9THK | pdb_00009thk

Structure of human CLN8 in an apo-state

PDB DOI: https://doi.org/10.2210/pdb9THK/pdb
EM Map EMD-55929: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Saccharomyces cerevisiae
Mutation(s): No

Deposited: 2025-12-03 Released: 2026-07-29
Deposition Author(s): Lacabanne, D., Sheokand, P.K., Ruprecht, J.J., Petkevicius, K.
Funding Organization(s): Medical Research Council (MRC, United Kingdom), Wellcome Trust

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9THK

This is version 1.0 of the entry. See complete history.

Literature

Stereospecific GPG acylation by CLN8 drives BMP biosynthesis and underpins Batten disease

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.

To be published.

Macromolecule Content

Total Structure Weight: 68.6 kDa
Atom Count: 4,136
Modeled Residue Count: 494
Deposited Residue Count: 586
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein CLN8	A [auth B], B [auth D]	293	Homo sapiens	Mutation(s): 0 Gene Names: CLN8, C8orf61
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBY8 (Homo sapiens) Explore Q9UBY8 Go to UniProtKB: Q9UBY8
GTEx: ENSG00000182372
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UBY8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COA (Subject of Investigation/LOI) Query on COA Download:Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D MOL2 format, chain C [auth B] MOL2 format, chain D mmCIF format, chain C [auth B] mmCIF format, chain D	C [auth B], D	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain C [auth B] Focus chain D Interactions & Density Focus chain C [auth B] Focus chain D

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-07-29

Deposition Author(s):

Petkevicius, K.

Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MC_UU_00028
Wellcome Trust	United Kingdom	SBF00101078

Revision History (Full details and data files)

Version 1.0: 2026-07-29
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.