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- PDB-2vis: INFLUENZA VIRUS HEMAGGLUTININ, (ESCAPE) MUTANT WITH THR 131 REPLA... -

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Basic information

Entry
Database: PDB / ID: 2vis
TitleINFLUENZA VIRUS HEMAGGLUTININ, (ESCAPE) MUTANT WITH THR 131 REPLACED BY ILE, COMPLEXED WITH A NEUTRALIZING ANTIBODY
Components
  • (IMMUNOGLOBULIN (IGG1, LAMBDA)) x 2
  • HEMAGGLUTININ
KeywordsCOMPLEX (HEMAGGLUTININ/IMMUNOGLOBULIN) / COMPLEX (HEMAGGLUTININ-IMMUNOGLOBULIN) / GLYCOPROTEIN / COMPLEX (HEMAGGLUTININ-IMMUNOGLOBULIN) complex
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 / metal ion binding / membrane
Similarity search - Function
Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / 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 / : ...Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / 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 / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Ribbon / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / : / Hemagglutinin / Igh protein
Similarity search - Component
Biological speciesInfluenza A virus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.25 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: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry / _struct_conn_type.id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 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
Revision 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IMMUNOGLOBULIN (IGG1, LAMBDA)
B: IMMUNOGLOBULIN (IGG1, LAMBDA)
C: HEMAGGLUTININ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9677
Polymers77,5503
Non-polymers4174
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.500, 85.500, 515.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Antibody IMMUNOGLOBULIN (IGG1, LAMBDA)


Mass: 22596.021 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: HYBRIDOMA / Strain: BALB/C / References: GenBank: 387376
#2: Antibody IMMUNOGLOBULIN (IGG1, LAMBDA)


Mass: 23777.783 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: HYBRIDOMA / Strain: BALB-C / References: GenBank: 4096752, UniProt: Q99LC4*PLUS
#3: Protein HEMAGGLUTININ


Mass: 31175.979 Da / Num. of mol.: 1
Fragment: PROTEOLYTIC FRAGMENT "HA TOP" CONTAINING HA1 RESIDUES 28 - 328
Mutation: T131I
Source method: isolated from a genetically manipulated source
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
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#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.: 1
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
Compound detailsTHE TWO MOLECULES (HEMAGGLUTININ "TOP" AND FAB FRAGMENT) ARE OBTAINED BY PROTEOLYSIS OF BIGGER ...THE TWO MOLECULES (HEMAGGLUTININ "TOP" AND FAB FRAGMENT) ARE OBTAINED BY PROTEOLYSIS OF BIGGER PROTEINS. FOR THIS REASON, THE C-TERMINI OF EACH OF THE THREE POLYPEPTIDE CHAINS ARE NOT UNIQUE (AS THE PROTEOLYSIS ARE NOT. ABSOLUTELY SPECIFIC). THE NUMBERING OF THE HEMAGGLUTININ FRAGMENT IS MADE ACCORDING TO THE ORIGINAL NUMBERING OF THE INTACT HEMAGGLUTININ MOLECULE: IT STARTS AT RESIDUE 28, BUT RESIDUES 28 - 42 ARE NOT VISIBLE IN THE ELECTRON DENSITY MAPS. THEREFORE, THE LISTED COORDINATES START AT RESIDUE 43.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.5 Å3/Da / Density % sol: 57 %
Crystal
*PLUS
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14 %PEG60001reservoir
250 mMMES1reservoir
3150 mM1reservoirNaCl
41 mM1reservoirZnCl2
50.05 %1reservoirNaN3
65 mg/mlprotein1drop
72 %PEG60001drop
825 mMMES1drop
975 mM1dropNaCl
100.5 mM1dropZnCl2
110.05 %1dropNaN3

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.85 / Wavelength: 0.85, 1.2
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.851
21.21
ReflectionResolution: 3.25→20 Å / Num. obs: 18144 / % possible obs: 96.4 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.109
Reflection
*PLUS
Num. measured all: 85445

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Processing

Software
NameVersionClassification
HKLdata collection
X-PLOR3.84model building
X-PLOR3.84refinement
HKLdata reduction
X-PLOR3.84phasing
RefinementResolution: 3.25→7 Å / σ(F): 0 /
Rfactor% reflection
Rfree0.267 5 %
Rwork0.188 -
obs0.188 -
Refinement stepCycle: LAST / Resolution: 3.25→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5337 0 17 0 5354
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.7
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
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.7

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