8CHA | pdb_00008cha

Fc gamma RIIa 27W/131H variant ectodomain

PDB DOI: https://doi.org/10.2210/pdb8CHA/pdb

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), 0.226 (DCC)
R-Value Work:
0.193 (Depositor), 0.195 (DCC)
R-Value Observed:
0.194 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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.

Macromolecule Content

Total Structure Weight: 25.4 kDa
Atom Count: 1,587
Modeled Residue Count: 168
Deposited Residue Count: 209
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Low affinity immunoglobulin gamma Fc region receptor II-a	A	209	Homo sapiens	Mutation(s): 1 Gene Names: FCGR2A, CD32, FCG2, FCGR2A1, IGFR2
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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12318
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A	Go to GlyGen: P12318-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	4	N/A	N-Glycosylation	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
16P Query on 16P Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	3,6,9,12,15,18-HEXAOXAICOSANE C₁₄ H₃₀ O₆ IXFAFGFZFQHRLB-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
FLC Query on FLC Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
FWN Query on FWN Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	2-[2-(2-ethoxyethoxy)ethoxy]ethanol C₈ H₁₈ O₄ WFSMVVDJSNMRAR-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	D [auth A], E [auth A], F [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
DXE Query on DXE Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	1,2-DIMETHOXYETHANE C₄ H₁₀ O₂ XTHFKEDIFFGKHM-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free: 0.225 (Depositor), 0.226 (DCC)
R-Value Work: 0.193 (Depositor), 0.195 (DCC)
R-Value Observed: 0.194 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.931	α = 90
b = 76.526	β = 90
c = 108.279	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-05-22

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private		19764
Wellcome Trust	United Kingdom	091322/2/10/2
European Research Council (ERC)	European Union	708051
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	ALERT-13
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/M021610/1
Academy of Finland	Finland	1252206
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/K015346/1