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- PDB-3ry5: Three-dimensional structure of glycosylated fcgammariia (high-res... -

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Basic information

Entry
Database: PDB / ID: 3ry5
TitleThree-dimensional structure of glycosylated fcgammariia (high-responder polymorphism)
ComponentsLOW AFFINITY IMMUNOGLOBULIN GAMMA FC REGION RECEPTOR II-A
KeywordsIMMUNE SYSTEM / FC RECEPTOR / CD32 / IMMUNOGLOBULIN SUPERFAMILY / HIGH RESPONDER POLYMORPHISM / CELL MEMBRANE / IGG-BINDING PROTEIN / IMMUNOGLOBULIN DOMAIN / MEMBRANE / RECEPTOR / TRANSMEMBRANE
Function / homology
Function and homology information


IgG receptor activity / antibody-dependent cellular cytotoxicity / IgG binding / FCGR activation / Role of phospholipids in phagocytosis / positive regulation of phagocytosis / FCGR3A-mediated IL10 synthesis / 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 / positive regulation of phagocytosis / FCGR3A-mediated IL10 synthesis / 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRamsland, P.A. / Farrugia, W. / Hogarth, P.M.
CitationJournal: J.Immunol. / Year: 2011
Title: Structural Basis for Fc{gamma}RIIa Recognition of Human IgG and Formation of Inflammatory Signaling Complexes.
Authors: Ramsland, P.A. / Farrugia, W. / Bradford, T.M. / Sardjono, C.T. / Esparon, S. / Trist, H.M. / Powell, M.S. / Tan, P.S. / Cendron, A.C. / Wines, B.D. / Scott, A.M. / Hogarth, P.M.
History
DepositionMay 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2011Group: Database references

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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 REGION RECEPTOR II-A


Theoretical massNumber of molelcules
Total (without water)19,1461
Polymers19,1461
Non-polymers00
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.036, 77.935, 88.104
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 19146.398 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, residues 114-327 / Mutation: H134R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD / Gene: FCGR2A, CD32, FCG2, FCGR2A1, IGFR2 / Plasmid: PVL1392 / Cell line (production host): SF21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P12318
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.24 Å3/Da / Density % sol: 45.13 %
Crystal growMethod: vapor diffusion / pH: 7.5
Details: 30% (W/V) PEG 4000, 0.2M AMMONIUM SULFATE, PH 7.50, VAPOR DIFFUSION, TEMPERATURE 291.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 3, 2003 / Details: MIRRORS
RadiationMonochromator: OSMIC BLUE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 7783 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 19.8 Å2 / Rsym value: 0.1 / Net I/σ(I): 13.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 4.9 / Rsym value: 0.27 / % possible all: 96

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→20.43 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.275 804 RANDOM
Rwork0.206 --
obs0.206 7554 -
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.3→20.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1350 0 0 85 1435
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
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
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0.029 /
RfactorNum. reflection
Rfree0.293 99
Rwork0.237 -

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