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- PDB-1jrh: COMPLEX (ANTIBODY/ANTIGEN) -

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Basic information

Entry
Database: PDB / ID: 1jrh
TitleCOMPLEX (ANTIBODY/ANTIGEN)
Components
  • (ANTIBODY A6) x 2
  • INTERFERON-GAMMA RECEPTOR ALPHA CHAIN
KeywordsCOMPLEX (ANTIBODY/ANTIGEN) / CYTOKINE RECEPTOR / COMPLEX (ANTIBODY-ANTIGEN) / TRANSMEMBRANE / GLYCOPROTEIN / COMPLEX (ANTIBODY-ANTIGEN) complex
Function / homology
Function and homology information


type II interferon receptor activity / Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / negative regulation of amyloid-beta clearance / type III interferon-mediated signaling pathway / Regulation of actin dynamics for phagocytic cup formation / humoral immune response mediated by circulating immunoglobulin ...type II interferon receptor activity / Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / negative regulation of amyloid-beta clearance / type III interferon-mediated signaling pathway / Regulation of actin dynamics for phagocytic cup formation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / cytokine receptor activity / phagocytosis, engulfment / IgG immunoglobulin complex / positive regulation of amyloid-beta formation / IFNG signaling activates MAPKs / cytokine binding / immunoglobulin mediated immune response / immunoglobulin complex, circulating / immunoglobulin receptor binding / type II interferon-mediated signaling pathway / Regulation of IFNG signaling / positive regulation of phagocytosis / B cell differentiation / complement activation, classical pathway / antigen binding / astrocyte activation / microglial cell activation / response to virus / cellular response to virus / cytokine-mediated signaling pathway / positive regulation of tumor necrosis factor production / Interferon gamma signaling / positive regulation of immune response / antibacterial humoral response / Potential therapeutics for SARS / defense response to bacterium / external side of plasma membrane / positive regulation of gene expression / signal transduction / extracellular space / extracellular region / membrane / plasma membrane / cytoplasm
Similarity search - Function
Interferon gamma receptor 1, transmembrane region / Interferon gamma receptor, D2 domain, poxvirus/mammal / Interferon gamma receptor (IFNGR1), D2 domain / Interferon gamma receptor alpha subunit / Tissue factor / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type ...Interferon gamma receptor 1, transmembrane region / Interferon gamma receptor, D2 domain, poxvirus/mammal / Interferon gamma receptor (IFNGR1), D2 domain / Interferon gamma receptor alpha subunit / Tissue factor / Fibronectin type III / Fibronectin type III superfamily / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Immunoglobulin kappa constant / Ig gamma-1 chain C region, membrane-bound form / Interferon gamma receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWinkler, F.K. / Sogabe, S.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: Neutralizing epitopes on the extracellular interferon gamma receptor (IFNgammaR) alpha-chain characterized by homolog scanning mutagenesis and X-ray crystal structure of the A6 fab-IFNgammaR1-108 complex.
Authors: Sogabe, S. / Stuart, F. / Henke, C. / Bridges, A. / Williams, G. / Birch, A. / Winkler, F.K. / Robinson, J.A.
#1: Journal: Biochemistry / Year: 1995
Title: Dissection of the Extracellular Human Interferon Gamma Receptor Alpha-Chain Into Two Immunoglobulin-Like Domains. Production in an Escherichia Coli Thioredoxin Gene Fusion Expression System ...Title: Dissection of the Extracellular Human Interferon Gamma Receptor Alpha-Chain Into Two Immunoglobulin-Like Domains. Production in an Escherichia Coli Thioredoxin Gene Fusion Expression System and Recognition by Neutralizing Antibodies
Authors: Williams, G. / Ruegg, N. / Birch, A. / Weber, C. / Hofstadter, K. / Robinson, J.A. / Aguet, M. / Garotta, G. / Schlatter, D. / Huber, W.
#2: Journal: Mol.Immunol. / Year: 1995
Title: Variable Region Cdna Sequences and Characterization of Murine Anti-Human Interferon Gamma Receptor Monoclonal Antibodies that Inhibit Receptor Binding by Interferon Gamma
Authors: Bridges, A. / Birch, A. / Williams, G. / Aguet, M. / Schlatter, D. / Huber, W. / Garotta, G. / Robinson, J.A.
History
DepositionSep 23, 1997Processing site: BNL
Revision 1.0Mar 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / struct_conn / struct_ref_seq_dif
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_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: ANTIBODY A6
H: ANTIBODY A6
I: INTERFERON-GAMMA RECEPTOR ALPHA CHAIN


Theoretical massNumber of molelcules
Total (without water)59,2783
Polymers59,2783
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-20 kcal/mol
Surface area22390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.740, 90.800, 101.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody ANTIBODY A6


Mass: 23600.936 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT;PEPSIN DIGESTION OF INTACT ANTIBODY / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: PIR: S01320, UniProt: P01837*PLUS
#2: Antibody ANTIBODY A6


Mass: 23570.543 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT;PEPSIN DIGESTION OF INTACT ANTIBODY / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01869*PLUS
#3: Protein INTERFERON-GAMMA RECEPTOR ALPHA CHAIN


Mass: 12106.464 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN / Mutation: C105S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: ESCHERICHIA COLI HIOREDOXIN GENE FUSION EXPRESSION SYSTEM, BOVINE ENTEROKINASE CLEAVAGE
Gene: CDNA / Production host: Escherichia coli (E. coli) / References: UniProt: P15260
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 61 %
Description: FOR FV_HEAVY AND FV_LIGHT, 1BBJ AND 1BBC, RESPECTIVELY. FOR FC, 2HFL. THESE ARE COMBINED AND OPTIMIZED. <I/SIGMA(I)> FOR THE DATA SET : 29.7 <I/SIGMA(I)> FOR SHELL : 5.9
Crystal growpH: 5.5
Details: 10%(W/V) PEG ME 5000, 0.5M NACL, 50MM BIS/TRIS, PH 5.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
117 mg/mlprotein1drop
221 mMTris1drop
393 mM1dropNaCl
40.4 mMEDTA1drop
51.4 %(w/v)PEG ME50001drop
67 mMBis-Tris1drop
710 %(w/v)PEG ME50001reservoir
80.5 M1reservoirNaCl
950 mMBis-Tris1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 19997 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 58 Å2 / Rsym value: 0.059
Reflection shellResolution: 2.82→2.95 Å / Redundancy: 3.6 % / Rsym value: 0.288 / % possible all: 98.1
Reflection
*PLUS
Num. measured all: 74824 / Rmerge(I) obs: 0.0588
Reflection shell
*PLUS
% possible obs: 98.1 % / Num. unique obs: 2465 / Num. measured obs: 8975 / Rmerge(I) obs: 0.2878

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Processing

Software
NameVersionClassification
MARXDSdata collection
X-PLOR3.1model building
X-PLOR3.1refinement
MARXDSdata reduction
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1BBJ, 1BBC, AND 2HFL

1bbj

1bbc

2hfl
PDB Unreleased entry


Resolution: 2.8→20 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Cross valid method: FREE R / σ(F): 0
Details: ATOMS WITH B-FACTORS > 80 A**2 MUST BE CONSIDERED DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.314 954 5 %RANDOM
Rwork0.246 ---
obs0.246 19997 99.3 %-
Displacement parametersBiso mean: 62.1 Å2
Refine analyzeLuzzati sigma a obs: 0.4 Å
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3454 0 0 30 3484
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.85
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_it2
X-RAY DIFFRACTIONx_mcangle_it3
X-RAY DIFFRACTIONx_scbond_it4.5
X-RAY DIFFRACTIONx_scangle_it20
LS refinement shellResolution: 2.8→2.9 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.399 99 5 %
Rwork0.322 1793 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Num. reflection all: 19997 / Num. reflection obs: 18723 / σ(F): 2 / Rfactor all: 0.255
Solvent computation
*PLUS
Displacement parameters
*PLUS

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