9GL6 | pdb_00009gl6

TRPC5 in complex with spin-labelled ligand SpinPico3

PDB DOI: https://doi.org/10.2210/pdb9GL6/pdb
EM Map EMD-51437: EMDB EMDataResource

Classification: PROTEIN TRANSPORT
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-08-27 Released: 2025-09-10
Deposition Author(s): Porav, S.A., Bon, R.S., Hammond, K.L.R.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

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

Validation slider image for 9GL6

This is version 1.1 of the entry. See complete history.

Literature

Non-covalent spin labelling of TRPC5 ion channels enables EPR studies of protein-ligand interactions

Johnson, A.J., Porav, S.A., Hammond, K.L.R., Shah, A., Hassane, E.M., Pask, C.M., Muench, S.P., Wilson, A.J., Pilotas, C., Bon, R.S.

To be published.

Macromolecule Content

Total Structure Weight: 360.36 kDa
Atom Count: 21,696
Modeled Residue Count: 2,624
Deposited Residue Count: 3,060
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Short transient receptor potential channel 5	A, B, C, D	765	Homo sapiens	Mutation(s): 0 Gene Names: TRPC5, TRP5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UL62 (Homo sapiens) Explore Q9UL62 Go to UniProtKB: Q9UL62
PHAROS: Q9UL62 GTEx: ENSG00000072315
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UL62
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1IMP (Subject of Investigation/LOI) Query on A1IMP Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain P [auth D] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D]	G [auth A], J [auth B], M [auth C], P [auth D]	7-[(4-chlorophenyl)methyl]-3-methyl-1-(3-oxidanylpropyl)-8-(1,1,3,3-tetramethyl-2-oxidanyl-isoindol-5-yl)oxy-purine-2,6-dione C₂₈ H₃₂ Cl N₅ O₅ KVWONESNCHOGAF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D]
Y01 Query on Y01 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain N [auth D]	E [auth A], H [auth B], K [auth C], N [auth D]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain O [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain O [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain O [auth D]	F [auth A], I [auth B], L [auth C], O [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286:

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-09-10

Deposition Author(s):

Hammond, K.L.R.

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/P020208/1

Revision History (Full details and data files)

Version 1.0: 2025-09-10
Type: Initial release
Version 1.1: 2026-04-01
Changes: Data collection, Database references

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.