4BYH | pdb_00004byh

Crystal structure of sialylated IgG Fc

• PDB DOI: https://doi.org/10.2210/pdb4BYH/pdb

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


• Deposited: 2013-07-19 Released: 2013-08-21 
• Deposition Author(s): Crispin, M., Yu, X., Bowden, T.A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.262 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.226 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Sialylated Igg Fc: Implications for the Mechanism of Intravenous Immunoglobulin Therapy.

Crispin, M., Yu, X., Bowden, T.A.

(2013) Proc Natl Acad Sci U S A 110: E3544

• PubMed: 23929778 
• DOI: https://doi.org/10.1073/pnas.1310657110
• Primary Citation Related Structures: 
  4BYH

---

Organizational Affiliation: 
• Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, Oxford OX1 3QU, United Kingdom.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 56.49 kDa 
• Atom Count: 3,780 
• Modeled Residue Count: 416 
• Deposited Residue Count: 466 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IG GAMMA-1 CHAIN C REGION	A, B	233	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01857 (Homo sapiens) Explore P01857  Go to UniProtKB:  P01857
PHAROS:  P01857 GTEx:  ENSG00000211896
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P01857-2

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-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	C	10		N-Glycosylation
Glycosylation Resources
GlyTouCan: G23295TF GlyCosmos: G23295TF GlyGen: G23295TF

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[beta-D-galactopyranose-(1-4)-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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D	10		N-Glycosylation
Glycosylation Resources
GlyTouCan: G78059CC GlyCosmos: G78059CC GlyGen: G78059CC

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	E [auth A], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.262 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.226 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153	α = 90
b = 153	β = 90
c = 111.85	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-21 
Deposition Author(s): Crispin, M., Yu, X., Bowden, T.A.

Revision History  

• Version 1.0: 2013-08-21
  Type: Initial release
  
• Version 1.1: 2013-10-02
  Changes: Database references
• Version 1.2: 2018-02-28
  Changes: Source and taxonomy
• Version 1.3: 2019-04-03
  Changes: Data collection, Derived calculations, Source and taxonomy
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 3.0: 2020-12-23
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 3.1: 2023-12-20
  Changes: Data collection, Database references, Refinement description
• Version 3.2: 2024-11-13
  Changes: Structure summary