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- PDB-28hy: Cryo-EM structure of human TMEM45A with a bound 2-Hydroxypalmitate -

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Basic information

Entry
Database: PDB / ID: 28hy
TitleCryo-EM structure of human TMEM45A with a bound 2-Hydroxypalmitate
ComponentsTransmembrane protein 45A
KeywordsMEMBRANE PROTEIN / orphan transmembrane 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsGrieben, M. / Inderhees, J.
Funding support1items
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, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 14, 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 45A
B: Transmembrane protein 45A
C: Transmembrane protein 45A
D: Transmembrane protein 45A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,43616
Polymers126,8384
Non-polymers1,59812
Water724
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 45A / DNA polymerase-transactivated protein 4 / Dermal papilla-derived protein 7


Mass: 31709.457 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TMEM45A, DERP7, DNAPTP4 / Production host: Homo sapiens (human) / References: UniProt: Q9NWC5
#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-A1JXZ / (R)-2-hydroxypalmitic acid / (2R)-2-oxidanylhexadecanoic acid / 2-hydroxypalmitate / 2-hydroxyhexadecanoate


Mass: 272.423 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H32O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 70071 / Symmetry type: POINT
RefinementCross valid method: NONE

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