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- EMDB-56022: Structure of human CLN8 in the presence of oleate -

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Basic information

Entry
Database: EMDB / ID: EMD-56022
TitleStructure of human CLN8 in the presence of oleate
Map data
Sample
  • Complex: CLN8 dimer
    • Protein or peptide: Protein CLN8
  • Ligand: COENZYME A
  • Ligand: OLEIC ACID
  • Ligand: water
KeywordsBis(monoacylglycero)phosphate / Batten disease / Glycerophosphoglycerol / Lysophosphatidylglycerol / Acyltransferase / Neurodegeneration / MEMBRANE PROTEIN
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
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsLacabanne D / Sheokand PK / Ruprecht JJ / Petkevicius K
Funding support United Kingdom, 2 items
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 PK / Lacabanne D / James AM / Ruprecht JJ / van der Kleij J / Muller-Niva J / Salo MH / Juneja N / Jenkins J / Shun Yu C / Pratt MA / King MS / Weimer JM / Koulman A / Hinttala R / ...Authors: Sheokand PK / Lacabanne D / James AM / Ruprecht JJ / van der Kleij J / Muller-Niva J / Salo MH / Juneja N / Jenkins J / Shun Yu C / Pratt MA / King MS / Weimer JM / Koulman A / Hinttala R / Santorelli FM / Murphy MP / Kunji ERS / Petkevicus K
History
DepositionDec 9, 2025-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56022.png

Downloads & links

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Map

FileDownload / File: emd_56022.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 360 pix.
= 262.44 Å		0.73 Å/pix.
x 360 pix.
= 262.44 Å		0.73 Å/pix.
x 360 pix.
= 262.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.729 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.169
Minimum - Maximum-0.9807984 - 1.6765627
Average (Standard dev.)0.00085645117 (±0.022371175)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 262.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_56022_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_56022_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_56022_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CLN8 dimer

EntireName: CLN8 dimer
Components
  • Complex: CLN8 dimer
    • Protein or peptide: Protein CLN8
  • Ligand: COENZYME A
  • Ligand: OLEIC ACID
  • Ligand: water

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Supramolecule #1: CLN8 dimer

SupramoleculeName: CLN8 dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Protein CLN8

MacromoleculeName: Protein CLN8 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.532996 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MNPASDGGTS ESIFDLDYAS WGIRSTLMVA GFVFYLGVFV VCHQLSSSLN ATYRSLVARE KVFWDLAATR AVFGVQSTAA GLWALLGDP VLHADKARGQ QNWCWFHITT ATGFFCFENV AVHLSNLIFR TFDLFLVIHH LFAFLGFLGC LVNLQAGHYL A MTTLLLEM ...String:
MNPASDGGTS ESIFDLDYAS WGIRSTLMVA GFVFYLGVFV VCHQLSSSLN ATYRSLVARE KVFWDLAATR AVFGVQSTAA GLWALLGDP VLHADKARGQ QNWCWFHITT ATGFFCFENV AVHLSNLIFR TFDLFLVIHH LFAFLGFLGC LVNLQAGHYL A MTTLLLEM STPFTCVSWM LLKAGWSESL FWKLNQWLMI HMFHCRMVLT YHMWWVCFWH WDGLVSSLYL PHLTLFLVGL AL LTLIINP YWTHKKTQQL LNPVDWNFAQ PEAKSRPEGN GQLLRKKRPD AAIEGR

UniProtKB: Protein CLN8

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Macromolecule #2: COENZYME A

MacromoleculeName: COENZYME A / type: ligand / ID: 2 / Number of copies: 1 / Formula: COA
Molecular weightTheoretical: 767.534 Da
Chemical component information

ChemComp-COA:
COENZYME A

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Macromolecule #3: OLEIC ACID

MacromoleculeName: OLEIC ACID / type: ligand / ID: 3 / Number of copies: 1 / Formula: OLA
Molecular weightTheoretical: 282.461 Da
Chemical component information

ChemComp-OLA:
OLEIC ACID

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 11 / 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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 51.05 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: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Warp / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 247856
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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