3WJL

Crystal structure of IIb selective Fc variant, Fc(V12), in complex with FcgRIIb

PDB DOI: https://doi.org/10.2210/pdb3WJL/pdb

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

Deposited: 2013-10-11 Released: 2013-11-13
Deposition Author(s): Kadono, S., Mimoto, F., Katada, H., Igawa, T., Kuramochi, T., Muraoka, M., Wada, Y., Haraya, K., Miyazaki, T., Hattori, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.86 Å
R-Value Free: 0.270
R-Value Work: 0.230
R-Value Observed: 0.232

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 75.6 kDa
Atom Count: 4,768
Modelled Residue Count: 580
Deposited Residue Count: 639
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ig gamma-1 chain C region	A, B	230	Homo sapiens	Mutation(s): 7 Gene Names: IGHG1
UniProt & NIH Common Fund Data Resources
Find proteins for P01857 (Homo sapiens) Explore P01857 Go to UniProtKB: P01857
PHAROS: P01857 GTEx: ENSG00000211896
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01857
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Low affinity immunoglobulin gamma Fc region receptor II-c	C	179	Homo sapiens	Mutation(s): 0 Gene Names: FCGR2C, CD32, FCG2, IGFR2
UniProt & NIH Common Fund Data Resources
Find proteins for P31995 (Homo sapiens) Explore P31995 Go to UniProtKB: P31995
PHAROS: P31995
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P31995
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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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)-[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	D	8		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G89993FE GlyCosmos: G89993FE GlyGen: G89993FE

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)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	E	9		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G33244HE GlyCosmos: G33244HE GlyGen: G33244HE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain F [auth C] MOL2 format, chain F [auth C]	F [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth C] Interactions & Density Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.86 Å
R-Value Free: 0.270
R-Value Work: 0.230
R-Value Observed: 0.232
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 156.71	α = 90
b = 260.2	β = 90
c = 56.86	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-11-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-11-13
Type: Initial release
Version 1.1: 2014-11-26
Changes: Other
Version 1.2: 2018-06-20
Changes: Data collection, Source and taxonomy
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2023-11-29
Changes: Data collection, Database references, Structure summary