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- PDB-2viu: INFLUENZA VIRUS HEMAGGLUTININ -

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Basic information

Entry
Database: PDB / ID: 2viu
TitleINFLUENZA VIRUS HEMAGGLUTININ
Components(HEMAGGLUTININ) x 2
KeywordsHEMAGGLUTININ / ENVELOPE PROTEIN / GLYCOPROTEIN
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B ...Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Ribbon / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
unidentified influenza virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsBizebard, T. / Fleury, D. / Gigant, B. / Wharton, S.A. / Skehel, J.J. / Knossow, M.
Citation
Journal: Nat.Struct.Biol. / Year: 1998
Title: Antigen distortion allows influenza virus to escape neutralization.
Authors: Fleury, D. / Wharton, S.A. / Skehel, J.J. / Knossow, M. / Bizebard, T.
#1: Journal: Nature / Year: 1995
Title: Structure of Influenza Virus Haemagglutinin Complexed with a Neutralizing Antibody
Authors: Bizebard, T. / Gigant, B. / Rigolet, P. / Rasmussen, B. / Diat, O. / Bosecke, P. / Wharton, S.A. / Skehel, J.J. / Knossow, M.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1994
Title: Refined Three-Dimensional Structure of the Fab Fragment of a Murine Iggl, Antibody
Authors: Bizebard, T. / Daniels, R. / Kahn, R. / Golinelli-Pimpaneau, B. / Skehel, J.J. / Knossow, M.
#3: Journal: Nature / Year: 1981
Title: Structure of the Haemagglutinin Membrane Glycoprotein of Influenza Virus at 3 A Resolution
Authors: Wilson, I.A. / Skehel, J.J. / Wiley, D.C.
History
DepositionDec 22, 1997Processing site: BNL
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.process_site / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 3, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEMAGGLUTININ
B: HEMAGGLUTININ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9828
Polymers56,2902
Non-polymers1,6936
Water1,856103
1
A: HEMAGGLUTININ
B: HEMAGGLUTININ
hetero molecules

A: HEMAGGLUTININ
B: HEMAGGLUTININ
hetero molecules

A: HEMAGGLUTININ
B: HEMAGGLUTININ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,94724
Polymers168,8706
Non-polymers5,07818
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_456z-1/2,-x+1/2,-y+11
crystal symmetry operation12_565-y+1/2,-z+1,x+1/21
Buried area39120 Å2
ΔGint-84 kcal/mol
Surface area56580 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)144.400, 144.400, 144.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein HEMAGGLUTININ /


Mass: 36077.512 Da / Num. of mol.: 1 / Mutation: CHAIN A, T131I
Source method: isolated from a genetically manipulated source
Details: BROMELAIN DIGESTED / Source: (gene. exp.) Influenza A virus (A/X-31(H3N2)) / Genus: Influenzavirus A / Species: Influenza A virus / Strain: X31
Description: A REASSORTANT INFLUENZA STRAIN CONTAINING A/AICHI/68 (H3N2) HEMAGGLUTININ
References: UniProt: P03437
#2: Protein HEMAGGLUTININ /


Mass: 20212.350 Da / Num. of mol.: 1 / Mutation: CHAIN A, T131I
Source method: isolated from a genetically manipulated source
Details: BROMELAIN DIGESTED / Source: (gene. exp.) unidentified influenza virus / Strain: X31
Description: A REASSORTANT INFLUENZA STRAIN CONTAINING A/AICHI/68 (H3N2) HEMAGGLUTININ
References: UniProt: P03437
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.46 Å3/Da / Density % sol: 66 %
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
170 mg/mlprotein1drop
20.15 M1dropNaCl
30.05 %1dropNaN3
41.18 Mcitrate1reservoir
50.05 %1reservoirNaN3

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.97
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 8, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.45→20 Å / Num. obs: 36234 / % possible obs: 99.9 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.055
Reflection
*PLUS
Num. measured all: 163053

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Processing

Software
NameVersionClassification
HKLdata collection
X-PLOR3.84model building
X-PLOR3.84refinement
HKLdata reduction
X-PLOR3.84phasing
RefinementResolution: 2.5→9 Å / σ(F): 0
Details: THERE IS ONE MONOMER OF THE TRIMERIC HEMAGGLUTININ MOLECULE IN THE ASYMMETRIC UNIT. THE MONOMER OF HEMAGGLUTININ CONSISTS OF TWO CHAINS, IDENTIFIED AS HA1 AND HA2 BY THE THE DEPOSITORS. ...Details: THERE IS ONE MONOMER OF THE TRIMERIC HEMAGGLUTININ MOLECULE IN THE ASYMMETRIC UNIT. THE MONOMER OF HEMAGGLUTININ CONSISTS OF TWO CHAINS, IDENTIFIED AS HA1 AND HA2 BY THE THE DEPOSITORS. CHAINS HA1 AND HA2 HAVE BEEN ASSIGNED CHAIN IDENTIFIERS *A* AND *B*, RESPECTIVELY.
RfactorNum. reflection% reflection
Rfree0.242 -5 %
Rwork0.21 --
obs0.21 36234 -
Refinement stepCycle: LAST / Resolution: 2.5→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3892 0 109 103 4104
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.5
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.84 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å / Rfactor obs: 0.213 / Rfactor Rfree: 0.239 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.5

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