4X4M

Structure of FcgammaRI in complex with Fc reveals the importance of glycan recognition for high affinity IgG binding

• PDB DOI: https://doi.org/10.2210/pdb4X4M/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus, Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-12-03 Released: 2015-04-08 
• Deposition Author(s): Lu, J., Sun, P.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.48 Å
• R-Value Free: 0.296 
• R-Value Work: 0.245 
• R-Value Observed: 0.249 

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.

Biological Assembly 2  

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 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 167.35 kDa 
• Atom Count: 11,366 
• Modelled Residue Count: 1,377 
• Deposited Residue Count: 1,426 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ig gamma-1 chain C region	A, B, C, D	219	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	E, F	275	Homo sapiens	Mutation(s): 18  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
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	G, H	8		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G59451NL GlyCosmos:  G59451NL GlyGen:  G59451NL

Entity ID: 4
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)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	I	9		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G33244HE GlyCosmos:  G33244HE GlyGen:  G33244HE

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J	6		N/A
Glycosylation Resources
GlyTouCan:  G55061AW GlyCosmos:  G55061AW GlyGen:  G55061AW

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose	K	2		N/A
Glycosylation Resources
GlyTouCan:  G30207PZ GlyCosmos:  G30207PZ GlyGen:  G30207PZ

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	L [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
FUL	M [auth D]	beta-L-fucopyranose C6 H12 O5 SHZGCJCMOBCMKK-KGJVWPDLSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.48 Å
• R-Value Free: 0.296 
• R-Value Work: 0.245 
• R-Value Observed: 0.249 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.921	α = 89.86
b = 67.991	β = 112.25
c = 125.028	γ = 89.96

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-08 
Deposition Author(s): Lu, J., Sun, P.D.

Revision History  

• Version 1.0: 2015-04-08
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary