9ZD2 | pdb_00009zd2

C1 local refinement of aquaporin 1 bound to endogenous human stomatin

PDB DOI: https://doi.org/10.2210/pdb9ZD2/pdb
EM Map EMD-74049: EMDB EMDataResource

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

Deposited: 2025-11-24 Released: 2026-02-25
Deposition Author(s): Vallese, F., Clarke, O.B.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.10 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

Stomatin encapsulates aquaporin-1 and urea transporter-B in the erythrocyte membrane

Vallese, F., Li, H., Clarke, O.B.

To be published.

Macromolecule Content

Total Structure Weight: 212.2 kDa
Atom Count: 14,799
Modeled Residue Count: 1,958
Deposited Residue Count: 1,958
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aquaporin-1	A [auth D], B, C, D [auth A]	247	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P29972 (Homo sapiens) Explore P29972 Go to UniProtKB: P29972
PHAROS: P29972 GTEx: ENSG00000240583
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P29972
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Stomatin	E [auth F], F [auth G], G [auth E], H [auth I], I [auth H]	194	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P27105 (Homo sapiens) Explore P27105 Go to UniProtKB: P27105
PHAROS: P27105 GTEx: ENSG00000148175
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P27105
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CLR (Subject of Investigation/LOI) Query on CLR Download Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain P [auth A] SDF format, chain N [auth C] SDF format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain P [auth A] MOL2 format, chain N [auth C] MOL2 format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain P [auth A] mmCIF format, chain N [auth C] mmCIF format, chain K [auth B]	K [auth B], M [auth C], N [auth C], P [auth A]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth A] Interactions & Density Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth A]
PLM (Subject of Investigation/LOI) Query on PLM Download Ideal Coordinates CCD File SDF format, chain J [auth D] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain Q [auth A] MOL2 format, chain J [auth D] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth A] mmCIF format, chain J [auth D] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain Q [auth A]	J [auth D], L [auth B], O [auth C], Q [auth A]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain J [auth D] Focus chain L [auth B] Focus chain O [auth C] Focus chain Q [auth A] Interactions & Density Focus chain J [auth D] Focus chain L [auth B] Focus chain O [auth C] Focus chain Q [auth A]