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- PDB-1h9v: Human Fc-gamma-Receptor IIa (FcgRIIa), monoclinic -

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Basic information

Entry
Database: PDB / ID: 1h9v
TitleHuman Fc-gamma-Receptor IIa (FcgRIIa), monoclinic
ComponentsLOW AFFINITY IMMUNOGLOBULIN GAMMA FC RECEPTOR II-A
KeywordsIMMUNE SYSTEM / MEMBRANE PROTEIN / FCR / FC-RECEPTOR / IMMUNOGLOBULIN / FCGR / FC-GAMMA-R
Function / homology
Function and homology information


IgG receptor activity / antibody-dependent cellular cytotoxicity / IgG binding / FCGR activation / Role of phospholipids in phagocytosis / FCGR3A-mediated IL10 synthesis / positive regulation of phagocytosis / secretory granule membrane / Regulation of actin dynamics for phagocytic cup formation / positive regulation of tumor necrosis factor production ...IgG receptor activity / antibody-dependent cellular cytotoxicity / IgG binding / FCGR activation / Role of phospholipids in phagocytosis / FCGR3A-mediated IL10 synthesis / positive regulation of phagocytosis / secretory granule membrane / Regulation of actin dynamics for phagocytic cup formation / positive regulation of tumor necrosis factor production / cell surface receptor signaling pathway / external side of plasma membrane / Neutrophil degranulation / plasma membrane
Similarity search - Function
: / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold ...: / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Low affinity immunoglobulin gamma Fc region receptor II-a
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSondermann, P. / Kaiser, J. / Jacob, U.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Molecular Basis for Immune Complex Recognition: A Comparison of Fc-Receptor Structures
Authors: Sondermann, P. / Kaiser, J. / Jacob, U.
History
DepositionMar 21, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2001Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 20, 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
A: LOW AFFINITY IMMUNOGLOBULIN GAMMA FC RECEPTOR II-A


Theoretical massNumber of molelcules
Total (without water)19,3431
Polymers19,3431
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)81.310, 50.000, 55.450
Angle α, β, γ (deg.)90.00, 128.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein LOW AFFINITY IMMUNOGLOBULIN GAMMA FC RECEPTOR II-A / FC-GAMMA RII-A / FCRII-A / IGG FC RECEPTOR II-A / FC-GAMMA-RIIA / CD32 / CDW32


Mass: 19342.645 Da / Num. of mol.: 1 / Fragment: IMMUNOGLOBULIN G BINDING DOMAIN RESIDUE 5-177
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: REFOLDED FROM INCLUSION BODIES / Cellular location: EXTRACELLULAR / Variant: HIGH RESPONDER / Plasmid: PET / Cellular location (production host): INCLUSION BODIES / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12318
Compound detailsBINDS TO THE FC REGION OF IMMUNOGLOBULINS GAMMA.
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46 %
Crystal growpH: 5.5 / Details: 0.2M NAOAC PH 4.6, 26% PEG 8000
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.2 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12 mMMOPS1drop
2150 mM1dropNaCl
30.02 %sodium azide1drop
40.2 Msodium acetate/acetic acid1reservoir
526 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 2000
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 3417 / % possible obs: 90.5 % / Observed criterion σ(I): 2 / Redundancy: 2.4 %
Reflection
*PLUS
Rmerge(I) obs: 0.111
Reflection shell
*PLUS
% possible obs: 69 % / Rmerge(I) obs: 0.242

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FCB

2fcb


Highest resolution: 3 Å / R Free selection details: RANDOM / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Details: ONE REFINEMENT CYCLE WAS CARRIED OUT ON THE MODEL
Refinement stepCycle: LAST / Highest resolution: 3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1364 0 0 0 1364
Refine LS restraints
Refine-IDType
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor obs: 0.246 / Rfactor Rfree: 0.327
Solvent computation
*PLUS
Displacement parameters
*PLUS

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