9G6C | pdb_00009g6c

CLC7/OSTM1 complex with bound PIP2 lipid

PDB DOI: https://doi.org/10.2210/pdb9G6C/pdb
EM Map EMD-51097: EMDB EMDataResource

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

Deposited: 2024-07-18 Released: 2025-07-30
Deposition Author(s): Lin, Y., Deme, J.C., Lea, S.M., Newstead, S.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 1.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Mechanism of phosphoinositide regulation of lysosomal pH via inhibition of CLC7

Hilton, J., Lin, Y., Sefah, E., Deme, J.C., Parker, J., Langton, M.J., Grabe, M., Lea, S., Newstead, S., Mindell, J.A.

To be published.

Macromolecule Content

Total Structure Weight: 258.79 kDa
Atom Count: 14,937
Modeled Residue Count: 1,802
Deposited Residue Count: 2,278
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H(+)/Cl(-) exchange transporter 7	A, C	805	Homo sapiens	Mutation(s): 0 Gene Names: CLCN7
UniProt & NIH Common Fund Data Resources
Find proteins for P51798 (Homo sapiens) Explore P51798 Go to UniProtKB: P51798
PHAROS: P51798 GTEx: ENSG00000103249
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P51798
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Osteopetrosis-associated transmembrane protein 1	B, D	334	Homo sapiens	Mutation(s): 0 Gene Names: OSTM1, GL, HSPC019, UNQ6098/PRO21201
UniProt & NIH Common Fund Data Resources
Find proteins for Q86WC4 (Homo sapiens) Explore Q86WC4 Go to UniProtKB: Q86WC4
PHAROS: Q86WC4 GTEx: ENSG00000081087
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q86WC4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1IIT (Subject of Investigation/LOI) Query on A1IIT Download Ideal Coordinates CCD File SDF format, chain T [auth C] SDF format, chain J [auth A] MOL2 format, chain T [auth C] MOL2 format, chain J [auth A] mmCIF format, chain T [auth C] mmCIF format, chain J [auth A]	J [auth A], T [auth C]	[(2R)-2-octanoyloxy-3-[oxidanyl-[(1S,2R,3S,4R,5R,6R)-2,4,5-tris(oxidanyl)-3,6-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate C₂₅ H₄₉ O₁₉ P₃ UKNJNTJYGDDGCJ-DDHCIDQLSA-N		Interactions Focus chain J [auth A] Focus chain T [auth C] Interactions & Density Focus chain J [auth A] Focus chain T [auth C]
ATP (Subject of Investigation/LOI) Query on ATP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain O [auth C] MOL2 format, chain E [auth A] MOL2 format, chain O [auth C] mmCIF format, chain E [auth A] mmCIF format, chain O [auth C]	E [auth A], O [auth C]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain O [auth C] Interactions & Density Focus chain E [auth A] Focus chain O [auth C]
Y01 Query on Y01 Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain X [auth D] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain X [auth D] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain X [auth D]	K [auth A] L [auth A] M [auth A] N [auth B] U [auth C] K [auth A], L [auth A], M [auth A], N [auth B], U [auth C], V [auth C], W [auth C], X [auth D]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth D] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth D]
CL (Subject of Investigation/LOI) Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain Q [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain Q [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain Q [auth C]	G [auth A] H [auth A] I [auth A] Q [auth C] R [auth C] G [auth A], H [auth A], I [auth A], Q [auth C], R [auth C], S [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain P [auth C] MOL2 format, chain F [auth A] MOL2 format, chain P [auth C] mmCIF format, chain F [auth A] mmCIF format, chain P [auth C]	F [auth A], P [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain P [auth C] Interactions & Density Focus chain F [auth A] Focus chain P [auth C]