9TYV | pdb_00009tyv

Cryo-EM structure of human TMEM45B with a bound GM3 (18:1;O2/24:1)

PDB DOI: https://doi.org/10.2210/pdb9TYV/pdb
EM Map EMD-56439: EMDB EMDataResource

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

Deposited: 2026-01-21 Released: 2026-10-07
Deposition Author(s): Grieben, M., Inderhees, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.82 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

Cryo-EM structure of human TMEM45B with a bound GM3 (18:1;O2/24:1).

Grieben, M., Inderhees, J., Ebersberger, N.

(2026) J Struct Biol 218: 108376-108376

PubMed: 42785650 Search on PubMed
DOI: https://doi.org/10.1016/j.jsb.2026.108376
Primary Citation Related Structures:
9TYV

PubMed Abstract:
The orphan transmembrane protein 45B (TMEM45B) has been reported to be involved in mechanical pain hypersensitivity, antiviral processes, and cancer. The structure of human TMEM45B with bound monosialodihexosylganglioside (GM3, 18:1;O2/24:1), presented here, determined by single-particle cryo-electron microscopy (cryo-EM) to 2.8 Å, reveals a homotetrameric assembly of seven-transmembrane-helix protomers. The first six transmembrane helices from each protomer create a central hydrophobic tunnel that accommodates metal ions and the C24:1 fatty acid component of the ganglioside GM3.

Organizational Affiliation

Institute of Biochemistry, Center of Structural and Cell Biology in Medicine, University of Lübeck, 23562 Lübeck, Germany. Electronic address: Mariana.Grieben@uni-luebeck.de.

Macromolecule Content

Total Structure Weight: 134.55 kDa
Atom Count: 8,360
Modeled Residue Count: 968
Deposited Residue Count: 1,100
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transmembrane protein 45B	A, B, C, D	275	Homo sapiens	Mutation(s): 0 Gene Names: TMEM45B
UniProt & NIH Common Fund Data Resources
Find proteins for Q96B21 (Homo sapiens) Explore Q96B21 Go to UniProtKB: Q96B21
PHAROS: Q96B21 GTEx: ENSG00000151715
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96B21
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1KB5( Subject of Investigation/LOI) Query on A1KB5 Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain P [auth C] SDF format, chain L [auth B] SDF format, chain G [auth A] MOL2 format, chain T [auth D] MOL2 format, chain P [auth C] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] mmCIF format, chain T [auth D] mmCIF format, chain P [auth C] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A]	G [auth A], L [auth B], P [auth C], T [auth D]	Neu5Ac-alpha2->3Gal-beta1->4Glc-beta1->1'Cer(d18:1/24:1 C₆₅ H₁₁₈ N₂ O₂₁ BGMMKNTYKZAIDF-KFCZHOSASA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D]
CLR (Subject of Investigation/LOI) Query on CLR Download:Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain M [auth C] SDF format, chain I [auth B] SDF format, chain H [auth A] MOL2 format, chain Q [auth D] MOL2 format, chain M [auth C] MOL2 format, chain I [auth B] MOL2 format, chain H [auth A] mmCIF format, chain Q [auth D] mmCIF format, chain M [auth C] mmCIF format, chain I [auth B] mmCIF format, chain H [auth A]	H [auth A], I [auth B], M [auth C], Q [auth D]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain H [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain Q [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain Q [auth D]
UNX (Subject of Investigation/LOI) Query on UNX Download:Ideal Coordinates CCD File SDF format, chain S [auth D] SDF format, chain R [auth D] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain S [auth D] MOL2 format, chain R [auth D] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain S [auth D] mmCIF format, chain R [auth D] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] J [auth B] K [auth B] N [auth C] E [auth A], F [auth A], J [auth B], K [auth B], N [auth C], O [auth C], R [auth D], S [auth D]	UNKNOWN ATOM OR ION X		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D]