6fs8

Influenza B/Memphis/13/03 endonuclease with bound inhibitor, baloxavir acid (BXA)

Method: X-RAY DIFFRACTION D_max: 67.5 Å Quality: EXCELLENT

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

Polymerase acidic protein

Influenza B virus (B/Memphis/13/2003)

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–197	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–197	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

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 6FS8	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 construct 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 construct 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 construct 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
5MSG Influenza B polymerase bound to vRNA promoter and capped RNA primer Deposited 2017-01-04	Different construct 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 1–726（726 aa）	Not recorded	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
6F5O A mechanism for the activation of the influenza virus transcriptase Deposited 2017-12-02	Different construct 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
6FS9 Influenza B/Memphis/13/03 endonuclease with I38T mutation with bound inhibitor, baloxavir acid (BXA) Deposited 2018-02-19	Different mutation/modification 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 mutation/modification 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 mutation/modification 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 construct 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: 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 construct 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: 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 construct 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 1–726（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 construct 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 1–726（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 construct 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 1–726（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 construct 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 construct 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: 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 construct 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 construct 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 construct 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 construct 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: 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 construct 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: 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 construct 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: 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 construct 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 construct 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 construct 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 construct 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 42 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 9–205； UniProt 1–197 Author chain B； PDBConstruct 9–205； UniProt 1–197

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	6fs8
Deposition date deposition_date	2018-02-19
Structure title title	Influenza B/Memphis/13/03 endonuclease with bound inhibitor, baloxavir acid (BXA)
Keywords keywords	Influenza, endonuclease, inhibitor, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	21.99 Å
Radius of gyration Rg (electron density) rg_electron	20.92 Å
Forward intensity I(0) i0	30689700.00
Molecular weight molecular_weight	43100.0 kDa
Excluded volume excluded_volume	54089 Å³
Envelope volume envelope_volume	63711 Å³
Hydration-shell volume shell_volume	24827 Å³
Envelope diameter envelope_diameter	68.2 Å
Shell Rg shell_rg	27.94 Å
Envelope Rg envelope_rg	21.08 Å
Shape Rg shape_rg	20.96 Å
Total Rg total_rg	21.72 Å
Total atoms total_atoms	3014
Residues n_residues	360
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	67.5 Å
Rg (real space) rg_real	21.84 Å
Rg uncertainty (real space) rg_real_error	0.32 Å
I(0) (real space) i0_real	3.0690e+07
I(0) uncertainty (real space) i0_real_error	3.5210e+05
Rg (reciprocal space) rg_reciprocal	21.87 Å
I(0) (reciprocal space) i0_reciprocal	30690000.0000
Solution quality estimate total_estimate	0.9047
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.2 Å
Skewness Skewness skewness	0.150
Kurtosis Kurtosis kurtosis	-0.466
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8900000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.926; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.985

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Polymerase acidic protein
Molecular weight formula_weight	23518.7 kDa
EC 编号 ec_number	3.1.-.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A
Atom count atom_count	3267

GAMGSGMAMDTFITRNFQTTIIQKAKNTMAEFSEDPELQPAMLFNICVHLEVCYVISDMNFLDEEGKSYTALEGQGKEQNLRPQYEVIEGMPRTIAWMVQRSLAQEHGIETPKYLADLFDYKTKRFIEVGITKGLADDYFWKKKEKLGNSMELMIFSYNQDYSLSNESSLDEEGKGRVLSRLTELQAELSLKNLWQVLIGEEDVE

来源 Source

来源生物 organism	Influenza B virus (B/Memphis/13/2003)
NCBI Class编号 ncbi_taxonomy_id	1601067
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	Baloxavir acid
Molecular weight formula_weight	483.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	176

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d6fs8a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.52 — Restriction endonuclease-like
Superfamily Superfamily superfamily	c.52.1 — Restriction endonuclease-like
Family Family family	c.52.1.34 — PA N-terminal domain

Domain ID domain_id	d6fs8a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6fs8b1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.52 — Restriction endonuclease-like
Superfamily Superfamily superfamily	c.52.1 — Restriction endonuclease-like
Family Family family	c.52.1.34 — PA N-terminal domain

Domain ID domain_id	d6fs8b2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

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8. Citations (1)

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Unit-cell length a length_a	59.820 Å
Unit-cell length b length_b	59.820 Å
Unit-cell length c length_c	125.890 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	8

Space group space_group	P 43
Space-group number int_tables_number	78
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	59.860 Å
R factor r_factor	0.1849
R_work r_work	0.1834
R_free r_free	0.2151

fit	/app/data/saxs_computation/fs/6fs8/6fs8.fit
pddf	/app/data/pr_computation/fs/6fs8/6fs8.pr.out
profile	/app/data/saxs_computation/fs/6fs8/6fs8.dat