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- PDB-1fcg: ECTODOMAIN OF HUMAN FC GAMMA RECEPTOR, FCGRIIA -

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Basic information

Entry
Database: PDB / ID: 1fcg
TitleECTODOMAIN OF HUMAN FC GAMMA RECEPTOR, FCGRIIA
ComponentsPROTEIN (FC RECEPTOR FC(GAMMA)RIIA)
KeywordsIMMUNE SYSTEM / MEMBRANE PROTEIN / FC RECEPTOR / IMMUNOGLOULIN / LEUKOCYTE / CD32
Function / homology
Function and homology information


IgG binding / immune system process / FCGR activation / regulation of immune response / Role of phospholipids in phagocytosis / FCGR3A-mediated IL10 synthesis / secretory granule membrane / Regulation of actin dynamics for phagocytic cup formation / transmembrane signaling receptor activity / cell surface receptor signaling pathway ...IgG binding / immune system process / FCGR activation / regulation of immune response / Role of phospholipids in phagocytosis / FCGR3A-mediated IL10 synthesis / secretory granule membrane / Regulation of actin dynamics for phagocytic cup formation / transmembrane signaling receptor activity / cell surface receptor signaling pathway / 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 / 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-a
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2 Å
AuthorsMaxwell, K.F. / Powell, M.S. / Garrett, T.P. / Hogarth, P.M.
Citation
Journal: Nat.Struct.Biol. / Year: 1999
Title: Crystal structure of the human leukocyte Fc receptor, Fc gammaRIIa.
Authors: Maxwell, K.F. / Powell, M.S. / Hulett, M.D. / Barton, P.A. / McKenzie, I.F. / Garrett, T.P. / Hogarth, P.M.
#1: Journal: Immunol.Lett. / Year: 1999
Title: Biochemical Analysis and Crystallisation of Fc(Gamma)RIIA, the Low Affinity Receptor for IgG
Authors: Powell, M.S. / Barton, P.A. / Emmanouilidis, D. / Wines, B.D. / Neumann, G.M. / Peitersz, G.A. / Maxwell, K.F. / Garrett, T.P. / Hogarth, P.M.
History
DepositionApr 7, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 12, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Apr 11, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.5Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 RECEPTOR FC(GAMMA)RIIA)


Theoretical massNumber of molelcules
Total (without water)19,5571
Polymers19,5571
Non-polymers00
Water1,63991
1
A: PROTEIN (FC RECEPTOR FC(GAMMA)RIIA)

A: PROTEIN (FC RECEPTOR FC(GAMMA)RIIA)


Theoretical massNumber of molelcules
Total (without water)39,1142
Polymers39,1142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Unit cell
Length a, b, c (Å)79.221, 100.866, 28.172
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-288-

HOH

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Components

#1: Protein PROTEIN (FC RECEPTOR FC(GAMMA)RIIA) / CD32


Mass: 19556.863 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAINS / Mutation: S88F, R134H
Source method: isolated from a genetically manipulated source
Details: LOW RESPONDER VARIANT OF FC(GAMMA)RIIA / Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD / Cell: MONOCYTE / Cellular location: CELL SURFACECell membrane / Plasmid: PVL1392 / Cell line (production host): SF21 / Cellular location (production host): SECRETED / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P12318
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growpH: 5.6
Details: HANGING DROP VAPOUR DIFFUSION WITH EQUAL VOLUMES OF FC(GAMMA)RIIA AT 6 MG/ML AND MOTHER LIQUOR (0.2 M AMMONIUM ACETATE, 30% W/V PEG 4000, 0.1 M SODIUM CITRATE PH 5.6) MIXED IN 3 MICRO L ...Details: HANGING DROP VAPOUR DIFFUSION WITH EQUAL VOLUMES OF FC(GAMMA)RIIA AT 6 MG/ML AND MOTHER LIQUOR (0.2 M AMMONIUM ACETATE, 30% W/V PEG 4000, 0.1 M SODIUM CITRATE PH 5.6) MIXED IN 3 MICRO L DROPLETS AND ALLOWED TO EQUILIBRATE AT 22 C FOR 3-9 DAYS.
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, hanging drop / Details: Powell, M.S., (1999) Immunol.Lett., 68, 17.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 mg/mlprotein1drop
20.2 Mammonium sulfate1reservoir
30.1 Msodium citrate1reservoir
430 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE M18X / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Apr 1, 1998 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→10 Å / Num. obs: 15024 / % possible obs: 94.9 % / Redundancy: 2.73 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 10.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.53 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 1.5 / % possible all: 95.9
Reflection shell
*PLUS
Highest resolution: 2 Å / % possible obs: 95.9 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DMmodel building
REFMACrefinement
DMphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2→6 Å / SU B: 4.65 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.21 / ESU R Free: 0.18
Details: NO ELECTRON DENSITY WAS OBSERVED FOR AMINO ACIDS 1-3 OR EITHER OF THE N-LINKED CARBOHYDRATE MOIETIES SO THESE RESIDUES HAVE NOT BEEN MODELLED. MASS SPECTROMETRY INDICATES THAT THESE RESIDUES ...Details: NO ELECTRON DENSITY WAS OBSERVED FOR AMINO ACIDS 1-3 OR EITHER OF THE N-LINKED CARBOHYDRATE MOIETIES SO THESE RESIDUES HAVE NOT BEEN MODELLED. MASS SPECTROMETRY INDICATES THAT THESE RESIDUES ARE PRESENT IN THE CRYSTAL.
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1038 8 %RANDOM
Rwork0.197 ---
obs0.218 11447 95.5 %-
Displacement parametersBiso mean: 25.1 Å2
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1392 0 0 91 1483
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.030.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0320.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.313
X-RAY DIFFRACTIONp_mcangle_it4.716
X-RAY DIFFRACTIONp_scbond_it3.015
X-RAY DIFFRACTIONp_scangle_it5.817
X-RAY DIFFRACTIONp_plane_restr0.020.03
X-RAY DIFFRACTIONp_chiral_restr0.1210.15
X-RAY DIFFRACTIONp_singtor_nbd0.1770.3
X-RAY DIFFRACTIONp_multtor_nbd0.2350.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1360.3
X-RAY DIFFRACTIONp_planar_tor4.17
X-RAY DIFFRACTIONp_staggered_tor19.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor27.420
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / σ(F): 0 / % reflection Rfree: 8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.04
X-RAY DIFFRACTIONp_planar_d0.05
X-RAY DIFFRACTIONp_plane_restr0.030.02
X-RAY DIFFRACTIONp_chiral_restr0.15
X-RAY DIFFRACTIONp_mcbond_it32.31
X-RAY DIFFRACTIONp_scbond_it53.01
X-RAY DIFFRACTIONp_mcangle_it64.71
X-RAY DIFFRACTIONp_scangle_it75.81

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