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5msg

Influenza B polymerase bound to vRNA promoter and capped RNA primer

Method: X-RAY DIFFRACTION Dmax: 130.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Polymerase acidic protein

Influenza B virus

UniProt Q5V8Z9

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 × 3 RNA 3 PDB declaration: hexameric（6） Consistent with all polymer counts Chain A； UniProt 1–726 Not recorded RNA-directed RNA polymerase catalytic subunit × 1 （Q5V8Y6） Polymerase basic protein 2 × 1 （Q5V8X3） ;RNA (5'-D(*(GDM))-R(P*AP*AP*UP*C)-3') ; × 1 ;RNA (5'-R(*UP*AP*UP*AP*CP*CP*UP*CP*UP*GP*CP*UP*UP*CP*UP*GP*CP*U)-3') ; × 1 ;RNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP*AP*G)-3') ; × 1 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4；277 K；35 microM of FluB polymerase was mixed with 40 microM of the vRNA promoter and 40 microM 13-mer capped RNA primer in a buffer containing 500 mM NaCl, 50 mM HEPES pH 7.5, 5% glycerol and 2 mM TCEP. The best diffracting crystals appeared in 100 mM sodium acetate pH 3.8 - 4.0 and 150 mM di-ammonium phosphate Resolution 3.80 Å R-free 0.267

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 5MSG Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4WRT Crystal structure of Influenza B polymerase with bound vRNA promoter (form FluB2) Deposited 2014-10-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 1–726（726 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；281 K；1 M LiCl, 10% PEG 6000 and 0.1 M bicine pH 9.0
Resolution 2.70 Å R-free 0.211
4WSA Crystal structure of Influenza B polymerase bound to the vRNA promoter (FluB1 form) Deposited 2014-10-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 1–726（726 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；281 K；FluB polymerase was concentrated to 9 mg per ml (37 microM) in a buffer containing 500 mM NaCl, 50 mM Hepes pH 7.5, 5% glycerol and 2mM Tris(2-carboxyethyl)phosphine (TCEP), and mixed with 40 microM vRNA for crystallization in hanging drops at 4 C. A trigonal crystal form (FluB1) was obtained by mixing polymerase with nucleotides 5-18 of the 3 prime end and 1-14 of the 5 prime end of the vRNA in a condition containing 0.1 M bicine pH 9.0, 10% MPD.
Resolution 3.40 Å R-free 0.265
5EPI CRYSTAL STRUCTURE OF INFLUENZA B POLYMERASE WITH BOUND 5' CRNA EXHIBITS A NOVEL DOMAIN ARRANGEMENT Deposited 2015-11-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain A 1–726（726 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；100 MM TRI SODIUM CITRATE PH 5.6, 10 OR 100 MM NACL AND 12% MPD
Resolution 4.10 Å R-free 0.287
5EPI CRYSTAL STRUCTURE OF INFLUENZA B POLYMERASE WITH BOUND 5' CRNA EXHIBITS A NOVEL DOMAIN ARRANGEMENT Deposited 2015-11-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain E 1–726（726 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；100 MM TRI SODIUM CITRATE PH 5.6, 10 OR 100 MM NACL AND 12% MPD
Resolution 4.10 Å R-free 0.287
5EPI CRYSTAL STRUCTURE OF INFLUENZA B POLYMERASE WITH BOUND 5' CRNA EXHIBITS A NOVEL DOMAIN ARRANGEMENT Deposited 2015-11-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain I 1–726（726 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；100 MM TRI SODIUM CITRATE PH 5.6, 10 OR 100 MM NACL AND 12% MPD
Resolution 4.10 Å R-free 0.287
5EPI CRYSTAL STRUCTURE OF INFLUENZA B POLYMERASE WITH BOUND 5' CRNA EXHIBITS A NOVEL DOMAIN ARRANGEMENT Deposited 2015-11-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain M 1–726（726 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；100 MM TRI SODIUM CITRATE PH 5.6, 10 OR 100 MM NACL AND 12% MPD
Resolution 4.10 Å R-free 0.287
5EPI CRYSTAL STRUCTURE OF INFLUENZA B POLYMERASE WITH BOUND 5' CRNA EXHIBITS A NOVEL DOMAIN ARRANGEMENT Deposited 2015-11-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain Q 1–726（726 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；100 MM TRI SODIUM CITRATE PH 5.6, 10 OR 100 MM NACL AND 12% MPD
Resolution 4.10 Å R-free 0.287
5EPI CRYSTAL STRUCTURE OF INFLUENZA B POLYMERASE WITH BOUND 5' CRNA EXHIBITS A NOVEL DOMAIN ARRANGEMENT Deposited 2015-11-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain U 1–726（726 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；100 MM TRI SODIUM CITRATE PH 5.6, 10 OR 100 MM NACL AND 12% MPD
Resolution 4.10 Å R-free 0.287
5FML Crystal structure of the endonuclease from the PA subunit of influenza B virus bound to the PB2 subunit NLS peptide Deposited 2015-11-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–197（197 aa） Fragment：ENDONUCLEASE DOMAIN RESIDUES 1-197
Not recorded MG MAGNESIUM ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；0.1 M MES PH 6.5, 25% PEG6000
Resolution 1.70 Å R-free 0.276
5FMZ Crystal structure of Influenza B polymerase with bound 5' vRNA Deposited 2015-11-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain D 1–726（726 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；0.1 M KCL, 10 MM MGCL2, 50 MM TRIS-HCL PH 8.5 AND 30% PEG400
Resolution 3.40 Å R-free 0.277
5FMZ Crystal structure of Influenza B polymerase with bound 5' vRNA Deposited 2015-11-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain A 1–726（726 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；0.1 M KCL, 10 MM MGCL2, 50 MM TRIS-HCL PH 8.5 AND 30% PEG400
Resolution 3.40 Å R-free 0.277
5M3J Influenza B polymerase bound to four heptad repeats of serine 5 phosphorylated Pol II CTD Deposited 2016-10-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain A 1–726（726 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；277 K；FluB polymerase in a buffer containing 500 mM NaCl, 50 mM Hepes pH 7.5, 5% glycerol and 2mM Tris(2-carboxyethyl)phosphine (TCEP) was mixed with 5' and 3' ends of vRNA promoter and CTD peptide. Reservoir solution contained 0.1 M bicine pH 9.0, 10% MPD.
Resolution 3.50 Å R-free 0.268
6F5O A mechanism for the activation of the influenza virus transcriptase Deposited 2017-12-02 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 1–726（726 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.80 Å
6FS8 Influenza B/Memphis/13/03 endonuclease with bound inhibitor, baloxavir acid (BXA) Deposited 2018-02-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–197（197 aa）
Not recorded E4Z Baloxavir acid × 1 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；Protein, at 15-17 mg/ml, was incubated with 10-fold molar excess of BXA for 30 min at RT, mixtures were centrifuged at RT for 5 minutes at 12000 g, and soluble fraction was used for crystallization trials (final protein concentration 8-10 mg/ml). Mother liquor was 0.2 M NaCl, 0.1 M Na(CH3)2AsO2 pH 6.5, 2 M (NH4)2SO4
Resolution 1.80 Å R-free 0.215
6FS8 Influenza B/Memphis/13/03 endonuclease with bound inhibitor, baloxavir acid (BXA) Deposited 2018-02-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–197（197 aa）
Not recorded E4Z Baloxavir acid × 1 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；Protein, at 15-17 mg/ml, was incubated with 10-fold molar excess of BXA for 30 min at RT, mixtures were centrifuged at RT for 5 minutes at 12000 g, and soluble fraction was used for crystallization trials (final protein concentration 8-10 mg/ml). Mother liquor was 0.2 M NaCl, 0.1 M Na(CH3)2AsO2 pH 6.5, 2 M (NH4)2SO4
Resolution 1.80 Å R-free 0.215
6FS9 Influenza B/Memphis/13/03 endonuclease with I38T mutation with bound inhibitor, baloxavir acid (BXA) Deposited 2018-02-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–197（197 aa）
Mutation：I38T MN MANGANESE (II) ION × 2 E4Z Baloxavir acid × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Protein, at 15-17 mg/ml, was incubated with 10-fold molar excess of BXA for 30 min at RT, mixtures were centrifuged at RT for 5 minutes at 12000 g, and soluble fraction was used for crystallization trials (final protein concentration 8-10 mg/ml). Mother liquor was 0.2 M CaCl2, 0.1 M MES pH 6.0, 20% (w/v) PEG6000
Resolution 2.28 Å R-free 0.235
6FSB Influenza B/Memphis/13/03 endonuclease with I38T mutation Deposited 2018-02-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–197（197 aa）
Mutation：I38T MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Protein, at 15-17 mg/ml, was incubated with 10-fold molar excess of BXA for 30 min at RT, mixtures were centrifuged at RT for 5 minutes at 12000 g, and soluble fraction was used for crystallization trials (final protein concentration 8-10 mg/ml). Mother liquor was
Resolution 1.80 Å R-free 0.236
6FSB Influenza B/Memphis/13/03 endonuclease with I38T mutation Deposited 2018-02-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–197（197 aa）
Mutation：I38T MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Protein, at 15-17 mg/ml, was incubated with 10-fold molar excess of BXA for 30 min at RT, mixtures were centrifuged at RT for 5 minutes at 12000 g, and soluble fraction was used for crystallization trials (final protein concentration 8-10 mg/ml). Mother liquor was
Resolution 1.80 Å R-free 0.236
6QCS Influenza B polymerase pre-initiation complex Deposited 2018-12-30 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: hexameric
Chain A 1–726（726 aa）
Not recorded MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6QCT Influenza B polymerase elongation complex Deposited 2018-12-30 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: hexameric
Chain A 1–726（726 aa）
Not recorded MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6QCV Crystal structure of influenza B polymerase initiation state with capped 14-mer RNA primer and CTP Deposited 2018-12-31 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: hexameric
Chain A 1–726（726 aa）
Not recorded PO4 PHOSPHATE ION × 1 CTP CYTIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.4；277 K；Influenza B polymerase at 9 mg per ml in was mixed with 40 microM vRNA 5 prime end 14-mer, 40 microM vRNA 3 prime end 21-mer and 80 microM 14-mer capped RNA. The mother liquor contained 200 mM di-ammonium phosphate and 100 mM sodium acetate between pH 4.0 and 4.4. CTP was soaked for 18 hours into grown crystals at a final concentration of 5 mM in the drop.
Resolution 3.24 Å R-free 0.234
6QCW Crystal structure of influenza B polymerase initiation state with capped 14-mer RNA primer Deposited 2018-12-31 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: hexameric
Chain A 1–726（726 aa）
Not recorded PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.4；277 K；Influenza B polymerase at 9 mg per ml in was mixed with 40 microM vRNA 5 prime end 14-mer, 40 microM vRNA 3 prime end 21-mer and 80 microM 14-mer capped RNA. The mother liquor contained 200 mM di-ammonium phosphate and 100 mM sodium acetate between pH 4.0 and 4.4.
Resolution 2.88 Å R-free 0.234
6QCX Crystal structure of influenza B polymerase initiation state with capped 15-mer RNA primer Deposited 2018-12-31 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: hexameric
Chain A 1–726（726 aa）
Not recorded PO4 PHOSPHATE ION × 1 POP PYROPHOSPHATE 2- × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.4；277 K；Influenza B polymerase at 9 mg per ml in was mixed with 40 microM vRNA 5 prime end 14-mer, 40 microM vRNA 3 prime end 21-mer and 80 microM 15-mer capped RNA. The mother liquor contained 200 mM di-ammonium phosphate and 100 mM sodium acetate between pH 4.0 and 4.4.
Resolution 3.08 Å R-free 0.226
6T0W Human Influenza B polymerase recycling complex Deposited 2019-10-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain A 1–726（726 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.18 Å
7R1F Early transcription elongation state of influenza B polymerase backtracked due to double incoproation of nucleotide analogue T1106 Deposited 2022-02-02 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: hexameric
Chain A 1–726（726 aa）
Not recorded MG MAGNESIUM ION × 3 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 2.58 Å
7Z42 Influenza B polymerase with Pol II pSer5 CTD peptide mimic bound in site 2B Deposited 2022-03-03 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 5 PDB declaration: hexameric
Chain A 1–726（726 aa）
Mutation：K135A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；FluPolB PA mutant K135A at 9 mg per ml was mixed with 40 microM of nucleotides 1-13 vRNA 5prime end, 5-pAGUAGUAACAAGA-3, and 1.8 mM 28-mer CTD peptide, YSPTpSPS x 4 in a buffer containing 50 mM HEPES pH 7.5, 500 mM NaCl, 5% glycerol, 2 mM TCEP. Hanging drops for crystallization were set up at 20 C.
Resolution 2.42 Å R-free 0.257
7Z42 Influenza B polymerase with Pol II pSer5 CTD peptide mimic bound in site 2B Deposited 2022-03-03 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 5 PDB declaration: hexameric
Chain D 1–726（726 aa）
Mutation：K135A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；FluPolB PA mutant K135A at 9 mg per ml was mixed with 40 microM of nucleotides 1-13 vRNA 5prime end, 5-pAGUAGUAACAAGA-3, and 1.8 mM 28-mer CTD peptide, YSPTpSPS x 4 in a buffer containing 50 mM HEPES pH 7.5, 500 mM NaCl, 5% glycerol, 2 mM TCEP. Hanging drops for crystallization were set up at 20 C.
Resolution 2.42 Å R-free 0.257
7Z43 Influenza B polymerase with Pol II pSer5 CTD peptide mimic bound in site 1B and 2B Deposited 2022-03-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 5 PDB declaration: octameric
Chain AAA 1–726（726 aa）
Not recorded PO4 PHOSPHATE ION × 1 IC5 [(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.4；277 K；200 mM di-ammonium phosphate, and 100 mM sodium acetate at pH 4.4
Resolution 3.12 Å R-free 0.272
8BDR Early transcription elongation state of influenza B/Mem polymerase backtracked due to double incoproation of nucleotide analogue T1106 and with singly incoporated T1106 at the U +1 position Deposited 2022-10-19 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: hexameric
Chain A 1–726（726 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 2.70 Å
8BE0 Early transcription elongation state of influenza B/Mem polymerase backtracked due to double incoproation of nucleotide analogue T1106 and with singly incoporated T1106 at the C +1 position Deposited 2022-10-20 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: hexameric
Chain A 1–726（726 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 2.34 Å
8BF5 Early transcription elongation state of influenza A/H7N9 polymerase stalled with incoming GTP analogue Deposited 2022-10-24 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: hexameric
Chain A 1–726（726 aa）
Not recorded MG MAGNESIUM ION × 3 G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 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 2.96 Å
8RN1 Influenza B polymerase, monomeric encapsidase with 5' cRNA hook bound Deposited 2024-01-09 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain A 1–726（726 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.64 Å
8RN2 Monomeric apo-influenza B polymerase, encapsidase conformation Deposited 2024-01-09 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–726（726 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.89 Å
8RN3 Pseudo-symmetrical influenza B polymerase apo-dimer, encapsidase moiety (from "Influenza B polymerase pseudo-symmetrical dimer" | Local refinement) Deposited 2024-01-09 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 × 5 PDB declaration: pentameric
Chain A 1–726（726 aa）
Chain D 1–726（726 aa）
Not recorded MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.78 Å
8RN4 Pseudo-symmetrical influenza B polymerase apo-dimer, ENDO(T) moiety (from "Influenza B polymerase pseudo-symmetrical dimer" | Local refinement) Deposited 2024-01-09 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 × 5 PDB declaration: pentameric
Chain A 1–726（726 aa）
Chain D 1–726（726 aa）
Not recorded MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å
8RN5 Pseudo-symmetrical influenza B polymerase apo-dimer, ENDO(R) moiety (from "Influenza B polymerase pseudo-symmetrical dimer" | Local refinement) Deposited 2024-01-09 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 × 5 PDB declaration: pentameric
Chain A 1–726（726 aa）
Chain E 1–726（726 aa）
Not recorded MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.88 Å
8RN6 Pseudo-symmetrical influenza B polymerase apo-dimer, ENDO(E) moiety (from "Influenza B polymerase pseudo-symmetrical dimer" | Local refinement) Deposited 2024-01-09 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–726（726 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.82 Å
8RN7 Pseudo-symmetrical influenza B polymerase apo-dimer, core-only moeity (from "Influenza B polymerase pseudo-symmetrical dimer" | Local refinement) Deposited 2024-01-09 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 × 5 PDB declaration: pentameric
Chain A 1–726（726 aa）
Chain E 1–726（726 aa）
Not recorded MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.09 Å
8RN8 Influenza B polymerase pseudo-symmetrical apo-dimer (FluPol(E)|FluPol(S)) Deposited 2024-01-09 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 A 1–726（726 aa）
Chain D 1–726（726 aa）
Not recorded MG MAGNESIUM ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.92 Å
8RN9 Influenza B polymerase, replicase (from "Influenza B polymerase apo-trimer" | Local refinement) Deposited 2024-01-09 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 × 5 PDB declaration: pentameric
Chain A 1–726（726 aa）
Chain E 1–726（726 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.31 Å
8RNA Influenza B polymerase apo-trimer Deposited 2024-01-09 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 × 10 PDB declaration: decameric
Chain A 1–726（726 aa）
Chain D 1–726（726 aa）
Chain X 1–726（726 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.57 Å
8RNB Influenza B polymerase, encapsidase plus 627(R) / human ANP32A (from "Influenza B polymerase apo-trimer" | Local refinement) Deposited 2024-01-09 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 1–726（726 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.31 Å
8RNC Influenza B polymerase, replication complex, an asymmetric polymerase dimer bound to human ANP32A (from "Influenza B polymerase apo-trimer" | Local refinement) Deposited 2024-01-09 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 × 9 PDB declaration: nonameric
Chain A 1–726（726 aa）
Chain D 1–726（726 aa）
Chain X 1–726（726 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.52 Å

34 other PDB entries and 43 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q5V8Z9_9INFB
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 15–740； UniProt 1–726

RNA-directed RNA polymerase catalytic subunit

Influenza B virus

UniProt Q5V8Y6

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 × 3 RNA 3 PDB declaration: hexameric（6） Consistent with all polymer counts Chain B； UniProt 1–752 Not recorded Polymerase acidic protein × 1 （Q5V8Z9） Polymerase basic protein 2 × 1 （Q5V8X3） ;RNA (5'-D(*(GDM))-R(P*AP*AP*UP*C)-3') ; × 1 ;RNA (5'-R(*UP*AP*UP*AP*CP*CP*UP*CP*UP*GP*CP*UP*UP*CP*UP*GP*CP*U)-3') ; × 1 ;RNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP*AP*G)-3') ; × 1 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4；277 K；35 microM of FluB polymerase was mixed with 40 microM of the vRNA promoter and 40 microM 13-mer capped RNA primer in a buffer containing 500 mM NaCl, 50 mM HEPES pH 7.5, 5% glycerol and 2 mM TCEP. The best diffracting crystals appeared in 100 mM sodium acetate pH 3.8 - 4.0 and 150 mM di-ammonium phosphate Resolution 3.80 Å R-free 0.267

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 5MSG Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4WRT Crystal structure of Influenza B polymerase with bound vRNA promoter (form FluB2) Deposited 2014-10-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain B 1–752（752 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；281 K；1 M LiCl, 10% PEG 6000 and 0.1 M bicine pH 9.0
Resolution 2.70 Å R-free 0.211
4WSA Crystal structure of Influenza B polymerase bound to the vRNA promoter (FluB1 form) Deposited 2014-10-26 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: pentameric
Chain B 1–752（752 aa）
Mutation：Trichoplusia ni No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；281 K；FluB polymerase was concentrated to 9 mg per ml (37 microM) in a buffer containing 500 mM NaCl, 50 mM Hepes pH 7.5, 5% glycerol and 2mM Tris(2-carboxyethyl)phosphine (TCEP), and mixed with 40 microM vRNA for crystallization in hanging drops at 4 C. A trigonal crystal form (FluB1) was obtained by mixing polymerase with nucleotides 5-18 of the 3 prime end and 1-14 of the 5 prime end of the vRNA in a condition containing 0.1 M bicine pH 9.0, 10% MPD.
Resolution 3.40 Å R-free 0.265
5EPI CRYSTAL STRUCTURE OF INFLUENZA B POLYMERASE WITH BOUND 5' CRNA EXHIBITS A NOVEL DOMAIN ARRANGEMENT Deposited 2015-11-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain B 1–752（752 aa） Fragment：PB1 SUBUNIT
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；100 MM TRI SODIUM CITRATE PH 5.6, 10 OR 100 MM NACL AND 12% MPD
Resolution 4.10 Å R-free 0.287
5EPI CRYSTAL STRUCTURE OF INFLUENZA B POLYMERASE WITH BOUND 5' CRNA EXHIBITS A NOVEL DOMAIN ARRANGEMENT Deposited 2015-11-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain F 1–752（752 aa） Fragment：PB1 SUBUNIT
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；100 MM TRI SODIUM CITRATE PH 5.6, 10 OR 100 MM NACL AND 12% MPD
Resolution 4.10 Å R-free 0.287
5EPI CRYSTAL STRUCTURE OF INFLUENZA B POLYMERASE WITH BOUND 5' CRNA EXHIBITS A NOVEL DOMAIN ARRANGEMENT Deposited 2015-11-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain J 1–752（752 aa） Fragment：PB1 SUBUNIT
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；100 MM TRI SODIUM CITRATE PH 5.6, 10 OR 100 MM NACL AND 12% MPD
Resolution 4.10 Å R-free 0.287
5EPI CRYSTAL STRUCTURE OF INFLUENZA B POLYMERASE WITH BOUND 5' CRNA EXHIBITS A NOVEL DOMAIN ARRANGEMENT Deposited 2015-11-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain N 1–752（752 aa） Fragment：PB1 SUBUNIT
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；100 MM TRI SODIUM CITRATE PH 5.6, 10 OR 100 MM NACL AND 12% MPD
Resolution 4.10 Å R-free 0.287
5EPI CRYSTAL STRUCTURE OF INFLUENZA B POLYMERASE WITH BOUND 5' CRNA EXHIBITS A NOVEL DOMAIN ARRANGEMENT Deposited 2015-11-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain R 1–752（752 aa） Fragment：PB1 SUBUNIT
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；100 MM TRI SODIUM CITRATE PH 5.6, 10 OR 100 MM NACL AND 12% MPD
Resolution 4.10 Å R-free 0.287
5EPI CRYSTAL STRUCTURE OF INFLUENZA B POLYMERASE WITH BOUND 5' CRNA EXHIBITS A NOVEL DOMAIN ARRANGEMENT Deposited 2015-11-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain V 1–752（752 aa） Fragment：PB1 SUBUNIT
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；100 MM TRI SODIUM CITRATE PH 5.6, 10 OR 100 MM NACL AND 12% MPD
Resolution 4.10 Å R-free 0.287
5FMZ Crystal structure of Influenza B polymerase with bound 5' vRNA Deposited 2015-11-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain E 1–752（752 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；0.1 M KCL, 10 MM MGCL2, 50 MM TRIS-HCL PH 8.5 AND 30% PEG400
Resolution 3.40 Å R-free 0.277
5FMZ Crystal structure of Influenza B polymerase with bound 5' vRNA Deposited 2015-11-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain B 1–752（752 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；0.1 M KCL, 10 MM MGCL2, 50 MM TRIS-HCL PH 8.5 AND 30% PEG400
Resolution 3.40 Å R-free 0.277
5M3J Influenza B polymerase bound to four heptad repeats of serine 5 phosphorylated Pol II CTD Deposited 2016-10-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain B 1–752（752 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；277 K；FluB polymerase in a buffer containing 500 mM NaCl, 50 mM Hepes pH 7.5, 5% glycerol and 2mM Tris(2-carboxyethyl)phosphine (TCEP) was mixed with 5' and 3' ends of vRNA promoter and CTD peptide. Reservoir solution contained 0.1 M bicine pH 9.0, 10% MPD.
Resolution 3.50 Å R-free 0.268
6F5O A mechanism for the activation of the influenza virus transcriptase Deposited 2017-12-02 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain B 1–752（752 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.80 Å
6QCS Influenza B polymerase pre-initiation complex Deposited 2018-12-30 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: hexameric
Chain B 1–752（752 aa）
Not recorded MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6QCT Influenza B polymerase elongation complex Deposited 2018-12-30 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: hexameric
Chain B 1–752（752 aa）
Not recorded MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6QCV Crystal structure of influenza B polymerase initiation state with capped 14-mer RNA primer and CTP Deposited 2018-12-31 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: hexameric
Chain B 1–752（752 aa）
Not recorded PO4 PHOSPHATE ION × 1 CTP CYTIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.4；277 K；Influenza B polymerase at 9 mg per ml in was mixed with 40 microM vRNA 5 prime end 14-mer, 40 microM vRNA 3 prime end 21-mer and 80 microM 14-mer capped RNA. The mother liquor contained 200 mM di-ammonium phosphate and 100 mM sodium acetate between pH 4.0 and 4.4. CTP was soaked for 18 hours into grown crystals at a final concentration of 5 mM in the drop.
Resolution 3.24 Å R-free 0.234
6QCW Crystal structure of influenza B polymerase initiation state with capped 14-mer RNA primer Deposited 2018-12-31 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: hexameric
Chain B 1–752（752 aa）
Not recorded PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.4；277 K；Influenza B polymerase at 9 mg per ml in was mixed with 40 microM vRNA 5 prime end 14-mer, 40 microM vRNA 3 prime end 21-mer and 80 microM 14-mer capped RNA. The mother liquor contained 200 mM di-ammonium phosphate and 100 mM sodium acetate between pH 4.0 and 4.4.
Resolution 2.88 Å R-free 0.234
6QCX Crystal structure of influenza B polymerase initiation state with capped 15-mer RNA primer Deposited 2018-12-31 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: hexameric
Chain B 1–752（752 aa）
Not recorded PO4 PHOSPHATE ION × 1 POP PYROPHOSPHATE 2- × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.4；277 K；Influenza B polymerase at 9 mg per ml in was mixed with 40 microM vRNA 5 prime end 14-mer, 40 microM vRNA 3 prime end 21-mer and 80 microM 15-mer capped RNA. The mother liquor contained 200 mM di-ammonium phosphate and 100 mM sodium acetate between pH 4.0 and 4.4.
Resolution 3.08 Å R-free 0.226
6T0W Human Influenza B polymerase recycling complex Deposited 2019-10-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain B 1–752（752 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.18 Å
7R1F Early transcription elongation state of influenza B polymerase backtracked due to double incoproation of nucleotide analogue T1106 Deposited 2022-02-02 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: hexameric
Chain B 1–752（752 aa）
Not recorded MG MAGNESIUM ION × 3 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 2.58 Å
7Z42 Influenza B polymerase with Pol II pSer5 CTD peptide mimic bound in site 2B Deposited 2022-03-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 5 PDB declaration: hexameric
Chain B 1–752（752 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；FluPolB PA mutant K135A at 9 mg per ml was mixed with 40 microM of nucleotides 1-13 vRNA 5prime end, 5-pAGUAGUAACAAGA-3, and 1.8 mM 28-mer CTD peptide, YSPTpSPS x 4 in a buffer containing 50 mM HEPES pH 7.5, 500 mM NaCl, 5% glycerol, 2 mM TCEP. Hanging drops for crystallization were set up at 20 C.
Resolution 2.42 Å R-free 0.257
7Z42 Influenza B polymerase with Pol II pSer5 CTD peptide mimic bound in site 2B Deposited 2022-03-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 5 PDB declaration: hexameric
Chain E 1–752（752 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；FluPolB PA mutant K135A at 9 mg per ml was mixed with 40 microM of nucleotides 1-13 vRNA 5prime end, 5-pAGUAGUAACAAGA-3, and 1.8 mM 28-mer CTD peptide, YSPTpSPS x 4 in a buffer containing 50 mM HEPES pH 7.5, 500 mM NaCl, 5% glycerol, 2 mM TCEP. Hanging drops for crystallization were set up at 20 C.
Resolution 2.42 Å R-free 0.257
7Z43 Influenza B polymerase with Pol II pSer5 CTD peptide mimic bound in site 1B and 2B Deposited 2022-03-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 5 PDB declaration: octameric
Chain BBB 1–752（752 aa）
Not recorded PO4 PHOSPHATE ION × 1 IC5 [(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.4；277 K；200 mM di-ammonium phosphate, and 100 mM sodium acetate at pH 4.4
Resolution 3.12 Å R-free 0.272
8BDR Early transcription elongation state of influenza B/Mem polymerase backtracked due to double incoproation of nucleotide analogue T1106 and with singly incoporated T1106 at the U +1 position Deposited 2022-10-19 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: hexameric
Chain B 1–752（752 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 2.70 Å
8BE0 Early transcription elongation state of influenza B/Mem polymerase backtracked due to double incoproation of nucleotide analogue T1106 and with singly incoporated T1106 at the C +1 position Deposited 2022-10-20 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: hexameric
Chain B 1–752（752 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 2.34 Å
8BF5 Early transcription elongation state of influenza A/H7N9 polymerase stalled with incoming GTP analogue Deposited 2022-10-24 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: hexameric
Chain B 1–752（752 aa）
Not recorded MG MAGNESIUM ION × 3 G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 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 2.96 Å
8RN1 Influenza B polymerase, monomeric encapsidase with 5' cRNA hook bound Deposited 2024-01-09 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain B 1–752（752 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.64 Å
8RN2 Monomeric apo-influenza B polymerase, encapsidase conformation Deposited 2024-01-09 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–752（752 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.89 Å
8RN3 Pseudo-symmetrical influenza B polymerase apo-dimer, encapsidase moiety (from "Influenza B polymerase pseudo-symmetrical dimer" | Local refinement) Deposited 2024-01-09 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 × 5 PDB declaration: pentameric
Chain B 1–752（752 aa）
Chain E 1–752（752 aa）
Not recorded MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.78 Å
8RN4 Pseudo-symmetrical influenza B polymerase apo-dimer, ENDO(T) moiety (from "Influenza B polymerase pseudo-symmetrical dimer" | Local refinement) Deposited 2024-01-09 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 × 5 PDB declaration: pentameric
Chain B 1–752（752 aa）
Chain E 1–752（752 aa）
Not recorded MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å
8RN5 Pseudo-symmetrical influenza B polymerase apo-dimer, ENDO(R) moiety (from "Influenza B polymerase pseudo-symmetrical dimer" | Local refinement) Deposited 2024-01-09 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 × 5 PDB declaration: pentameric
Chain B 1–752（752 aa）
Chain D 1–752（752 aa）
Not recorded MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.88 Å
8RN6 Pseudo-symmetrical influenza B polymerase apo-dimer, ENDO(E) moiety (from "Influenza B polymerase pseudo-symmetrical dimer" | Local refinement) Deposited 2024-01-09 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–752（752 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.82 Å
8RN7 Pseudo-symmetrical influenza B polymerase apo-dimer, core-only moeity (from "Influenza B polymerase pseudo-symmetrical dimer" | Local refinement) Deposited 2024-01-09 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 × 5 PDB declaration: pentameric
Chain B 1–752（752 aa）
Chain D 1–752（752 aa）
Not recorded MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.09 Å
8RN8 Influenza B polymerase pseudo-symmetrical apo-dimer (FluPol(E)|FluPol(S)) Deposited 2024-01-09 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 B 1–752（752 aa）
Chain E 1–752（752 aa）
Not recorded MG MAGNESIUM ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.92 Å
8RN9 Influenza B polymerase, replicase (from "Influenza B polymerase apo-trimer" | Local refinement) Deposited 2024-01-09 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 × 5 PDB declaration: pentameric
Chain B 1–752（752 aa）
Chain D 1–752（752 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.31 Å
8RNA Influenza B polymerase apo-trimer Deposited 2024-01-09 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 × 10 PDB declaration: decameric
Chain B 1–752（752 aa）
Chain E 1–752（752 aa）
Chain Y 1–752（752 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.57 Å
8RNB Influenza B polymerase, encapsidase plus 627(R) / human ANP32A (from "Influenza B polymerase apo-trimer" | Local refinement) Deposited 2024-01-09 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain E 1–752（752 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.31 Å
8RNC Influenza B polymerase, replication complex, an asymmetric polymerase dimer bound to human ANP32A (from "Influenza B polymerase apo-trimer" | Local refinement) Deposited 2024-01-09 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 × 9 PDB declaration: nonameric
Chain B 1–752（752 aa）
Chain E 1–752（752 aa）
Chain Y 1–752（752 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.52 Å

30 other PDB entries and 37 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q5V8Y6_9INFB
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 10–761； UniProt 1–752

Polymerase basic protein 2

Influenza B virus

UniProt Q5V8X3

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 × 3 RNA 3 PDB declaration: hexameric（6） Consistent with all polymer counts Chain C； UniProt 1–770 Not recorded Polymerase acidic protein × 1 （Q5V8Z9） RNA-directed RNA polymerase catalytic subunit × 1 （Q5V8Y6） ;RNA (5'-D(*(GDM))-R(P*AP*AP*UP*C)-3') ; × 1 ;RNA (5'-R(*UP*AP*UP*AP*CP*CP*UP*CP*UP*GP*CP*UP*UP*CP*UP*GP*CP*U)-3') ; × 1 ;RNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP*AP*G)-3') ; × 1 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4；277 K；35 microM of FluB polymerase was mixed with 40 microM of the vRNA promoter and 40 microM 13-mer capped RNA primer in a buffer containing 500 mM NaCl, 50 mM HEPES pH 7.5, 5% glycerol and 2 mM TCEP. The best diffracting crystals appeared in 100 mM sodium acetate pH 3.8 - 4.0 and 150 mM di-ammonium phosphate Resolution 3.80 Å R-free 0.267

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 5MSG Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4WRT Crystal structure of Influenza B polymerase with bound vRNA promoter (form FluB2) Deposited 2014-10-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain C 1–770（770 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；281 K；1 M LiCl, 10% PEG 6000 and 0.1 M bicine pH 9.0
Resolution 2.70 Å R-free 0.211
4WSA Crystal structure of Influenza B polymerase bound to the vRNA promoter (FluB1 form) Deposited 2014-10-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain C 1–770（770 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；281 K；FluB polymerase was concentrated to 9 mg per ml (37 microM) in a buffer containing 500 mM NaCl, 50 mM Hepes pH 7.5, 5% glycerol and 2mM Tris(2-carboxyethyl)phosphine (TCEP), and mixed with 40 microM vRNA for crystallization in hanging drops at 4 C. A trigonal crystal form (FluB1) was obtained by mixing polymerase with nucleotides 5-18 of the 3 prime end and 1-14 of the 5 prime end of the vRNA in a condition containing 0.1 M bicine pH 9.0, 10% MPD.
Resolution 3.40 Å R-free 0.265
5EPI CRYSTAL STRUCTURE OF INFLUENZA B POLYMERASE WITH BOUND 5' CRNA EXHIBITS A NOVEL DOMAIN ARRANGEMENT Deposited 2015-11-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain C 1–770（770 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；100 MM TRI SODIUM CITRATE PH 5.6, 10 OR 100 MM NACL AND 12% MPD
Resolution 4.10 Å R-free 0.287
5EPI CRYSTAL STRUCTURE OF INFLUENZA B POLYMERASE WITH BOUND 5' CRNA EXHIBITS A NOVEL DOMAIN ARRANGEMENT Deposited 2015-11-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain G 1–770（770 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；100 MM TRI SODIUM CITRATE PH 5.6, 10 OR 100 MM NACL AND 12% MPD
Resolution 4.10 Å R-free 0.287
5EPI CRYSTAL STRUCTURE OF INFLUENZA B POLYMERASE WITH BOUND 5' CRNA EXHIBITS A NOVEL DOMAIN ARRANGEMENT Deposited 2015-11-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain K 1–770（770 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；100 MM TRI SODIUM CITRATE PH 5.6, 10 OR 100 MM NACL AND 12% MPD
Resolution 4.10 Å R-free 0.287
5EPI CRYSTAL STRUCTURE OF INFLUENZA B POLYMERASE WITH BOUND 5' CRNA EXHIBITS A NOVEL DOMAIN ARRANGEMENT Deposited 2015-11-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain O 1–770（770 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；100 MM TRI SODIUM CITRATE PH 5.6, 10 OR 100 MM NACL AND 12% MPD
Resolution 4.10 Å R-free 0.287
5EPI CRYSTAL STRUCTURE OF INFLUENZA B POLYMERASE WITH BOUND 5' CRNA EXHIBITS A NOVEL DOMAIN ARRANGEMENT Deposited 2015-11-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain S 1–770（770 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；100 MM TRI SODIUM CITRATE PH 5.6, 10 OR 100 MM NACL AND 12% MPD
Resolution 4.10 Å R-free 0.287
5EPI CRYSTAL STRUCTURE OF INFLUENZA B POLYMERASE WITH BOUND 5' CRNA EXHIBITS A NOVEL DOMAIN ARRANGEMENT Deposited 2015-11-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain W 1–770（770 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；100 MM TRI SODIUM CITRATE PH 5.6, 10 OR 100 MM NACL AND 12% MPD
Resolution 4.10 Å R-free 0.287
5FML Crystal structure of the endonuclease from the PA subunit of influenza B virus bound to the PB2 subunit NLS peptide Deposited 2015-11-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 742–770（29 aa） Fragment：NLS PEPTIDE RESIDUES 742-770
Not recorded MG MAGNESIUM ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；0.1 M MES PH 6.5, 25% PEG6000
Resolution 1.70 Å R-free 0.276
5FMZ Crystal structure of Influenza B polymerase with bound 5' vRNA Deposited 2015-11-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain F 1–770（770 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；0.1 M KCL, 10 MM MGCL2, 50 MM TRIS-HCL PH 8.5 AND 30% PEG400
Resolution 3.40 Å R-free 0.277
5FMZ Crystal structure of Influenza B polymerase with bound 5' vRNA Deposited 2015-11-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain C 1–770（770 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；0.1 M KCL, 10 MM MGCL2, 50 MM TRIS-HCL PH 8.5 AND 30% PEG400
Resolution 3.40 Å R-free 0.277
5M3J Influenza B polymerase bound to four heptad repeats of serine 5 phosphorylated Pol II CTD Deposited 2016-10-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain C 1–770（770 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；277 K；FluB polymerase in a buffer containing 500 mM NaCl, 50 mM Hepes pH 7.5, 5% glycerol and 2mM Tris(2-carboxyethyl)phosphine (TCEP) was mixed with 5' and 3' ends of vRNA promoter and CTD peptide. Reservoir solution contained 0.1 M bicine pH 9.0, 10% MPD.
Resolution 3.50 Å R-free 0.268
6EUX Structure of the midlink and cap-binding domains of influenza B polymerase PB2 subunit with a bound azaindazole cap-binding inhibitor Deposited 2017-10-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 249–540（292 aa） Fragment：cap-midlink double domain (residues 249-540)
Not recorded BYB (2~{S},3~{S})-3-[[5-fluoranyl-2-(5-fluoranyl-1~{H}-pyrazolo[3,4-b]pyridin-3-yl)pyrimidin-4-yl]amino]bicyclo[2.2.2]octane-2-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；Crystals were obtained by mixing FluB double domain at 15 mg/ml in 50 mM Tris pH 7.5 and 10% glycerol and 5 mM of VX-787 with 0.1 M PTCP and 25% PEG1500.
Resolution 2.05 Å R-free 0.254
6F5O A mechanism for the activation of the influenza virus transcriptase Deposited 2017-12-02 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain C 1–770（770 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.80 Å
6QCS Influenza B polymerase pre-initiation complex Deposited 2018-12-30 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: hexameric
Chain C 1–770（770 aa）
Not recorded MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6QCT Influenza B polymerase elongation complex Deposited 2018-12-30 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: hexameric
Chain C 1–770（770 aa）
Not recorded MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6QCV Crystal structure of influenza B polymerase initiation state with capped 14-mer RNA primer and CTP Deposited 2018-12-31 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: hexameric
Chain C 1–770（770 aa）
Not recorded PO4 PHOSPHATE ION × 1 CTP CYTIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.4；277 K；Influenza B polymerase at 9 mg per ml in was mixed with 40 microM vRNA 5 prime end 14-mer, 40 microM vRNA 3 prime end 21-mer and 80 microM 14-mer capped RNA. The mother liquor contained 200 mM di-ammonium phosphate and 100 mM sodium acetate between pH 4.0 and 4.4. CTP was soaked for 18 hours into grown crystals at a final concentration of 5 mM in the drop.
Resolution 3.24 Å R-free 0.234
6QCW Crystal structure of influenza B polymerase initiation state with capped 14-mer RNA primer Deposited 2018-12-31 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: hexameric
Chain C 1–770（770 aa）
Not recorded PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.4；277 K；Influenza B polymerase at 9 mg per ml in was mixed with 40 microM vRNA 5 prime end 14-mer, 40 microM vRNA 3 prime end 21-mer and 80 microM 14-mer capped RNA. The mother liquor contained 200 mM di-ammonium phosphate and 100 mM sodium acetate between pH 4.0 and 4.4.
Resolution 2.88 Å R-free 0.234
6QCX Crystal structure of influenza B polymerase initiation state with capped 15-mer RNA primer Deposited 2018-12-31 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: hexameric
Chain C 1–770（770 aa）
Not recorded PO4 PHOSPHATE ION × 1 POP PYROPHOSPHATE 2- × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.4；277 K；Influenza B polymerase at 9 mg per ml in was mixed with 40 microM vRNA 5 prime end 14-mer, 40 microM vRNA 3 prime end 21-mer and 80 microM 15-mer capped RNA. The mother liquor contained 200 mM di-ammonium phosphate and 100 mM sodium acetate between pH 4.0 and 4.4.
Resolution 3.08 Å R-free 0.226
7R1F Early transcription elongation state of influenza B polymerase backtracked due to double incoproation of nucleotide analogue T1106 Deposited 2022-02-02 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: hexameric
Chain C 1–770（770 aa）
Not recorded MG MAGNESIUM ION × 3 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 2.58 Å
7Z42 Influenza B polymerase with Pol II pSer5 CTD peptide mimic bound in site 2B Deposited 2022-03-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 5 PDB declaration: hexameric
Chain C 1–770（770 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；FluPolB PA mutant K135A at 9 mg per ml was mixed with 40 microM of nucleotides 1-13 vRNA 5prime end, 5-pAGUAGUAACAAGA-3, and 1.8 mM 28-mer CTD peptide, YSPTpSPS x 4 in a buffer containing 50 mM HEPES pH 7.5, 500 mM NaCl, 5% glycerol, 2 mM TCEP. Hanging drops for crystallization were set up at 20 C.
Resolution 2.42 Å R-free 0.257
7Z42 Influenza B polymerase with Pol II pSer5 CTD peptide mimic bound in site 2B Deposited 2022-03-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 5 PDB declaration: hexameric
Chain F 1–770（770 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；FluPolB PA mutant K135A at 9 mg per ml was mixed with 40 microM of nucleotides 1-13 vRNA 5prime end, 5-pAGUAGUAACAAGA-3, and 1.8 mM 28-mer CTD peptide, YSPTpSPS x 4 in a buffer containing 50 mM HEPES pH 7.5, 500 mM NaCl, 5% glycerol, 2 mM TCEP. Hanging drops for crystallization were set up at 20 C.
Resolution 2.42 Å R-free 0.257
7Z43 Influenza B polymerase with Pol II pSer5 CTD peptide mimic bound in site 1B and 2B Deposited 2022-03-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 5 PDB declaration: octameric
Chain CCC 1–770（770 aa）
Not recorded PO4 PHOSPHATE ION × 1 IC5 [(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.4；277 K；200 mM di-ammonium phosphate, and 100 mM sodium acetate at pH 4.4
Resolution 3.12 Å R-free 0.272
8BDR Early transcription elongation state of influenza B/Mem polymerase backtracked due to double incoproation of nucleotide analogue T1106 and with singly incoporated T1106 at the U +1 position Deposited 2022-10-19 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: hexameric
Chain C 1–770（770 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 2.70 Å
8BE0 Early transcription elongation state of influenza B/Mem polymerase backtracked due to double incoproation of nucleotide analogue T1106 and with singly incoporated T1106 at the C +1 position Deposited 2022-10-20 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: hexameric
Chain C 1–770（770 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 2.34 Å
8BF5 Early transcription elongation state of influenza A/H7N9 polymerase stalled with incoming GTP analogue Deposited 2022-10-24 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: hexameric
Chain C 1–770（770 aa）
Not recorded MG MAGNESIUM ION × 3 G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 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 2.96 Å
8RN1 Influenza B polymerase, monomeric encapsidase with 5' cRNA hook bound Deposited 2024-01-09 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain C 1–770（770 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.64 Å
8RN2 Monomeric apo-influenza B polymerase, encapsidase conformation Deposited 2024-01-09 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–770（770 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.89 Å
8RN3 Pseudo-symmetrical influenza B polymerase apo-dimer, encapsidase moiety (from "Influenza B polymerase pseudo-symmetrical dimer" | Local refinement) Deposited 2024-01-09 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 1–770（770 aa）
Not recorded MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.78 Å
8RN4 Pseudo-symmetrical influenza B polymerase apo-dimer, ENDO(T) moiety (from "Influenza B polymerase pseudo-symmetrical dimer" | Local refinement) Deposited 2024-01-09 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 1–770（770 aa）
Not recorded MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å
8RN5 Pseudo-symmetrical influenza B polymerase apo-dimer, ENDO(R) moiety (from "Influenza B polymerase pseudo-symmetrical dimer" | Local refinement) Deposited 2024-01-09 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 1–770（770 aa）
Not recorded MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.88 Å
8RN6 Pseudo-symmetrical influenza B polymerase apo-dimer, ENDO(E) moiety (from "Influenza B polymerase pseudo-symmetrical dimer" | Local refinement) Deposited 2024-01-09 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–770（770 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.82 Å
8RN7 Pseudo-symmetrical influenza B polymerase apo-dimer, core-only moeity (from "Influenza B polymerase pseudo-symmetrical dimer" | Local refinement) Deposited 2024-01-09 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 1–770（770 aa）
Not recorded MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.09 Å
8RN8 Influenza B polymerase pseudo-symmetrical apo-dimer (FluPol(E)|FluPol(S)) Deposited 2024-01-09 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 C 1–770（770 aa）
Chain F 1–770（770 aa）
Not recorded MG MAGNESIUM ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.92 Å
8RN9 Influenza B polymerase, replicase (from "Influenza B polymerase apo-trimer" | Local refinement) Deposited 2024-01-09 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 1–770（770 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.31 Å
8RNA Influenza B polymerase apo-trimer Deposited 2024-01-09 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 × 10 PDB declaration: decameric
Chain C 1–770（770 aa）
Chain F 1–770（770 aa）
Chain Z 1–770（770 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.57 Å
8RNB Influenza B polymerase, encapsidase plus 627(R) / human ANP32A (from "Influenza B polymerase apo-trimer" | Local refinement) Deposited 2024-01-09 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 × 5 PDB declaration: pentameric
Chain C 1–770（770 aa）
Chain F 1–770（770 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.31 Å
8RNC Influenza B polymerase, replication complex, an asymmetric polymerase dimer bound to human ANP32A (from "Influenza B polymerase apo-trimer" | Local refinement) Deposited 2024-01-09 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 × 9 PDB declaration: nonameric
Chain C 1–770（770 aa）
Chain F 1–770（770 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.52 Å

31 other PDB entries and 38 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q5V8X3_9INFB
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 10–779； UniProt 1–770

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

SAXS profile for 5msg

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5msg
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5msg
Deposition date deposition_date2017-01-04
Structure title titleInfluenza B polymerase bound to vRNA promoter and capped RNA primer
Keywords keywordsinfluenza B virus RNA-dependent RNA polymerase, vRNA promoter, capped RNA primer, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier40.92 Å
Radius of gyration Rg (electron density) rg_electron40.46 Å
Forward intensity I(0) i01062630000.00
Molecular weight molecular_weight260950.0 kDa
Excluded volume excluded_volume323710 ų
Envelope volume envelope_volume431390 ų
Hydration-shell volume shell_volume84218 ų
Envelope diameter envelope_diameter135.2 Å
Shell Rg shell_rg49.11 Å
Envelope Rg envelope_rg40.33 Å
Shape Rg shape_rg40.48 Å
Total Rg total_rg40.81 Å
Total atoms total_atoms18236
Residues n_residues2230
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax130.8 Å
Rg (real space) rg_real40.75 Å
Rg uncertainty (real space) rg_real_error0.89 Å
I(0) (real space) i0_real1.0630e+09
I(0) uncertainty (real space) i0_real_error1.7710e+07
Rg (reciprocal space) rg_reciprocal40.92 Å
I(0) (reciprocal space) i0_reciprocal1063000000.0000
Solution quality estimate total_estimate0.8846
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary53.7 Å
Skewness Skewness skewness0.197
Kurtosis Kurtosis kurtosis-0.384
Angular range angular_range— – 0.1950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha234800000.0000
Real-space data points n_real_points40
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.872; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.893
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

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8. Citations (1)

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9. Files and Curves (10)