4W4O

High-resolution crystal structure of Fc bound to its human receptor Fc-gamma-RI

• PDB DOI: https://doi.org/10.2210/pdb4W4O/pdb

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


• Deposited: 2014-08-15 Released: 2015-04-29 
• Deposition Author(s): Caaveiro, J.M.M., Kiyoshi, M., Tsumoto, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.215 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 87.85 kDa 
• Atom Count: 6,420 
• Modelled Residue Count: 683 
• Deposited Residue Count: 728 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ig gamma-1 chain C region	A, B	224	Homo sapiens	Mutation(s): 0  Gene Names: IGHG1
UniProt & NIH Common Fund Data Resources
Find proteins for P01857 (Homo sapiens) Explore P01857  Go to UniProtKB:  P01857
PHAROS:  P01857 GTEx:  ENSG00000211896

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
High affinity immunoglobulin gamma Fc receptor I	C	280	Homo sapiens	Mutation(s): 19  Gene Names: FCGR1A, FCG1, FCGR1, IGFR1
UniProt & NIH Common Fund Data Resources
Find proteins for P12314 (Homo sapiens) Explore P12314  Go to UniProtKB:  P12314
PHAROS:  P12314 GTEx:  ENSG00000150337

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D, E	9		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G27919IH GlyCosmos:  G27919IH GlyGen:  G27919IH

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-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	G	6		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G01760ZU GlyCosmos:  G01760ZU GlyGen:  G01760ZU

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	Q [auth A], U [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	H [auth A], I [auth A], J [auth A], R [auth B], S [auth B], V [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], T [auth B], W [auth C], X [auth C]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.215 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.98	α = 90
b = 126.5	β = 118.95
c = 71.61	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-29 
Deposition Author(s): Caaveiro, J.M.M., Kiyoshi, M., Tsumoto, K.

Revision History  

• Version 1.0: 2015-04-29
  Type: Initial release
  
• Version 1.1: 2015-05-20
  Changes: Database references
• Version 1.2: 2020-01-29
  Changes: Advisory, Data collection, Derived calculations, Source and taxonomy, Structure summary
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary