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- PDB-9tyv: Cryo-EM structure of human TMEM45B with a bound GM3 (18:1;O2/24:1) -

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Basic information

Entry
Database: PDB / ID: 9tyv
TitleCryo-EM structure of human TMEM45B with a bound GM3 (18:1;O2/24:1)
ComponentsTransmembrane protein 45B
KeywordsMEMBRANE PROTEIN / orphan transmembrane protein
Function / homology
Function and homology information


response to pain / trans-Golgi network / endosome membrane / lysosomal membrane
Similarity search - Function
Protein of unknown function DUF716 / Transmembrane protein 45 / Family of unknown function (DUF716)
Similarity search - Domain/homology
: / CHOLESTEROL / Transmembrane protein 45B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.82 Å
AuthorsGrieben, M. / Inderhees, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Struct Biol / Year: 2026
Title: Cryo-EM structure of human TMEM45B with a bound GM3 (18:1;O2/24:1).
Authors: Mariana Grieben / Julica Inderhees / Niklas Ebersberger /
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 ...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.
History
DepositionJan 21, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 7, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transmembrane protein 45B
B: Transmembrane protein 45B
C: Transmembrane protein 45B
D: Transmembrane protein 45B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,55020
Polymers127,4404
Non-polymers7,11016
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Transmembrane protein 45B


Mass: 31860.082 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TMEM45B / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q96B21
#2: Chemical
ChemComp-UNX / UNKNOWN LIGAND


Mass: 63.546 Da / Num. of mol.: 8 / Source method: obtained synthetically / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-A1KB5 / Neu5Ac-alpha2->3Gal-beta1->4Glc-beta1->1'Cer(d18:1/24:1 / 5-acetamido-2-[2-(hydroxymethyl)-6-[(2~{R},3~{S},4~{R},5~{R},6~{R})-2-(hydroxymethyl)-4,5-bis(oxidanyl)-6-[(~{E},2~{S},3~{R})-3-oxidanyl-2-(tetracos-14-enoylamino)octadec-4-enoxy]oxan-3-yl]oxy-3,5-bis(oxidanyl)oxan-4-yl]oxy-4-oxidanyl-6-[1,2,3-tris(oxidanyl)propyl]oxane-2-carboxylic acid


Mass: 1263.633 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C65H118N2O21 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H46O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: orphan transmembrane protein 45B / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 45 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 134004 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 33.82 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00548640
ELECTRON MICROSCOPYf_angle_d0.815711744
ELECTRON MICROSCOPYf_chiral_restr0.04021296
ELECTRON MICROSCOPYf_plane_restr0.00541388
ELECTRON MICROSCOPYf_dihedral_angle_d13.28141316

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