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- PDB-5hmg: REFINEMENT OF THE INFLUENZA VIRUS HEMAGGLUTININ BY SIMULATED ANNEALING -

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Basic information

Entry
Database: PDB / ID: 5hmg
TitleREFINEMENT OF THE INFLUENZA VIRUS HEMAGGLUTININ BY SIMULATED ANNEALING
Components(Hemagglutinin ...) x 2
KeywordsVIRAL PROTEIN / INFLUENZA VIRUS HEMAGGLUTININ
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 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
N-acetyl-alpha-neuraminic acid / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / Resolution: 3.2 Å
AuthorsWeis, W.I. / Bruenger, A.T. / Skehel, J.J. / Wiley, D.C.
Citation
Journal: J.Mol.Biol. / Year: 1990
Title: Refinement of the influenza virus hemagglutinin by simulated annealing.
Authors: Weis, W.I. / Brunger, A.T. / Skehel, J.J. / Wiley, D.C.
#1: Journal: Nature / Year: 1988
Title: Structure of the Influenza Virus Haemagglutinin Complexes with its Receptor, Sialic Acid
Authors: Weis, W. / Brown, J.H. / Cusack, S. / Paulson, J.C. / Skehel, J.J. / Wiley, D.C.
#2: Journal: Nature / Year: 1984
Title: Three-Dimensional Structure of an Antigenic Mutant of the Influenza Virus Haemagglutinin
Authors: Knossow, M. / Daniels, R.S. / Douglas, A.R. / Skehel, J.J. / Wiley, D.C.
#3: Journal: Nature / Year: 1981
Title: Structure of the Haemagglutinin Membrane Glycoprotein of Influenza Virus at 3 Angstroms Resolution
Authors: Wilson, I.A. / Skehel, J.J. / Wiley, D.C.
#4: Journal: Nature / Year: 1981
Title: Structural Identification of the Antibody-Binding Sites of Hong Kong Influenza Haemagglutinin and Their Involvement in Antigenic Variation
Authors: Wiley, D.C. / Wilson, I.A. / Skehel, J.J.
#5: Journal: J.Mol.Biol. / Year: 1977
Title: Crystallization and X-Ray Diffraction Studies on the Haemagglutinin Glycoprotein from the Membrane of Influenza Virus
Authors: Wiley, D.C. / Skehel, J.J.
History
DepositionSep 11, 1989Processing site: BNL
Revision 1.0Jan 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_validate_chiral / struct_asym / struct_conn / struct_ref_seq_dif / 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.occupancy / _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_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
C: Hemagglutinin HA1 chain
D: Hemagglutinin HA2 chain
E: Hemagglutinin HA1 chain
F: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,00124
Polymers168,6596
Non-polymers5,34218
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40580 Å2
ΔGint-84 kcal/mol
Surface area58690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.600, 162.600, 177.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Atom site foot note1: RESIDUES PRO A 55, PRO C 55, PRO E 55 ARE CIS PROLINES.
2: A TEMPERATURE FACTOR OF 65.0 OR LARGER SIGNIFIES AN ATOM WHOSE COORDINATES WERE GENERATED USING STEREOCHEMICAL CRITERIA.
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.034333, -0.550874, 0.833882), (-0.851708, 0.420417, 0.3128), (-0.522891, -0.720963, -0.454749)41.4187, 45.2807, 61.8898
2given(0.034333, -0.851708, -0.522891), (-0.550874, 0.420417, -0.720963), (0.833882, 0.3128, -0.454749)69.5055, 48.3999, -20.5577
Details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Components

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Hemagglutinin ... , 2 types, 6 molecules ACEBDF

#1: Protein Hemagglutinin HA1 chain / Hemagglutinin


Mass: 36065.457 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Aichi/2/1968(H3N2))
Genus: Influenzavirus A / Species: Influenza A virus / Strain: (A/Aichi/2/1968(H3N2)) / Gene: HA / References: UniProt: P03437
#2: Protein Hemagglutinin HA2 chain / Hemagglutinin


Mass: 20154.314 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Aichi/2/1968(H3N2))
Genus: Influenzavirus A / Species: Influenza A virus / Strain: (A/Aichi/2/1968(H3N2)) / Gene: HA / References: UniProt: P03437

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Sugars , 3 types, 18 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-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.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_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-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 12
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

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Non-polymers , 1 types, 39 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal grow
*PLUS
pH: 7.5 / Method: microdialysis
Details: referred to 'Weis, W.', (1988) Nature, 333, 426-431
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
135 mg/mlprotein11
21.30-1.34 MNa3 citrate12
30.1 %12NaN3

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 7 Å / Num. obs: 54098 / % possible obs: 64.7 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.16

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementRfactor Rwork: 0.22 / Highest resolution: 3.2 Å
Details: A TEMPERATURE FACTOR OF 65.0 OR LARGER SIGNIFIES AN ATOM WHOSE COORDINATES WERE GENERATED USING STEREOCHEMICAL CRITERIA.
Refinement stepCycle: LAST / Highest resolution: 3.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11847 0 348 39 12234
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg2.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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: XPLOR / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d2.8
X-RAY DIFFRACTIONx_dihedral_angle_d27
X-RAY DIFFRACTIONx_improper_angle_d1.5
X-RAY DIFFRACTIONx_chiral_restr0.09

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