2WAH | pdb_00002wah

Crystal Structure of an IgG1 Fc Glycoform (Man9GlcNAc2)

• PDB DOI: https://doi.org/10.2210/pdb2WAH/pdb

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


• Deposited: 2009-02-06 Released: 2009-03-10 
• Deposition Author(s): Crispin, M., Bowden, T.A., Coles, C.H., Harlos, K., Aricescu, A.R., Harvey, D.J., Stuart, D.I., Jones, E.Y.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 
  0.268 (Depositor), 0.307 (DCC) 
• R-Value Work: 
  0.216 (Depositor) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

Carbohydrate and Domain Architecture of an Immature Antibody Glycoform Exhibiting Enhanced Effector Functions

Crispin, M., Bowden, T.A., Coles, C.H., Harlos, K., Aricescu, A.R., Harvey, D.J., Stuart, D.I., Jones, E.Y.

(2009) J Mol Biology 387: 1061

• PubMed: 19236877 
• DOI: https://doi.org/10.1016/j.jmb.2009.02.033
• Primary Citation Related Structures: 
  2WAH


• PubMed Abstract: 
  

  Antibodies contain a conserved glycosylation site that has emerged as a target for the modulation of antibody effector functions. The crystal structure of a biosynthetic intermediate of human IgG1, bearing immature oligomannose-type glycans and reported to display increased antibody-dependent cellular cytotoxicity, demonstrates that glycan engineering can bias the Fc to an open conformation primed for receptor binding.

---

Organizational Affiliation: 
• Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Headington, Oxford OX3 7BN, UK.

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 PQS (software)

Macromolecule Content 

• Total Structure Weight: 49.55 kDa 
• Atom Count: 3,565 
• Modeled Residue Count: 416 
• Deposited Residue Count: 418 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IG GAMMA-1 CHAIN C REGION	A, B	209	Homo sapiens	Mutation(s): 1
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
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[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	C	9		N-Glycosylation
Glycosylation Resources
GlyTouCan: G83161QT GlyCosmos: G83161QT GlyGen: G83161QT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free:  0.268 (Depositor), 0.307 (DCC) 
• R-Value Work:  0.216 (Depositor) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.391	α = 90
b = 74.977	β = 90
c = 149.2	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-10 
Deposition Author(s): Crispin, M., Bowden, T.A., Coles, C.H., Harlos, K., Aricescu, A.R., Harvey, D.J., Stuart, D.I., Jones, E.Y.

Revision History  

• Version 1.0: 2009-03-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2018-02-28
  Changes: 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 2.1: 2023-12-13
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-13
  Changes: Structure summary