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- EMDB-56439: Cryo-EM structure of human TMEM45B with a bound GM3 (18:1;O2/24:1) -

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Basic information

Entry
Database: EMDB / ID: EMD-56439
TitleCryo-EM structure of human TMEM45B with a bound GM3 (18:1;O2/24:1)
Map datamap sharp
Sample
  • Organelle or cellular component: orphan transmembrane protein 45B
    • Protein or peptide: Transmembrane protein 45B
  • Ligand: UNKNOWN LIGAND
  • Ligand: Neu5Ac-alpha2->3Gal-beta1->4Glc-beta1->1'Cer(d18:1/24:1
  • Ligand: CHOLESTEROL
  • Ligand: water
Keywordsorphan transmembrane protein / MEMBRANE PROTEIN
Function / homologyProtein of unknown function DUF716 / Transmembrane protein 45 / Family of unknown function (DUF716) / response to pain / trans-Golgi network / endosome membrane / lysosomal membrane / Transmembrane protein 45B
Function and homology information
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.82 Å
AuthorsGrieben M / Inderhees J
Funding support1 items
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, 2026-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56439.png

Downloads & links

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Map

FileDownload / File: emd_56439.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap sharp
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.37 Å/pix.
x 640 pix.
= 233.92 Å		0.37 Å/pix.
x 640 pix.
= 233.92 Å		0.37 Å/pix.
x 640 pix.
= 233.92 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.3655 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.038
Minimum - Maximum-0.27107546 - 0.4070446
Average (Standard dev.)0.00029212632 (±0.01028728)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 233.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_56439_msk_1.map
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Half map: half map A

Fileemd_56439_half_map_1.map
Annotationhalf map A
Projections & Slices
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Half map: half map B

Fileemd_56439_half_map_2.map
Annotationhalf map B
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Sample components

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Entire : orphan transmembrane protein 45B

EntireName: orphan transmembrane protein 45B
Components
  • Organelle or cellular component: orphan transmembrane protein 45B
    • Protein or peptide: Transmembrane protein 45B
  • Ligand: UNKNOWN LIGAND
  • Ligand: Neu5Ac-alpha2->3Gal-beta1->4Glc-beta1->1'Cer(d18:1/24:1
  • Ligand: CHOLESTEROL
  • Ligand: water

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Supramolecule #1: orphan transmembrane protein 45B

SupramoleculeName: orphan transmembrane protein 45B / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Transmembrane protein 45B

MacromoleculeName: Transmembrane protein 45B / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.860082 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MANFKGHALP GSFFLIIGLC WSVKYPLKYF SHTRKNSPLH YYQRLEIVEA AIRTLFSVTG ILAEQFVPDG PHLHLYHENH WIKLMNWQH STMYLFFAVS GIVDMLTYLV SHVPLGVDRL VMAVAVFMEG FLFYYHVHNR PPLDQHIHSL LLYALFGGCV S ISLEVIFR ...String:
MANFKGHALP GSFFLIIGLC WSVKYPLKYF SHTRKNSPLH YYQRLEIVEA AIRTLFSVTG ILAEQFVPDG PHLHLYHENH WIKLMNWQH STMYLFFAVS GIVDMLTYLV SHVPLGVDRL VMAVAVFMEG FLFYYHVHNR PPLDQHIHSL LLYALFGGCV S ISLEVIFR DHIVLELFRT SLIILQGTWF WQIGFVLFPP FGTPEWDQKD DANLMFITMC FCWHYLAALS IVAVNYSLVY CL LTRMKRH GRGEIIGIQK LNSDDTYQTA LLSGSDEE

UniProtKB: Transmembrane protein 45B

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Macromolecule #2: UNKNOWN LIGAND

MacromoleculeName: UNKNOWN LIGAND / type: ligand / ID: 2 / Number of copies: 8 / Formula: UNX
Molecular weightTheoretical: 63.546 Da
Chemical component information


ChemComp, No image

ChemComp-UNL:
Unknown ligand

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Macromolecule #3: Neu5Ac-alpha2->3Gal-beta1->4Glc-beta1->1'Cer(d18:1/24:1

MacromoleculeName: Neu5Ac-alpha2->3Gal-beta1->4Glc-beta1->1'Cer(d18:1/24:1
type: ligand / ID: 3 / Number of copies: 4 / Formula: A1KB5
Molecular weightTheoretical: 1.263633 KDa

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Macromolecule #4: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 4 / Number of copies: 4 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 12 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 134004
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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