8XXX | pdb_00008xxx

Structure of CXCR2 bound to CXCL6 (Composite map)

PDB DOI: https://doi.org/10.2210/pdb8XXX/pdb
EM Map EMD-38764: EMDB EMDataResource

Classification: SIGNALING PROTEIN/IMMUNE SYSTEM
Organism(s): Homo sapiens, Mus musculus
Expression System: Escherichia coli, Spodoptera frugiperda
Mutation(s): Yes
Membrane Protein: Yes PDBTM

Deposited: 2024-01-19 Released: 2025-01-15
Deposition Author(s): Sano, F.K., Saha, S., Sharma, S., Ganguly, M., Shihoya, W., Nureki, O., Shukla, A.K., Banerjee, R.
Funding Organization(s): Science and Engineering Research Board (SERB)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.17 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structure of CXCR2 bound to CXCL6 (Composite map)

Sano, F.K., Saha, S., Sharma, S., Ganguly, M., Shihoya, W., Nureki, O., Shukla, A.K., Banerjee, R.

To be published.

Macromolecule Content

Total Structure Weight: 154.92 kDa
Atom Count: 9,083
Modelled Residue Count: 1,196
Deposited Residue Count: 1,402
Unique protein chains: 6

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C-X-C motif chemokine 6	A [auth D]	77	Homo sapiens	Mutation(s): 0 Gene Names: CXCL6, GCP2, SCYB6 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P80162 (Homo sapiens) Explore P80162 Go to UniProtKB: P80162
PHAROS: P80162 GTEx: ENSG00000124875
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P80162
Sequence Annotations Expand
Reference Sequence LOADING

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
C-X-C chemokine receptor type 2	B [auth R]	416	Homo sapiens	Mutation(s): 0 Gene Names: CXCR2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P25025 (Homo sapiens) Explore P25025 Go to UniProtKB: P25025
PHAROS: P25025 GTEx: ENSG00000180871
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P25025
Sequence Annotations Expand
Reference Sequence LOADING

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(o) subunit alpha	C [auth A]	240	Homo sapiens	Mutation(s): 6 Gene Names: GNAO1 EC: 3.6.5 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P09471 (Homo sapiens) Explore P09471 Go to UniProtKB: P09471
PHAROS: P09471 GTEx: ENSG00000087258
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P09471
Sequence Annotations Expand
Reference Sequence LOADING

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	D [auth B]	350	Homo sapiens	Mutation(s): 0 Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens) Explore P62873 Go to UniProtKB: P62873
PHAROS: P62873 GTEx: ENSG00000078369
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62873
Sequence Annotations Expand
Reference Sequence LOADING

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	E [auth G]	71	Homo sapiens	Mutation(s): 0 Gene Names: GNG2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens) Explore P59768 Go to UniProtKB: P59768
PHAROS: P59768 GTEx: ENSG00000186469
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P59768
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody fragment ScFv16	F [auth S]	248	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.17 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC	4.4
RECONSTRUCTION	RELION	4

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-01-15

Deposition Author(s):

Funding Organization	Location	Grant Number
Science and Engineering Research Board (SERB)	India	IPA/2020/000405

Revision History (Full details and data files)

Version 1.0: 2025-01-15
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.