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6y5k

Extended Intermediate form of X-31 Influenza Haemagglutinin at pH 5 (State IV)

Method: ELECTRON MICROSCOPY Dmax: 145.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

X-31 Influenza Haemagglutinin HA1

unidentified influenza virus

UniProt P03437

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 homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain A； UniProt 24–341 Chain B； UniProt 346–517 Chain C； UniProt 24–341 Chain D； UniProt 346–517 Chain E； UniProt 24–341 Chain F； UniProt 346–517 Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ELECTRON MICROSCOPY cryo-EM buffer：pH 5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.20 Å

Other States of the Same Protein in the Database

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

Other PDB Difference from Current Entry 6Y5K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1EO8 INFLUENZA VIRUS HEMAGGLUTININ COMPLEXED WITH A NEUTRALIZING ANTIBODY Deposited 2000-03-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 17–344（328 aa） Fragment：BROMELAIN RELEASED FRAGMENT
Chain B 346–520（175 aa） Fragment：BROMELAIN RELEASED FRAGMENT
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；28%(w:v) PEG 600, 100 mM Sodium Phosphate, 150 mM NaCl, 0.05% NaN3 , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.298
1FYT CRYSTAL STRUCTURE OF A COMPLEX OF A HUMAN ALPHA/BETA-T CELL RECEPTOR, INFLUENZA HA ANTIGEN PEPTIDE, AND MHC CLASS II MOLECULE, HLA-DR1 Deposited 2000-10-03 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 322–334（13 aa） Fragment：ANTIGEN PEPTIDE
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；11% PEG 8000, 1 M NaCl, 100 mM HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 18K
Resolution 2.60 Å R-free 0.255
1HA0 HEMAGGLUTININ PRECURSOR HA0 Deposited 1998-10-08 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 25–518（494 aa） Fragment：HA1, HA2
Mutation：R329Q NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.50
Resolution 2.80 Å R-free 0.302
1HGD BINDING OF INFLUENZA VIRUS HEMAGGLUTININ TO ANALOGS OF ITS CELL-SURFACE RECEPTOR, SIALIC ACID: ANALYSIS BY PROTON NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY AND X-RAY CRYSTALLOGRAPHY Deposited 1991-11-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 17–344（328 aa）
Chain B 346–520（175 aa）
Chain C 17–344（328 aa）
Chain D 346–520（175 aa）
Chain E 17–344（328 aa）
Chain F 346–520（175 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.70 Å
1HGE BINDING OF INFLUENZA VIRUS HEMAGGLUTININ TO ANALOGS OF ITS CELL-SURFACE RECEPTOR, SIALIC ACID: ANALYSIS BY PROTON NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY AND X-RAY CRYSTALLOGRAPHY Deposited 1991-11-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 17–344（328 aa）
Chain B 346–520（175 aa）
Chain C 17–344（328 aa）
Chain D 346–520（175 aa）
Chain E 17–344（328 aa）
Chain F 346–520（175 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 MNA 2-O-methyl-5-N-acetyl-alpha-D-neuraminic acid × 3 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.60 Å
1HGF BINDING OF INFLUENZA VIRUS HEMAGGLUTININ TO ANALOGS OF ITS CELL-SURFACE RECEPTOR, SIALIC ACID: ANALYSIS BY PROTON NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY AND X-RAY CRYSTALLOGRAPHY Deposited 1991-11-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 17–344（328 aa）
Chain B 346–520（175 aa）
Chain C 17–344（328 aa）
Chain D 346–520（175 aa）
Chain E 17–344（328 aa）
Chain F 346–520（175 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å
1HGG BINDING OF INFLUENZA VIRUS HEMAGGLUTININ TO ANALOGS OF ITS CELL-SURFACE RECEPTOR, SIALIC ACID: ANALYSIS BY PROTON NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY AND X-RAY CRYSTALLOGRAPHY Deposited 1991-11-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 17–344（328 aa）
Chain B 346–520（175 aa）
Chain C 17–344（328 aa）
Chain D 346–520（175 aa）
Chain E 17–344（328 aa）
Chain F 346–520（175 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.90 Å
1HGH BINDING OF INFLUENZA VIRUS HEMAGGLUTININ TO ANALOGS OF ITS CELL-SURFACE RECEPTOR, SIALIC ACID: ANALYSIS BY PROTON NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY AND X-RAY CRYSTALLOGRAPHY Deposited 1991-11-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 17–344（328 aa）
Chain B 346–520（175 aa）
Chain C 17–344（328 aa）
Chain D 346–520（175 aa）
Chain E 17–344（328 aa）
Chain F 346–520（175 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 MNA 2-O-methyl-5-N-acetyl-alpha-D-neuraminic acid × 6 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.70 Å
1HGI BINDING OF INFLUENZA VIRUS HEMAGGLUTININ TO ANALOGS OF ITS CELL-SURFACE RECEPTOR, SIALIC ACID: ANALYSIS BY PROTON NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY AND X-RAY CRYSTALLOGRAPHY Deposited 1991-11-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 17–344（328 aa）
Chain B 346–520（175 aa）
Chain C 17–344（328 aa）
Chain D 346–520（175 aa）
Chain E 17–344（328 aa）
Chain F 346–520（175 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 ANA methyl 4-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid × 3 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.70 Å
1HGJ BINDING OF INFLUENZA VIRUS HEMAGGLUTININ TO ANALOGS OF ITS CELL-SURFACE RECEPTOR, SIALIC ACID: ANALYSIS BY PROTON NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY AND X-RAY CRYSTALLOGRAPHY Deposited 1991-11-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 17–344（328 aa）
Chain B 346–520（175 aa）
Chain C 17–344（328 aa）
Chain D 346–520（175 aa）
Chain E 17–344（328 aa）
Chain F 346–520（175 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 AMN methyl 5-acetamido-9-amino-3,5,9-trideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid × 3 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.70 Å
1HTM STRUCTURE OF INFLUENZA HAEMAGGLUTININ AT THE PH OF MEMBRANE FUSION Deposited 1994-11-02 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 17–43（27 aa）
Chain B 383–520（138 aa）
Chain C 17–43（27 aa）
Chain D 383–520（138 aa）
Chain E 17–43（27 aa）
Chain F 383–520（138 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å R-free 0.291
1J8H Crystal Structure of a Complex of a Human alpha/beta-T cell Receptor, Influenza HA Antigen Peptide, and MHC Class II Molecule, HLA-DR4 Deposited 2001-05-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 322–334（13 aa） Fragment：Antigen Peptide
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；13% PEG 8000, 1 M NaCl, 100 mM HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 2.40 Å R-free 0.246
1KEN INFLUENZA VIRUS HEMAGGLUTININ COMPLEXED WITH AN ANTIBODY THAT PREVENTS THE HEMAGGLUTININ LOW PH FUSOGENIC TRANSITION Deposited 2001-11-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: decameric
Chain B 346–520（175 aa） Fragment：FAB fragment of antibody
Chain D 346–520（175 aa） Fragment：FAB fragment of antibody
Chain F 346–520（175 aa） Fragment：FAB fragment of antibody
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；peg 20000, calcium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.50 Å R-free 0.323
1QFU INFLUENZA VIRUS HEMAGGLUTININ COMPLEXED WITH A NEUTRALIZING ANTIBODY Deposited 1999-04-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 17–344（328 aa） Fragment：BROMELAIN DIGESTED
Chain B 346–520（175 aa） Fragment：BROMELAIN DIGESTED
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；pH 7.0
Resolution 2.80 Å R-free 0.284
1QU1 CRYSTAL STRUCTURE OF EHA2 (23-185) Deposited 1999-07-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 376–530（155 aa）
Chain B 376–530（155 aa）
Chain C 376–530（155 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.4；2% PEG 4000, 30-150 MM NACL, pH 4.40
Resolution 1.90 Å R-free 0.250
1QU1 CRYSTAL STRUCTURE OF EHA2 (23-185) Deposited 1999-07-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain D 376–530（155 aa）
Chain E 376–530（155 aa）
Chain F 376–530（155 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.4；2% PEG 4000, 30-150 MM NACL, pH 4.40
Resolution 1.90 Å R-free 0.250
2HMG REFINEMENT OF THE INFLUENZA VIRUS HEMAGGLUTININ BY SIMULATED ANNEALING Deposited 1989-09-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 17–344（328 aa）
Chain B 346–520（175 aa）
Chain C 17–344（328 aa）
Chain D 346–520（175 aa）
Chain E 17–344（328 aa）
Chain F 346–520（175 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å
2VIR INFLUENZA VIRUS HEMAGGLUTININ COMPLEXED WITH A NEUTRALIZING ANTIBODY Deposited 1997-12-22 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 × 3 PDB declaration: trimeric
Chain C 44–325（282 aa） Fragment：;PROTEOLYTIC FRAGMENT "HA TOP" CONTAINING HA1 RESIDUES 28 - 328 ;
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.25 Å R-free 0.249
2VIS INFLUENZA VIRUS HEMAGGLUTININ, (ESCAPE) MUTANT WITH THR 131 REPLACED BY ILE, COMPLEXED WITH A NEUTRALIZING ANTIBODY Deposited 1997-12-22 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 × 3 PDB declaration: trimeric
Chain C 44–325（282 aa） Fragment：;PROTEOLYTIC FRAGMENT "HA TOP" CONTAINING HA1 RESIDUES 28 - 328 ;
Mutation：T131I ZN ZINC ION × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.25 Å R-free 0.267
2VIT INFLUENZA VIRUS HEMAGGLUTININ, MUTANT WITH THR 155 REPLACED BY ILE, COMPLEXED WITH A NEUTRALIZING ANTIBODY Deposited 1997-12-22 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 × 3 PDB declaration: trimeric
Chain C 44–325（282 aa） Fragment：;PROTEOLYTIC FRAGMENT "HA TOP" CONTAINING HA1 RESIDUES 28 - 328 ;
Mutation：T155I ZN ZINC ION × 3 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.25 Å R-free 0.237
2VIU INFLUENZA VIRUS HEMAGGLUTININ Deposited 1997-12-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 17–344（328 aa）
Chain B 346–520（175 aa）
Mutation：CHAIN A, T131I Mutation：CHAIN A, T131I NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å R-free 0.242
2YPG Haemagglutinin of 1968 Human H3N2 Virus in Complex with Human Receptor Analogue LSTc Deposited 2012-10-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 17–344（328 aa）
Chain B 346–520（175 aa） Fragment：HA2 OF BROMELAIN RELEASED ECTODOMAIN, RESIDUES 346-520
Chain C 17–344（328 aa）
Chain D 346–520（175 aa） Fragment：HA2 OF BROMELAIN RELEASED ECTODOMAIN, RESIDUES 346-520
Chain E 17–344（328 aa）
Chain F 346–520（175 aa） Fragment：HA2 OF BROMELAIN RELEASED ECTODOMAIN, RESIDUES 346-520
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 FLC CITRATE ANION × 13 X-RAY DIFFRACTION
X-ray crystallization conditions 1.7-2 M TRIAMMONIUM CITRATE PH 6.5
Resolution 2.85 Å R-free 0.190
3EYM Structure of Influenza Haemagglutinin in complex with an inhibitor of membrane fusion Deposited 2008-10-21 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 25–345（321 aa）
Chain B 346–517（172 aa）
Chain C 25–345（321 aa）
Chain D 346–517（172 aa）
Chain E 25–345（321 aa）
Chain F 346–517（172 aa）
Not recorded EYK 2-tert-butylbenzene-1,4-diol × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；Ammonium citratre, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.217
3HMG REFINEMENT OF THE INFLUENZA VIRUS HEMAGGLUTININ BY SIMULATED ANNEALING Deposited 1989-09-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 17–344（328 aa）
Chain B 346–520（175 aa）
Chain C 17–344（328 aa）
Chain D 346–520（175 aa）
Chain E 17–344（328 aa）
Chain F 346–520（175 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.90 Å
3VUN Crystal structure of a influenza A virus (A/Aichi/2/1968 H3N2) hemagglutinin in C2 space group. Deposited 2012-07-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 17–345（329 aa）
Chain B 346–520（175 aa）
Chain C 17–345（329 aa）
Chain D 346–520（175 aa）
Chain E 17–345（329 aa）
Chain F 346–520（175 aa）
Mutation：G144S, I182V Mutation：E132D Mutation：G144S, I182V Mutation：E132D Mutation：G144S, I182V Mutation：E132D NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.25；293 K；0.2M imidazole (pH 7.0), 27% Jeffamine ED-2001 (pH 7.0), VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.00 Å R-free 0.275
3ZTJ Structure of influenza A neutralizing antibody selected from cultures of single human plasma cells in complex with human H3 Influenza haemagglutinin. Deposited 2011-07-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 17–345（329 aa）
Chain B 346–520（175 aa） Fragment：RESIDUES 346-520
Chain C 17–345（329 aa）
Chain D 346–520（175 aa） Fragment：RESIDUES 346-520
Chain E 17–345（329 aa）
Chain F 346–520（175 aa） Fragment：RESIDUES 346-520
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.41 Å R-free 0.284
4HMG REFINEMENT OF THE INFLUENZA VIRUS HEMAGGLUTININ BY SIMULATED ANNEALING Deposited 1989-09-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 17–344（328 aa）
Chain B 346–520（175 aa）
Chain C 17–344（328 aa）
Chain D 346–520（175 aa）
Chain E 17–344（328 aa）
Chain F 346–520（175 aa）
Not recorded SIA N-acetyl-alpha-neuraminic acid × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å
5HMG REFINEMENT OF THE INFLUENZA VIRUS HEMAGGLUTININ BY SIMULATED ANNEALING Deposited 1989-09-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 17–344（328 aa）
Chain B 346–520（175 aa）
Chain C 17–344（328 aa）
Chain D 346–520（175 aa）
Chain E 17–344（328 aa）
Chain F 346–520（175 aa）
Not recorded SIA N-acetyl-alpha-neuraminic acid × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.20 Å
5Y2L Crystal structure of a group 2 HA binding antibody AF4H1K1 Fab in complex with the 1968 H3N2 pandemic (H3-AC/68) hemagglutinin Deposited 2017-07-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 17–345（329 aa）
Chain B 346–521（176 aa） Fragment：UNP residues 346-521
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；0.19 mM CYMAL7, 0.1M HEPES pH 7.5, 40% ployethylene glycol 400
Resolution 2.90 Å R-free 0.244
6E56 Human antibody H2214 in complex with influenza hemagglutinin A/Aichi/2/1968 (X-31) (H3N2) Deposited 2018-07-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 53–335（283 aa） Fragment：head domain (UNP residues 53-335)
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291.15 K；100 mM sodium chloride, 100 mM sodium acetate, pH 5.0, 20% w/v PEG2000 MME
Resolution 2.00 Å R-free 0.214
6E56 Human antibody H2214 in complex with influenza hemagglutinin A/Aichi/2/1968 (X-31) (H3N2) Deposited 2018-07-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 53–335（283 aa） Fragment：head domain (UNP residues 53-335)
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291.15 K；100 mM sodium chloride, 100 mM sodium acetate, pH 5.0, 20% w/v PEG2000 MME
Resolution 2.00 Å R-free 0.214
6N5D Broadly protective antibodies directed to a subdominant influenza hemagglutinin epitope Deposited 2018-11-21 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 × 3 PDB declaration: trimeric
Chain A 53–334（282 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.2 M sodium bromide, 0.1 M Bis-Tris propane, pH 6.5, 20% w/v PEG3350
Resolution 3.00 Å R-free 0.244
6N5D Broadly protective antibodies directed to a subdominant influenza hemagglutinin epitope Deposited 2018-11-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 53–334（282 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.2 M sodium bromide, 0.1 M Bis-Tris propane, pH 6.5, 20% w/v PEG3350
Resolution 3.00 Å R-free 0.244
6N5D Broadly protective antibodies directed to a subdominant influenza hemagglutinin epitope Deposited 2018-11-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain K 53–334（282 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.2 M sodium bromide, 0.1 M Bis-Tris propane, pH 6.5, 20% w/v PEG3350
Resolution 3.00 Å R-free 0.244
6N5E Broadly protective antibodies directed to a subdominant influenza hemagglutinin epitope Deposited 2018-11-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 53–334（282 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.2 M ammonium sulfate, 0.1 M MES, pH 6.5, 20% w/v PEG8000
Resolution 3.00 Å R-free 0.287
6N5E Broadly protective antibodies directed to a subdominant influenza hemagglutinin epitope Deposited 2018-11-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 53–334（282 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.2 M ammonium sulfate, 0.1 M MES, pH 6.5, 20% w/v PEG8000
Resolution 3.00 Å R-free 0.287
6N5E Broadly protective antibodies directed to a subdominant influenza hemagglutinin epitope Deposited 2018-11-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 53–334（282 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.2 M ammonium sulfate, 0.1 M MES, pH 6.5, 20% w/v PEG8000
Resolution 3.00 Å R-free 0.287
6XPX Human antibody S1V2-51 in complex with the influenza hemagglutinin head domain of A/Aichi/2/1968 (X-31)(H3N2) Deposited 2020-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 53–335（283 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 BCN BICINE × 2 GOL GLYCEROL × 7 1PE PENTAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；291.15 K；0.3 M Magnesium chloride, 25% (w/v) PEG 2000, 15% (w/v) Glycerol, 0.1 M BICINE, pH 9.0
Resolution 2.60 Å R-free 0.215
6Y5G Ectodomain of X-31 Haemagglutinin at pH 8 Deposited 2020-02-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 24–341（318 aa）
Chain B 346–517（172 aa）
Chain C 24–341（318 aa）
Chain D 346–517（172 aa）
Chain E 24–341（318 aa）
Chain F 346–517（172 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6Y5H Ectodomain of X-31 Haemagglutinin at pH 5 (State I) Deposited 2020-02-25 Different oligomeric state Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 24–341（318 aa）
Chain B 346–517（172 aa）
Chain C 24–341（318 aa）
Chain D 346–517（172 aa）
Chain E 24–341（318 aa）
Chain F 346–517（172 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6Y5I Dilated form 1 of X-31 Influenza Haemagglutinin at pH 5 (State II) Deposited 2020-02-25 Different oligomeric state Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 24–341（318 aa）
Chain B 346–517（172 aa）
Chain C 24–341（318 aa）
Chain D 346–517（172 aa）
Chain E 24–341（318 aa）
Chain F 346–517（172 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.50 Å
6Y5J Dilated form 2 of X-31 Influenza Haemagglutinin at pH 5 (State III) Deposited 2020-02-25 Different oligomeric state Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 24–341（318 aa）
Chain B 346–517（172 aa）
Chain C 24–341（318 aa）
Chain D 346–517（172 aa）
Chain E 24–341（318 aa）
Chain F 346–517（172 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.60 Å
6Y5L Signal Subtracted Extended Intermediate form of X-31 Influenza Haemagglutinin at pH 5 (State IV) Deposited 2020-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 346–517（172 aa）
Chain D 346–517（172 aa）
Chain F 346–517（172 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7ZJ6 X-31 Hemagglutinin Precursor HA0 at pH 7.5 Deposited 2022-04-08 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 17–520（504 aa）
Chain B 17–520（504 aa）
Chain C 17–520（504 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；4s blot
Resolution 2.60 Å
7ZJ7 X-31 Hemagglutinin Precursor HA0 at pH 4.8 Deposited 2022-04-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 17–520（504 aa）
Chain B 17–520（504 aa）
Chain C 17–520（504 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 4.8
cryo-EM vitrification conditions Cryogen ETHANE；4s blot
Resolution 3.95 Å
7ZJ8 X-31 Hemagglutinin Precursor HA0 at pH 7.5 after reneutralization Deposited 2022-04-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 17–520（504 aa）
Chain B 17–520（504 aa）
Chain C 17–520（504 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 BOG octyl beta-D-glucopyranoside × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE；4s blot
Resolution 3.10 Å
8G5B Influenza A H3N2 X-31 Hemagglutinin in complex with FL-1061 Deposited 2023-02-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain A 53–335（283 aa） Fragment：head fragment
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8PK3 CryoEM reconstruction of hemagglutinin HK68 of Influenza A virus bound to an Affimer reagent Deposited 2023-06-24 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric
Chain D 346–520（175 aa）
Chain E 346–520（175 aa）
Chain F 346–520（175 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å

42 other PDB entries and 48 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HEMA_I68A0
Isoform —
PDB entities 1, 2
Chains and sequence ranges Author chain A； PDBConstruct 1–318； UniProt 24–341 Author chain C； PDBConstruct 1–318； UniProt 24–341 Author chain E； PDBConstruct 1–318； UniProt 24–341 Author chain B； PDBConstruct 1–172； UniProt 346–517 Author chain D； PDBConstruct 1–172； UniProt 346–517 Author chain F； PDBConstruct 1–172； UniProt 346–517

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 6y5k

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6y5k
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6y5k
Deposition date deposition_date2020-02-25
Structure title titleExtended Intermediate form of X-31 Influenza Haemagglutinin at pH 5 (State IV)
Keywords keywordsHaemagglutinin, Hemagglutinin, Fusion protein, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier43.43 Å
Radius of gyration Rg (electron density) rg_electron42.77 Å
Forward intensity I(0) i0368862000.00
Molecular weight molecular_weight151080.0 kDa
Excluded volume excluded_volume186990 ų
Envelope volume envelope_volume281420 ų
Hydration-shell volume shell_volume57300 ų
Envelope diameter envelope_diameter152.7 Å
Shell Rg shell_rg45.52 Å
Envelope Rg envelope_rg41.84 Å
Shape Rg shape_rg42.75 Å
Total Rg total_rg42.97 Å
Total atoms total_atoms10614
Residues n_residues1335
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 dmax145.5 Å
Rg (real space) rg_real43.51 Å
Rg uncertainty (real space) rg_real_error1.88 Å
I(0) (real space) i0_real3.6890e+08
I(0) uncertainty (real space) i0_real_error6.9340e+06
Rg (reciprocal space) rg_reciprocal43.43 Å
I(0) (reciprocal space) i0_reciprocal368800000.0000
Solution quality estimate total_estimate0.8631
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary52.6 Å
Skewness Skewness skewness0.420
Kurtosis Kurtosis kurtosis-0.182
Angular range angular_range— – 0.1800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha29080000.0000
Real-space data points n_real_points37
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.799; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.819
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)