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- EMDB-56534: Cryo-EM structure of human TMEM45A with a bound 2-Hydroxypalmitate -

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Basic information

Entry
Database: EMDB / ID: EMD-56534
TitleCryo-EM structure of human TMEM45A with a bound 2-Hydroxypalmitate
Map data
Sample
  • Organelle or cellular component: orphan transmembrane protein 45B
    • Protein or peptide: Transmembrane protein 45A
  • Ligand: UNKNOWN LIGAND
  • Ligand: (R)-2-hydroxypalmitic acid
  • Ligand: water
Keywordsorphan transmembrane protein / MEMBRANE PROTEIN
Function / homologyProtein of unknown function DUF716 / Transmembrane protein 45 / Family of unknown function (DUF716) / membrane / Transmembrane protein 45A
Function and homology information
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsGrieben M / Inderhees J
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Struct Biol / Year: 2026
Title: Cryo-EM structure of human TMEM45A with a bound 2-Hydroxypalmitate.
Authors: Mariana Grieben / Julica Inderhees / Niklas Ebersberger /
Abstract: The orphan transmembrane protein 45 A (TMEM45A) is highly expressed in keratinocytes as well as cancer cells under hypoxic conditions, where it contributes to metastasis and chemoresistance. The ...The orphan transmembrane protein 45 A (TMEM45A) is highly expressed in keratinocytes as well as cancer cells under hypoxic conditions, where it contributes to metastasis and chemoresistance. The structure of human TMEM45A, determined with single-particle cryo-electron microscopy (cryo-EM) to 3.27 Å, reveals a homotetrameric assembly of seven-transmembrane-helix protomers. The first six transmembrane helices (TMHs) of each protomer assemble to form a central hydrophobic tunnel containing a 2-hydroxypalmitate.
History
DepositionFeb 1, 2026-
Header (metadata) releaseOct 14, 2026-
Map releaseOct 14, 2026-
UpdateOct 14, 2026-
Current statusOct 14, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56534.png

Downloads & links

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Map

FileDownload / File: emd_56534.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.37 Å/pix.
x 640 pix.
= 233.6 Å		0.37 Å/pix.
x 640 pix.
= 233.6 Å		0.37 Å/pix.
x 640 pix.
= 233.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.365 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.15437926 - 0.21920618
Average (Standard dev.)0.0003204503 (±0.0056152083)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 233.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_56534_msk_1.map
Projections & Slices
AxesZYX

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Half map: None

Fileemd_56534_half_map_1.map
AnnotationNone
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: None

Fileemd_56534_half_map_2.map
AnnotationNone
Projections & Slices
AxesZYX

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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 45A
  • Ligand: UNKNOWN LIGAND
  • Ligand: (R)-2-hydroxypalmitic acid
  • 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 45A

MacromoleculeName: Transmembrane protein 45A / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.709457 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGNFRGHALP GTFFFIIGLW WCTKSILKYI CKKQKRTCYL GSKTLFYRLE ILEGITIVGM ALTGMAGEQF IPGGPHLMLY DYKQGHWNQ LLGWHHFTMY FFFGLLGVAD ILCFTISSLP VSLTKLMLSN ALFVEAFIFY NHTHGREMLD IFVHQLLVLV V FLTGLVAF ...String:
MGNFRGHALP GTFFFIIGLW WCTKSILKYI CKKQKRTCYL GSKTLFYRLE ILEGITIVGM ALTGMAGEQF IPGGPHLMLY DYKQGHWNQ LLGWHHFTMY FFFGLLGVAD ILCFTISSLP VSLTKLMLSN ALFVEAFIFY NHTHGREMLD IFVHQLLVLV V FLTGLVAF LEFLVRNNVL LELLRSSLIL LQGSWFFQIG FVLYPPSGGP AWDLMDHENI LFLTICFCWH YAVTIVIVGM NY AFITWLV KSRLKRLCSS EVGLLKNAER EQESEEEM

UniProtKB: Transmembrane protein 45A

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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: (R)-2-hydroxypalmitic acid

MacromoleculeName: (R)-2-hydroxypalmitic acid / type: ligand / ID: 3 / Number of copies: 4 / Formula: A1JXZ
Molecular weightTheoretical: 272.423 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 4 / 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: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 70071
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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