4GKO

Crystal structure of the calcium2+-bound human IgE-Fc(epsilon)3-4 bound to its B cell receptor derCD23

• PDB DOI: https://doi.org/10.2210/pdb4GKO/pdb

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


• Deposited: 2012-08-13 Released: 2013-06-26 
• Deposition Author(s): Yuan, D., Sutton, B.J., Dhaliwal, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.312 
• R-Value Work: 0.273 
• R-Value Observed: 0.275 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 252.58 kDa 
• Atom Count: 16,217 
• Modelled Residue Count: 1,987 
• Deposited Residue Count: 2,196 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ig epsilon chain C region	A, B, C, D, E, F	223	Homo sapiens	Mutation(s): 0  Gene Names: IGHE
UniProt & NIH Common Fund Data Resources
Find proteins for P01854 (Homo sapiens) Explore P01854  Go to UniProtKB:  P01854
PHAROS:  P01854 GTEx:  ENSG00000211891

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Low affinity immunoglobulin epsilon Fc receptor	G, H, I, J, K, L	143	Homo sapiens	Mutation(s): 0  Gene Names: FCER2, CD23A, CLEC4J, FCE2, IGEBF
UniProt & NIH Common Fund Data Resources
Find proteins for P06734 (Homo sapiens) Explore P06734  Go to UniProtKB:  P06734
PHAROS:  P06734 GTEx:  ENSG00000104921

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M, N, O, P, Q, R	5		N/A
Glycosylation Resources
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MAN	S [auth C], T [auth C]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
CA	U [auth G], V [auth H], W [auth I], X [auth J], Y [auth K], Z [auth L]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.312 
• R-Value Work: 0.273 
• R-Value Observed: 0.275 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.83	α = 90
b = 110.13	β = 90
c = 367.41	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-06-26 
Deposition Author(s): Yuan, D., Sutton, B.J., Dhaliwal, B.

Revision History  

• Version 1.0: 2013-06-26
  Type: Initial release
  
• Version 1.1: 2013-08-14
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-09-13
  Changes: Data collection, Database references, Refinement description, Structure summary