6D58 | pdb_00006d58

Crystal structure of a Fc fragment of Human IgG3

• PDB DOI: https://doi.org/10.2210/pdb6D58/pdb

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


• Deposited: 2018-04-19 Released: 2019-05-15 
• Deposition Author(s): Gohain, N., Tolbert, W.D., Pazgier, M.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 
  0.286 (Depositor), 0.287 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.236 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a Fc fragment of Human IgG3.

Gohain, N., Tolbert, W.D., Pazgier, M.

To be published.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 51.43 kDa 
• Atom Count: 3,538 
• Modeled Residue Count: 414 
• Deposited Residue Count: 428 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin heavy constant gamma 3	A, B	214	Homo sapiens	Mutation(s): 1  Gene Names: IGHG3
UniProt & NIH Common Fund Data Resources
Find proteins for P01860 (Homo sapiens) Explore P01860  Go to UniProtKB:  P01860
PHAROS:  P01860
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P01860-2

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	8		N-Glycosylation
Glycosylation Resources
GlyTouCan: G80858MF GlyCosmos: G80858MF GlyGen: G80858MF

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free:  0.286 (Depositor), 0.287 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.236 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.59	α = 90
b = 80.678	β = 90
c = 136.029	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-05-15 
Deposition Author(s): Gohain, N., Tolbert, W.D., Pazgier, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	P01 AI120756

Revision History  

• Version 1.0: 2019-05-15
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence, Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 2.2: 2024-11-20
  Changes: Structure summary