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- PDB-1hgh: BINDING OF INFLUENZA VIRUS HEMAGGLUTININ TO ANALOGS OF ITS CELL-S... -

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Entry
Database: PDB / ID: 1hgh
TitleBINDING OF INFLUENZA VIRUS HEMAGGLUTININ TO ANALOGS OF ITS CELL-SURFACE RECEPTOR, SIALIC ACID: ANALYSIS BY PROTON NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY AND X-RAY CRYSTALLOGRAPHY
Components(HEMAGGLUTININ, CHAIN ...) 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
2-O-methyl-5-N-acetyl-alpha-D-neuraminic acid / Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsSauter, N.K. / Hanson, J.E. / Glick, G.D. / Brown, J.H. / Crowther, R.L. / Park, S.-J. / Skehel, J.J. / Wiley, D.C.
Citation
Journal: Biochemistry / Year: 1992
Title: 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.
Authors: Sauter, N.K. / Hanson, J.E. / Glick, G.D. / Brown, J.H. / Crowther, R.L. / Park, S.J. / Skehel, J.J. / Wiley, D.C.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1992
Title: Crystallographic Detection of a Second Ligand Binding Site in Influenza Virus Hemagglutinin
Authors: Sauter, N.K. / Glick, G.D. / Crowther, R.L. / Park, S.-J. / Eisen, M.B. / Skehel, J.J. / Knowles, J.R. / Wiley, D.C.
#2: 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.
#3: Journal: Nature / Year: 1988
Title: Structure of the Influenza Virus Hemagglutinin Complexed with its Receptor, Sialic Acid
Authors: Weis, W.I. / Brown, J.H. / Cusack, S. / Paulson, J.C. / Skehel, J.J. / Wiley, D.C.
#4: Journal: Acta Crystallogr.,Sect.B / Year: 1986
Title: The Refinement of the Hemagglutinin Membrane Glycoprotein of Influenza Virus
Authors: Knossow, M. / Lewis, M. / Rees, D. / Wilson, I.A. / Skehel, J.J. / Wiley, D.C.
#5: Journal: Nature / Year: 1984
Title: Three-Dimensional Structure of an Antigenic Mutant of the Influenza Virus Hemagglutinin
Authors: Knossow, M. / Daniels, R.S. / Douglas, A.R. / Skehel, J.J. / Wiley, D.C.
#6: Journal: Nature / Year: 1981
Title: Structure of the Hemagglutinin Membrane Glycoprotein of Influenza Virus at 3 Angstroms Resolution
Authors: Wilson, I.A. / Skehel, J.J. / Wiley, D.C.
#7: Journal: Nature / Year: 1981
Title: Structural Identification of the Antibody-Binding Sites of Hong Kong Influenza Hemagglutinin and Their Involvement in Antigenic Variation
Authors: Wiley, D.C. / Wilson, I.A. / Skehel, J.J.
#8: Journal: J.Mol.Biol. / Year: 1977
Title: Crystallization and X-Ray Diffraction Studies on the Hemagglutinin Glycoprotein from the Membrane of Influenza Virus
Authors: Wiley, D.C. / Skehel, J.J.
History
DepositionNov 1, 1991Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / 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.occupancy / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _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 / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HEMAGGLUTININ, CHAIN HA1
B: HEMAGGLUTININ, CHAIN HA1
C: HEMAGGLUTININ, CHAIN HA1
D: HEMAGGLUTININ, CHAIN HA1
E: HEMAGGLUTININ, CHAIN HA1
F: HEMAGGLUTININ, CHAIN HA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,18727
Polymers168,8336
Non-polymers6,35421
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area42400 Å2
ΔGint-83 kcal/mol
Surface area57570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.800, 162.800, 178.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Atom site foot note1: DISORDERED RESIDUES WITH LITTLE OR NO VISIBLE ELECTRON DENSITY: CHAIN A: 1 - 8, 326 - 328 B: 58, 172 - 175 CHAIN C: 1 - 8, 328 D: 58, 172 - 175 CHAIN E: 1 - 8, 327 - 328 F: 58, 172 - 175
2: CIS PROLINE - PRO A 55 / 3: CIS PROLINE - PRO C 55 / 4: CIS PROLINE - PRO E 55
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.034333, -0.851708, -0.522891), (-0.550874, 0.420417, -0.720963), (0.833882, 0.3128, -0.454749)69.5055, 48.3999, -20.5577
2given(0.034333, -0.550874, 0.833882), (-0.851708, 0.420417, 0.3128), (-0.522891, -0.720963, -0.454749)41.4187, 45.2807, 61.8898
Details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Components

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HEMAGGLUTININ, CHAIN ... , 2 types, 6 molecules ACEBDF

#1: Protein HEMAGGLUTININ, CHAIN HA1 /


Mass: 36065.457 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Genus: Influenzavirus A / Strain: (A/X-31(H3N2)) / References: UniProt: P03437, UniProt: P03438*PLUS
#2: Protein HEMAGGLUTININ, CHAIN HA1 /


Mass: 20212.350 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Genus: Influenzavirus A / Strain: (A/X-31(H3N2)) / References: UniProt: P03437, UniProt: P03438*PLUS

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Sugars , 3 types, 21 molecules

#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.: 3
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-Acetylglucosamine


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
#5: Sugar
ChemComp-MNA / 2-O-methyl-5-N-acetyl-alpha-D-neuraminic acid


Type: D-saccharide / Mass: 323.296 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C12H21NO9
IdentifierTypeProgram
2-O-methyl-5-N-acetyl-a-D-neuraminic acidIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 1 types, 72 molecules

#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsSINCE THE ELECTRON DENSITY DOES NOT CLEARLY ESTABLISH THE CONFORMATION OF THE GLYCOSIDIC SIDE CHAIN ...SINCE THE ELECTRON DENSITY DOES NOT CLEARLY ESTABLISH THE CONFORMATION OF THE GLYCOSIDIC SIDE CHAIN OF THE LIGAND [ALPHA-2-O-(4'-BENZYLAMIDOCARBOXYBUTYL)-5-N- ACETYLNEURAMINIC ACID], A REFINED MODEL OF ALPHA-2-O-METHYL-5-N-ACETYL-ALPHA-D-NEURAMINIC ACID IS GIVEN INSTEAD.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Num. obs: 85146 / Num. measured all: 157204 / Rmerge(I) obs: 0.087

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.7→7 Å / Rfactor Rwork: 0.226 / Rfactor obs: 0.226
Refinement stepCycle: LAST / Resolution: 2.7→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11859 0 417 72 12348
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg2.9
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
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 7 Å / Num. reflection obs: 73501 / Rfactor obs: 0.226
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.9

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