6EAQ
Glycosylated FCGR3B / CD16b in complex with afucosylated IgG1 Fc
- PDB DOI: https://doi.org/10.2210/pdb6EAQ/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): Yes 
- Deposited: 2018-08-03 Released: 2018-11-07 
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.22 Å
- R-Value Free: 0.244 
- R-Value Work: 0.213 
- R-Value Observed: 0.215 
wwPDB Validation   3D Report Full Report
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Immunoglobulin gamma-1 heavy chain | 220 | Homo sapiens | Mutation(s): 0  | ||
UniProt | |||||
Find proteins for P0DOX5 (Homo sapiens) Explore P0DOX5  Go to UniProtKB:  P0DOX5 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P0DOX5 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Low affinity immunoglobulin gamma Fc region receptor III-B | 175 | Homo sapiens | Mutation(s): 4  Gene Names: FCGR3B, CD16B, FCG3, FCGR3, IGFR3 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for O75015 (Homo sapiens) Explore O75015  Go to UniProtKB:  O75015 | |||||
PHAROS:  O75015 GTEx:  ENSG00000162747  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | O75015 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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 | D | 7 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G28663KH GlyCosmos:  G28663KH GlyGen:  G28663KH |
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
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)-2-acetamido-2-deoxy-beta-D-glucopyranose | E | 8 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G89993FE GlyCosmos:  G89993FE GlyGen:  G89993FE |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.22 Å
- R-Value Free: 0.244 
- R-Value Work: 0.213 
- R-Value Observed: 0.215 
- Space Group: C 1 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 123.629 | α = 90 |
b = 49.388 | β = 103.04 |
c = 139.415 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2018-11-07  Deposition Author(s): Roberts, J.T., Barb, A.W.
Funding Organization | Location | Grant Number |
---|---|---|
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | R01 GM115489 |
Department of Energy (DOE, United States) | United States | GUP-48455 |
Revision History (Full details and data files)
- Version 1.0: 2018-11-07
Type: Initial release - Version 1.1: 2018-11-14
Changes: Data collection, Database references - Version 1.2: 2019-01-09
Changes: Data collection, Database references - Version 1.3: 2019-12-04
Changes: Author supporting evidence - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary