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- PDB-1him: STRUCTURAL EVIDENCE FOR INDUCED FIT AS A MECHANISM FOR ANTIBODY-A... -

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Basic information

Entry
Database: PDB / ID: 1him
TitleSTRUCTURAL EVIDENCE FOR INDUCED FIT AS A MECHANISM FOR ANTIBODY-ANTIGEN RECOGNITION
Components
  • (INFLUENZA HEMAGGLUTININ HA1 (STRAIN X47) (RESIDUES 100-108)) x 2
  • IGG2A-KAPPA 17/9 FAB (HEAVY CHAIN)
  • IGG2A-KAPPA 17/9 FAB (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN
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
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsSchulze-Gahmen, U. / Wilson, I.A.
Citation
Journal: Science / Year: 1992
Title: Structural evidence for induced fit as a mechanism for antibody-antigen recognition.
Authors: Rini, J.M. / Schulze-Gahmen, U. / Wilson, I.A.
#1: Journal: J.Biol.Chem. / Year: 1988
Title: Preliminary Crystallographic Data, Primary Sequence, and Binding Data for an Anti-Peptide Fab and its Complex with a Synthetic Peptide from Influenza Virus Hemagglutinin
Authors: Schulze-Gahmen, U. / Rini, J.M. / Arevalo, J. / Stura, E.A. / Kenten, J.H. / Wilson, I.A.
History
DepositionJul 8, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 23, 2015Group: Database references / Structure summary
Revision 1.4Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: IGG2A-KAPPA 17/9 FAB (LIGHT CHAIN)
L: IGG2A-KAPPA 17/9 FAB (HEAVY CHAIN)
P: INFLUENZA HEMAGGLUTININ HA1 (STRAIN X47) (RESIDUES 100-108)
J: IGG2A-KAPPA 17/9 FAB (LIGHT CHAIN)
M: IGG2A-KAPPA 17/9 FAB (HEAVY CHAIN)
R: INFLUENZA HEMAGGLUTININ HA1 (STRAIN X47) (RESIDUES 100-108)


Theoretical massNumber of molelcules
Total (without water)97,1456
Polymers97,1456
Non-polymers00
Water00
1
H: IGG2A-KAPPA 17/9 FAB (LIGHT CHAIN)
L: IGG2A-KAPPA 17/9 FAB (HEAVY CHAIN)
P: INFLUENZA HEMAGGLUTININ HA1 (STRAIN X47) (RESIDUES 100-108)


Theoretical massNumber of molelcules
Total (without water)48,5163
Polymers48,5163
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-21 kcal/mol
Surface area19350 Å2
MethodPISA
2
J: IGG2A-KAPPA 17/9 FAB (LIGHT CHAIN)
M: IGG2A-KAPPA 17/9 FAB (HEAVY CHAIN)
R: INFLUENZA HEMAGGLUTININ HA1 (STRAIN X47) (RESIDUES 100-108)


Theoretical massNumber of molelcules
Total (without water)48,6293
Polymers48,6293
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-23 kcal/mol
Surface area19500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.080, 67.070, 73.240
Angle α, β, γ (deg.)89.90, 101.80, 96.50
Int Tables number1
Space group name H-MP1
Atom site foot note1: RESIDUES PRO 8, PRO 95, AND PRO 141 OF LIGHT CHAINS AND RESIDUES PRO 149, PRO 151 AND PRO 200 OF HEAVY CHAINS ARE CIS PROLINES.

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Components

#1: Antibody IGG2A-KAPPA 17/9 FAB (LIGHT CHAIN)


Mass: 23911.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
#2: Antibody IGG2A-KAPPA 17/9 FAB (HEAVY CHAIN)


Mass: 23677.441 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
#3: Protein/peptide INFLUENZA HEMAGGLUTININ HA1 (STRAIN X47) (RESIDUES 100-108)


Mass: 926.947 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: I6SHA6*PLUS
#4: Protein/peptide INFLUENZA HEMAGGLUTININ HA1 (STRAIN X47) (RESIDUES 100-108)


Mass: 1040.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: I6SHA6*PLUS
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: 2.95 Å3/Da / Density % sol: 58.34 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: using macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMammonium acetate1reservoir
250 mM1reservoirMnCl2
32-4 %PEG6001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.9 Å / % possible obs: 87 % / Rmerge(I) obs: 0.12

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.9→8 Å / Rfactor Rwork: 0.2 / Rfactor obs: 0.2 / σ(F): 2
Refinement stepCycle: LAST / Resolution: 2.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6742 0 0 0 6742
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
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_deg3.7
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: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 8 Å / σ(F): 2 / Rfactor obs: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.7

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