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- PDB-2fcb: HUMAN FC GAMMA RECEPTOR IIB ECTODOMAIN (CD32) -

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Basic information

Entry
Database: PDB / ID: 2fcb
TitleHUMAN FC GAMMA RECEPTOR IIB ECTODOMAIN (CD32)
ComponentsPROTEIN (FC GAMMA RIIB)
KeywordsIMMUNE SYSTEM / RECEPTOR / FC / CD32
Function / homology
Function and homology information


negative regulation of type I hypersensitivity / negative regulation of antibody-dependent cellular cytotoxicity / immune effector process / follicular dendritic cell activation / immune complex clearance by monocytes and macrophages / regulation of B cell antigen processing and presentation / regulation of immune complex clearance by monocytes and macrophages / negative regulation of acute inflammatory response to antigenic stimulus / positive regulation of humoral immune response / negative regulation of neutrophil activation ...negative regulation of type I hypersensitivity / negative regulation of antibody-dependent cellular cytotoxicity / immune effector process / follicular dendritic cell activation / immune complex clearance by monocytes and macrophages / regulation of B cell antigen processing and presentation / regulation of immune complex clearance by monocytes and macrophages / negative regulation of acute inflammatory response to antigenic stimulus / positive regulation of humoral immune response / negative regulation of neutrophil activation / regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of response to endoplasmic reticulum stress / negative regulation of dendritic cell antigen processing and presentation / negative regulation of B cell receptor signaling pathway / negative regulation of humoral immune response mediated by circulating immunoglobulin / low-affinity IgG receptor activity / follicular B cell differentiation / negative regulation of cytotoxic T cell degranulation / IgG receptor activity / negative regulation of immunoglobulin production / cellular response to molecule of bacterial origin / negative regulation of dendritic cell differentiation / negative regulation of B cell activation / regulation of dendritic spine maintenance / regulation of adaptive immune response / mature B cell differentiation involved in immune response / negative regulation of macrophage activation / Fc-gamma receptor signaling pathway / negative regulation of immune response / regulation of signaling receptor activity / negative regulation of phagocytosis / antibody-dependent cellular cytotoxicity / IgG binding / negative regulation of cytokine production / phagocytosis, engulfment / negative regulation of interleukin-10 production / regulation of innate immune response / negative regulation of B cell proliferation / immunoglobulin mediated immune response / phagocytosis / positive regulation of phagocytosis / cerebellum development / receptor-mediated endocytosis / positive regulation of JNK cascade / response to bacterium / defense response / cellular response to amyloid-beta / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of tumor necrosis factor production / amyloid-beta binding / cell body / dendritic spine / cell surface receptor signaling pathway / inflammatory response / external side of plasma membrane / protein-containing complex binding / 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 / Immunoglobulins / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Low affinity immunoglobulin gamma Fc region receptor II-b
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.74 Å
AuthorsSondermann, P. / Huber, R. / Jacob, U.
CitationJournal: EMBO J. / Year: 1999
Title: Crystal structure of the soluble form of the human fcgamma-receptor IIb: a new member of the immunoglobulin superfamily at 1.7 A resolution.
Authors: Sondermann, P. / Huber, R. / Jacob, U.
History
DepositionJan 7, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 1, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Advisory / Data collection
Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _diffrn_source.type
Revision 1.4Feb 21, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (FC GAMMA RIIB)


Theoretical massNumber of molelcules
Total (without water)19,4291
Polymers19,4291
Non-polymers00
Water2,702150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.830, 50.920, 80.520
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: Protein PROTEIN (FC GAMMA RIIB) / CD32


Mass: 19428.633 Da / Num. of mol.: 1 / Fragment: ECTODOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: B-LYMPHOCYTE / Plasmid: PET11D / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P31994
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.15 Å3/Da / Density % sol: 42.86 %
Crystal growpH: 5.3 / Details: 33% PEG 2000, 0.2M NAOAC, PH5.4, pH 5.3
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5.4 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17 mg/mlprotein1drop
22 mMMPS1drop
3150 mM1dropNaCl
40.02 %sodium azide1drop
533 %PEG20001reservoir
60.2 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.74→99 Å / Num. obs: 18009 / % possible obs: 93 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.055
Reflection shellHighest resolution: 1.74 Å / % possible all: 86.4
Reflection shell
*PLUS
% possible obs: 86.4 %

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Processing

Software
NameClassification
MOSFLMdata reduction
CCP4data reduction
X-PLORrefinement
CCP4data scaling
RefinementMethod to determine structure: MIR / Resolution: 1.74→8 Å / Data cutoff high absF: 100000000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.279 -5 %RANDOM
Rwork0.194 ---
obs0.194 18009 93 %-
Refinement stepCycle: LAST / Resolution: 1.74→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1371 0 0 150 1521
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg2.007
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_it18.8
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it25.2
X-RAY DIFFRACTIONx_scangle_it

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