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- PDB-1frg: CRYSTAL STRUCTURE, SEQUENCE, AND EPITOPE MAPPING OF A PEPTIDE COM... -

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Basic information

Entry
Database: PDB / ID: 1frg
TitleCRYSTAL STRUCTURE, SEQUENCE, AND EPITOPE MAPPING OF A PEPTIDE COMPLEX OF AN ANTI-INFLUENZA HA PEPTIDE ANTIBODY FAB 26(SLASH)9: FINE-TUNING ANTIBODY SPECIFICITY
Components
  • IGG2A 26/9 FAB (HEAVY CHAIN)
  • IGG2A 26/9 FAB (LIGHT CHAIN)
  • INFLUENZA HEMAGGLUTININ HA1 (STRAIN X47) (RESIDUES 101 - 108)
KeywordsViral protein/Immune system / IMMUNOGLOBULIN/VIRUS HEMAGGLUTININ / Viral protein-Immune system COMPLEX
Function / homology
Function and homology information


immunoglobulin receptor binding / immunoglobulin complex, circulating / complement activation, classical pathway / antigen binding / B cell differentiation / antibacterial humoral response / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope ...immunoglobulin receptor binding / immunoglobulin complex, circulating / complement activation, classical pathway / antigen binding / B cell differentiation / antibacterial humoral response / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / extracellular region / membrane / plasma membrane
Similarity search - Function
Haemagglutinin, HA1 chain, alpha/beta domain superfamily / : / Viral capsid/haemagglutinin protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain ...Haemagglutinin, HA1 chain, alpha/beta domain superfamily / : / Viral capsid/haemagglutinin protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / : / Hemagglutinin / Immunoglobulin kappa constant / Ig gamma-2A chain C region secreted form
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsChurchill, M.E.A. / Wilson, I.A.
Citation
Journal: J.Mol.Biol. / Year: 1994
Title: Crystal structure of a peptide complex of anti-influenza peptide antibody Fab 26/9. Comparison of two different antibodies bound to the same peptide antigen.
Authors: Churchill, M.E. / Stura, E.A. / Pinilla, C. / Appel, J.R. / Houghten, R.A. / Kono, D.H. / Balderas, R.S. / Fieser, G.G. / Schulze-Gahmen, U. / Wilson, I.A.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Detailed Analysis of the Free and Bound Conformations of an Antibody: X-Ray Structures of Fab 17(Slash)9 and Three Different Fab-Peptide Complexes
Authors: Schulze-Gahmen, U. / Rini, J.M. / Wilson, I.A.
#2: 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.
#3: Journal: J.Biol.Chem. / Year: 1988
Title: Preliminary Crystallographic Data, Primary Sequence, and Binding Data for the Anti-Peptide Fab and its Complex with a Synthetic Peptide from Influenza Hemagglutinin
Authors: Schulze-Gahmen, U. / Rini, J.M. / Arevalo, J. / Stura, E.A. / Kenten, J.H. / Wilson, I.A.
History
DepositionJan 17, 1994Processing site: BNL
Revision 1.0May 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 18, 2013Group: Source and taxonomy
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_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: 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
L: IGG2A 26/9 FAB (LIGHT CHAIN)
H: IGG2A 26/9 FAB (HEAVY CHAIN)
P: INFLUENZA HEMAGGLUTININ HA1 (STRAIN X47) (RESIDUES 101 - 108)


Theoretical massNumber of molelcules
Total (without water)48,6883
Polymers48,6883
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-21 kcal/mol
Surface area19660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.600, 115.100, 73.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO L 8 / 2: CIS PROLINE - PRO L 101 / 3: CIS PROLINE - PRO L 147 / 4: CIS PROLINE - PRO H 371 / 5: CIS PROLINE - PRO H 373 / 6: CIS PROLINE - PRO H 413

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Components

#1: Antibody IGG2A 26/9 FAB (LIGHT CHAIN)


Mass: 24028.650 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: PIR: A31790, UniProt: P01837*PLUS
#2: Antibody IGG2A 26/9 FAB (HEAVY CHAIN)


Mass: 23756.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: GenBank: 533229, UniProt: P01864*PLUS
#3: Protein/peptide INFLUENZA HEMAGGLUTININ HA1 (STRAIN X47) (RESIDUES 101 - 108)


Mass: 902.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
References: UniProt: E3W6A8*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsONE BOUND WATER IS INCLUDED IN THE PEPTIDE BINDING SITE OF THE FAB.
Sequence detailsTHE LIGHT CHAIN IS NUMBERED AS CHAIN L 1 - 217. THE HEAVY CHAIN IS NUMBERED AS CHAIN H 218 - 437. ...THE LIGHT CHAIN IS NUMBERED AS CHAIN L 1 - 217. THE HEAVY CHAIN IS NUMBERED AS CHAIN H 218 - 437. THE PEPTIDE IS NUMBERED AS CHAIN P 1 - 9.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.35 %
Crystal grow
*PLUS
Temperature: 22.5 ℃ / Method: vapor diffusion, sitting drop / PH range low: 9 / PH range high: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15-10 mg/mlFab1drop
217 %(w/v)PEG100001reservoir
30.2 Mimidazole malate1reservoir
40.8 mg/mlpeptide1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 9999 Å / Num. obs: 15290 / % possible obs: 87 % / Num. measured all: 45397 / Rmerge(I) obs: 0.1
Reflection shell
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 2.8 Å / % possible obs: 43 % / Num. unique obs: 1237 / Num. measured obs: 2555 / Rmerge(I) obs: 0.48

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.8→8 Å / Rfactor Rwork: 0.19 / Rfactor obs: 0.19
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3426 0 0 1 3427
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_deg3.48
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.4
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
Rfactor obs: 0.19 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d3.48
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg

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