8CHA

Fc gamma RIIa 27W/131H variant ectodomain

  • Classification: IMMUNE SYSTEM
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): Yes 

  • Deposited: 2023-02-07 Released: 2024-05-22 
  • Deposition Author(s): Foy, E.G., Thomsen, M., Goldman, A., Robinson, J.I.
  • Funding Organization(s): Other private, Wellcome Trust, European Research Council (ERC), Biotechnology and Biological Sciences Research Council (BBSRC), Academy of Finland, Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 
    0.225 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 16PClick on this verticalbar to view detailsBest fitted FWNClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

Fc gamma RIIa 27W/131H variant ectodomain

Foy, E.G.Thomsen, M.Goldman, A.Robinson, J.I.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Low affinity immunoglobulin gamma Fc region receptor II-a209Homo sapiensMutation(s): 1 
Gene Names: FCGR2ACD32FCG2FCGR2A1IGFR2
UniProt & NIH Common Fund Data Resources
Find proteins for P12318 (Homo sapiens)
Explore P12318 
Go to UniProtKB:  P12318
PHAROS:  P12318
GTEx:  ENSG00000143226 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12318
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P12318-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
4N/AN-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
16P
Query on 16P

Download Ideal Coordinates CCD File 
G [auth A]3,6,9,12,15,18-HEXAOXAICOSANE
C14 H30 O6
IXFAFGFZFQHRLB-UHFFFAOYSA-N
FLC
Query on FLC

Download Ideal Coordinates CCD File 
C [auth A]CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
FWN
Query on FWN

Download Ideal Coordinates CCD File 
J [auth A]2-[2-(2-ethoxyethoxy)ethoxy]ethanol
C8 H18 O4
WFSMVVDJSNMRAR-UHFFFAOYSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
H [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
DXE
Query on DXE

Download Ideal Coordinates CCD File 
I [auth A]1,2-DIMETHOXYETHANE
C4 H10 O2
XTHFKEDIFFGKHM-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
K [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free:  0.225 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.931α = 90
b = 76.526β = 90
c = 108.279γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 16PClick on this verticalbar to view detailsBest fitted FWNClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private19764
Wellcome TrustUnited Kingdom091322/2/10/2
European Research Council (ERC)European Union708051
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomALERT-13
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/M021610/1
Academy of FinlandFinland1252206
Medical Research Council (MRC, United Kingdom)United KingdomMR/K015346/1

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-22
    Type: Initial release
  • Version 1.1: 2024-10-09
    Changes: Structure summary