6YAX

Crystal structure of CD32b (Fc Gamma Receptor IIb) in complex with Human IgG1 Fab fragment (5C05)

• PDB DOI: https://doi.org/10.2210/pdb6YAX/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2020-03-14 Released: 2021-10-06 
• Deposition Author(s): Fisher, H., Tews, I., Orr, C.
• Funding Organization(s): Cancer Research UK

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.264 
• R-Value Work: 0.230 

Starting Model: experimental

Literature

Crystal structure of CD32b (Fc Gamma Receptor IIb) in complex with Human IgG1 Fab fragment (5C05)

Fisher, H., Tews, I., Orr, C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration, native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 134.42 kDa 
• Atom Count: 8,665 
• Modelled Residue Count: 1,096 
• Deposited Residue Count: 1,234 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5C05 F(ab) heavy chain	A [auth HHH], E [auth III]	218	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
5C05 F(ab) light chain	B [auth MMM], D [auth LLL]	218	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Low affinity immunoglobulin gamma Fc region receptor II-c	C [auth AAA], F [auth BBB]	181	Homo sapiens	Mutation(s): 0  Gene Names: FCGR2C, CD32, FCG2, IGFR2
UniProt & NIH Common Fund Data Resources
Find proteins for P31995 (Homo sapiens) Explore P31995  Go to UniProtKB:  P31995
PHAROS:  P31995
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P31995-1

Oligosaccharides

Help

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	G [auth A]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	I [auth AAA]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PG4	H [auth HHH], K [auth III]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
GOL	J [auth LLL]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.264 
• R-Value Work: 0.230 
• Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.728	α = 90
b = 95.728	β = 90
c = 186.038	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-10-06 
Deposition Author(s): Fisher, H., Tews, I., Orr, C.

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Funding Organization	Location	Grant Number
Cancer Research UK	United Kingdom	S_3591

Revision History  

• Version 1.0: 2021-10-06
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Derived calculations, Refinement description