4I2X

Crystal structure of Signal Regulatory Protein gamma (SIRP-gamma) in complex with FabOX117

PDB DOI: https://doi.org/10.2210/pdb4I2X/pdb

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

Deposited: 2012-11-23 Released: 2013-12-18
Deposition Author(s): Nettleship, J.E., Ren, J., Stuart, D.I., Owens, R.J., Oxford Protein Production Facility (OPPF)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free: 0.260
R-Value Work: 0.196
R-Value Observed: 0.199

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of signal regulatory protein gamma (SIRP gamma) in complex with an antibody Fab fragment.

Nettleship, J.E., Ren, J., Scott, D.J., Rahman, N., Hatherley, D., Zhao, Y., Stuart, D.I., Barclay, A.N., Owens, R.J.

(2013) BMC Struct Biol 13: 13-13

PubMed: 23826770 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1186/1472-6807-13-13
Primary Citation of Related Structures:
4I2X

PubMed Abstract:
Signal Regulatory Protein γ (SIRPγ) is a member of a closely related family of three cell surface receptors implicated in modulating immune/inflammatory responses. SIRPγ is expressed on T lymphocytes where it appears to be involved in the integrin-independent adhesion of lymphocytes to antigen-presenting cells. Here we describe the first full length structure of the extracellular region of human SIRPγ.

Macromolecule Content

Total Structure Weight: 170.6 kDa
Atom Count: 11,813
Modelled Residue Count: 1,486
Deposited Residue Count: 1,542
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FabOX117 light chain	A, C	214	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
FabOX117 heavy chain	B, D	229	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Signal-regulatory protein gamma	E, F	328	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P1W8 (Homo sapiens) Explore Q9P1W8 Go to UniProtKB: Q9P1W8
PHAROS: Q9P1W8 GTEx: ENSG00000089012
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9P1W8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain I [auth E] SDF format, chain K [auth F] MOL2 format, chain I [auth E] MOL2 format, chain K [auth F]	I [auth E], K [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth E] Focus chain K [auth F] Interactions & Density Focus chain I [auth E] Focus chain K [auth F]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B]	G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain J [auth E] MOL2 format, chain H [auth D] MOL2 format, chain J [auth E]	H [auth D], J [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth D] Focus chain J [auth E] Interactions & Density Focus chain H [auth D] Focus chain J [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free: 0.260
R-Value Work: 0.196
R-Value Observed: 0.199
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.361	α = 90
b = 174.191	β = 90
c = 81.734	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-12-18

Deposition Author(s):

Oxford Protein Production Facility (OPPF)

Revision History (Full details and data files)

Version 1.0: 2013-12-18
Type: Initial release
Version 1.1: 2014-12-24
Changes: Database references
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.3: 2023-09-20
Changes: Data collection, Database references, Refinement description, Structure summary