYLEKANKIKSEKTHIHIFSFTGEEMATKADYTLDEESRARIKTRLFTIRQEMASRGLWDSFRQSERGEETIEERFEITGTMRRLADQSLPPNFSSLENFRAYVDGFEPNGCIEGKLSQMSKEVNARIEPFLRTTPRPLRLPDGPPCSQRSKFLLMDALKLSIEDPSHEGEGIPLYDAIKCMKTFFGWKEPNIIKPHEKGINPNYLLTWKQVLAELQDIKNEEKIPRTKNMKKTSQLKWALGENMAPEKVDFEDCKDVNDLKQYDSDEPEPRSLACWIQSEFNKACELTDSSWVELDEIGEDVAPIEHIASMRRNYFTAEVSHCRATEYIMKGVYINTALLNASCAAMDDFQLIPMISKCITKEGRRKTNLYGFIIKGRSHLRNDTDVVNFVSMEFSLTDPRLEPHKWEKYCVLEIGDMLLRTAVGQVSRPMFLYVRTNGTSKIKMKWGMEMRRCLLQSLQQIESMIEAESSVKEKDLTKEFFENKSETWPIGESPKGVEEGSIGKVCRTLLAKSVFNSLYASPQLEGFSAESRKLLLIVQALRDNLEPGTFDLEGLYEAIEECLINDPWVLLNASWFNSFLTHALR

来源 Source

来源生物 organism	Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))
NCBI Class编号 ncbi_taxonomy_id	1318616
宿主生物 host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Polymerase basic protein 2
Molecular weight formula_weight	89038.6 kDa
Mutation mutation	G74R; K627; D701
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MERIKELRDLMSQSRTREILTKTTVDHMAIIKKYTSGRQEKNPALRMKWMMAMKYPITADKRIMEMIPERNEQRQTLWSKTNDAGSDRVMVSPLAVTWWNRNGPTTSTVHYPKVYKTYFEKVERLKHGTFGPVHFRNQVKIRRRVDINPGHADLSAKEAQDVIMEVVFPNEVGARILTSESQLTITKEKKKELQDCKIAPLMVAYMLERELVRKTRFLPVAGGTSSVYIEVLHLTQGTCWEQMYTPGGEVRNDDVDQSLIIAARNIVRRATVSADPLASLLEMCHSTQIGGVRMVDILRQNPTEEQAVDICKAAMGLRISSSFSFGGFTFKRTSGSSVKREEEVLTGNLQTLKIRVHEGYEEFTMVGRRATAILRKATRRLIQLIVSGKDEQSIAEAIIVAMVFSQEDCMIKAVRGDLNFVNRANQRLNPMHQLLRHFQKDAKVLFQNWGIEPIDNVMGMIGILPDMTPSTEMSLRGVRVSKMGVDEYSSTERVVVSIDRFLRVRDQRGNVLLSPEEVSETQGTEKLTITYSSSMMWEINGPESVLVNTYQWIIRNWENVKIQWSQDPTMLYNKMEFEPFQSLVPKAARGQYSGFVRVLFQQMRDVLGTFDTVQIIKLLPFAAAPPKQSRMQFSSLTVNVRGSGMRIVVRGNSPVFNYNKATKRLTVLGKDAGALMEDPDEGTAGVESAVLRGFLILGKEDKRYGPALSINELSNLAKGEKANVLIGQGDVVLVMKRKRDSSILTDSQTATKRIRMAINGWSHPQFEKGGGSGGGSGGSAWSHPQFEK

来源 Source

来源生物 organism	Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))
NCBI Class编号 ncbi_taxonomy_id	1318616
宿主生物 host_organism	Trichoplusia ni

Entity 3 Entity 3 polymer

Description description	RNA Pol II CTD 6 repeats (site 1A/2A)
Molecular weight formula_weight	4816.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

YSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS

Entity 4 Entity 4 polymer

Description description	RNA product
Molecular weight formula_weight	3560.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	M

CCGCAGGGAGC

Entity 5 Entity 5 polymer

Description description	RNA-directed RNA polymerase catalytic subunit
Molecular weight formula_weight	86424.0 kDa
Mutation mutation	K577G
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MDVNPTLLFLKVPVQNAISTTFPYTGDPPYSHGTGTGYTMDTVNRTHKYSEKGKWTTNTETGAPQLNPIDGPLPEDNEPSGYAQTDCVLEAMAFLEESHPGIFENSCLETMEIVQQTRVDKLTQGRQTYDWTLNRNQPAATALANTIEVFRSNGLTANESGRLIDFLKDVMDSMDKEEMEITTHFQRKRRVRDNMTKKMVTQRTIGKKKQRLNKRSYLIRALTLNTMTKDAERGKLKRRAIATPGMQIRGFVYFVEALARSICEKLEQSGLPVGGNEKKAKLANVVRKMMTNSQDTELSFTITGDNTKWNENQNPRMFLAMITYITRNQPEWFRNVLSIAPIMFSNKMARLGKGYMFESKSMKLRTQVPAEMLANIDLKYFNKSTREKIEKIRPLLIDGTASLSPGMMMGMFNMLSTVLGVSILNLGQKKYTKTTYWWDGLQSSDDFALIVNAPNHEGIQAGVDRFYRTCKLVGINMSKKKSYINRTGTFEFTSFFYRYGFVANFSMELPSFGVSGINESADMSVGVTVIKNNMINNDLGPATAQMALQLFIKDYRYTYRCHRGDTQIQTRRAFELGKLWEQTRSKAGLLVSDGGPNLYNIRNLHIPEVCLKWELMDEDYQGRLCNPMNPFVSHKEIDSVNNAVVMPAHGPAKSMEYDAVATTHSWIPKRNRSILNTSQRGILEDEQMYQKCCNLFEKFFPSSSYRRPVGISSMVEAMVSRARIDARIDFESGRIKKEEFAEIMKICSTIEELRRQK

来源 Source

来源生物 organism	Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))
NCBI Class编号 ncbi_taxonomy_id	1318616
宿主生物 host_organism	Trichoplusia ni

Entity 6 Entity 6 polymer

Description description	RNA template (70-mer)
Molecular weight formula_weight	22480.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	T

AGUAGAAACAAGGAUCAGGAAUGUCCCACAAAGAGCUCCCUGCGGUCUUUGUGGGGCUCCUGCUUUUGCU

Entity 7 Entity 7 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 8 Entity 8 non-polymer

Description description	PYROPHOSPHATE 2-
Molecular weight formula_weight	176.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	667

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	1.990 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	1.99 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	1030984

fit	/app/data/saxs_computation/ra/9rag/9rag.fit
pddf	/app/data/pr_computation/ra/9rag/9rag.pr.out
profile	/app/data/saxs_computation/ra/9rag/9rag.dat

Influenza A/H7N9 polymerase in complex with a 70-mer RNA template, in stalled elongation.

1. Protein Identity and Related Structures Protein Identity & Related Structures

Polymerase acidic protein

State in the Current Structure

Other States of the Same Protein in the Database

Polymerase basic protein 2

State in the Current Structure

Other States of the Same Protein in the Database

RNA-directed RNA polymerase catalytic subunit

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

来源 Source

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)