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- PDB-9thk: Structure of human CLN8 in an apo-state -

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Basic information

Entry
Database: PDB / ID: 9thk
TitleStructure of human CLN8 in an apo-state
ComponentsProtein CLN8
KeywordsMEMBRANE PROTEIN / Bis(monoacylglycero)phosphate / Batten disease / Glycerophosphoglycerol / Lysophosphatidylglycerol / Acyltransferase / Neurodegeneration
Function / homology
Function and homology information


ceramide metabolic process / ceramide binding / ceramide biosynthetic process / lipid transport / lipid biosynthetic process / lipid homeostasis / endoplasmic reticulum-Golgi intermediate compartment / phospholipid metabolic process / cholesterol metabolic process / negative regulation of proteolysis ...ceramide metabolic process / ceramide binding / ceramide biosynthetic process / lipid transport / lipid biosynthetic process / lipid homeostasis / endoplasmic reticulum-Golgi intermediate compartment / phospholipid metabolic process / cholesterol metabolic process / negative regulation of proteolysis / endoplasmic reticulum-Golgi intermediate compartment membrane / protein catabolic process / nervous system development / endoplasmic reticulum membrane / endoplasmic reticulum / membrane
Similarity search - Function
: / TRAM/LAG1/CLN8 homology domain / TLC domain / TLC domain profile. / TRAM, LAG1 and CLN8 homology domains.
Similarity search - Domain/homology
COENZYME A / Protein CLN8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLacabanne, D. / Sheokand, P.K. / Ruprecht, J.J. / Petkevicius, K.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UU_00028 United Kingdom
Wellcome TrustSBF00101078 United Kingdom
CitationJournal: To Be Published
Title: Stereospecific GPG acylation by CLN8 drives BMP biosynthesis and underpins Batten disease
Authors: Sheokand, P.K. / Lacabanne, D. / James, A.M. / Ruprecht, J.J. / van der Kleij, J. / Muller-Niva, J. / Salo, M.H. / Juneja, N. / Jenkins, J. / Shun Yu, C. / Pratt, M.A. / King, M.S. / Weimer, ...Authors: Sheokand, P.K. / Lacabanne, D. / James, A.M. / Ruprecht, J.J. / van der Kleij, J. / Muller-Niva, J. / Salo, M.H. / Juneja, N. / Jenkins, J. / Shun Yu, C. / Pratt, M.A. / King, M.S. / Weimer, J.M. / Koulman, A. / Hinttala, R. / Santorelli, F.M. / Murphy, M.P. / Kunji, E.R.S. / Petkevicus, K.
History
DepositionDec 3, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Protein CLN8
D: Protein CLN8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6014
Polymers67,0662
Non-polymers1,5352
Water00
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 Protein CLN8


Mass: 33532.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLN8, C8orf61 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q9UBY8
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
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: CLN8 dimer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.4
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: 600 nm
Image recordingElectron dose: 51.05 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameCategory
1Warpparticle selection
2EPUimage acquisition
4WarpCTF correction
10cryoSPARCinitial Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 258739 / Symmetry type: POINT

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