9DNW | pdb_00009dnw

Human ClC-3:noTMEM9

PDB DOI: https://doi.org/10.2210/pdb9DNW/pdb
EM Map EMD-47066: EMDB EMDataResource

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

Deposited: 2024-09-18 Released: 2025-04-02
Deposition Author(s): Son, Y., Schrecker, M., Hite, R.K.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.90 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

Structural basis of ClC-3 inhibition by TMEM9 and PI(3,5)P 2.

Schrecker, M., Son, Y., Planells-Cases, R., Kar, S., Vorobeva, V., Schulte, U., Fakler, B., Jentsch, T.J., Hite, R.K.

(2025) bioRxiv

PubMed: 40093093 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1101/2025.02.28.640562
Primary Citation of Related Structures:
9DNW, 9DNX, 9DNY, 9DNZ, 9DO0

PubMed Abstract:
The trafficking and activity of endosomes relies on the exchange of chloride ions and protons by members of the CLC family of chloride channels and transporters, whose mutations are associated with numerous diseases. Despite their critical roles, the mechanisms by which CLC transporters are regulated are poorly understood. Here, we show that two related accessory β-subunits, TMEM9 and TMEM9B, directly interact with ClC-3, -4 and -5. Cryo-EM structures reveal that TMEM9 inhibits ClC-3 by sealing the cytosolic entrance to the Cl ^- ion pathway. Unexpectedly, we find that PI(3,5)P ₂ stabilizes the interaction between TMEM9 and ClC-3 and is required for proper regulation of ClC-3 by TMEM9. Collectively, our findings reveal that TMEM9 and PI(3,5)P ₂ collaborate to regulate endosomal ion homeostasis by modulating the activity of ClC-3.

Organizational Affiliation

Structural Biology Program, Memorial Sloan Kettering Cancer Center; New York, NY, USA.

Macromolecule Content

Total Structure Weight: 185.89 kDa
Atom Count: 11,198
Modelled Residue Count: 1,398
Deposited Residue Count: 1,636
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H(+)/Cl(-) exchange transporter 3	A, B	818	Homo sapiens	Mutation(s): 0 Gene Names: CLCN3
UniProt & NIH Common Fund Data Resources
Find proteins for P51790 (Homo sapiens) Explore P51790 Go to UniProtKB: P51790
PHAROS: P51790 GTEx: ENSG00000109572
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P51790
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1A8I (Subject of Investigation/LOI) Query on A1A8I Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A]	G [auth A], L [auth B]	(2R)-1-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,4,6-trihydroxy-3,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}-3-(octadecanoyloxy)propan-2-yl (5E,8E,11E,13E)-icosa-5,8,11,13-tetraenoate C₄₇ H₈₅ O₁₉ P₃ LNUAYACWRWQKIB-QHILECHRSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain L [auth B]
CLR (Subject of Investigation/LOI) Query on CLR Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B]	E [auth A], F [auth A], J [auth B], K [auth B]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B]
CL (Subject of Investigation/LOI) Query on CL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	C [auth A], D [auth A], H [auth B], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-04-02

Deposition Author(s):

Son, Y.

Schrecker, M.

Hite, R.K.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	141553
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	008748