[English] 日本語
Yorodumi
- EMDB-56021: Structure of human CLN8 in the presence of docosahexaenoate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-56021
TitleStructure of human CLN8 in the presence of docosahexaenoate
Map data
Sample
  • Complex: CLN8 dimer
    • Protein or peptide: Protein CLN8
  • Ligand: DOCOSA-4,7,10,13,16,19-HEXAENOIC ACID
  • Ligand: COENZYME A
  • 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: 2.73 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

-
Structure visualization

Supplemental images

emd_56021.png

Downloads & links

-
Map

FileDownload / File: emd_56021.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: 0.255
Minimum - Maximum-0.90456927 - 1.7318975
Average (Standard dev.)0.00040466766 (±0.023324896)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Mask #1

Fileemd_56021_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_56021_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_56021_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : CLN8 dimer

EntireName: CLN8 dimer
Components
  • Complex: CLN8 dimer
    • Protein or peptide: Protein CLN8
  • Ligand: DOCOSA-4,7,10,13,16,19-HEXAENOIC ACID
  • Ligand: COENZYME A
  • Ligand: water

-
Supramolecule #1: CLN8 dimer

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

-
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

-
Macromolecule #2: DOCOSA-4,7,10,13,16,19-HEXAENOIC ACID

MacromoleculeName: DOCOSA-4,7,10,13,16,19-HEXAENOIC ACID / type: ligand / ID: 2 / Number of copies: 1 / Formula: HXA
Molecular weightTheoretical: 328.488 Da
Chemical component information

ChemComp-HXA:
DOCOSA-4,7,10,13,16,19-HEXAENOIC ACID

-
Macromolecule #3: COENZYME A

MacromoleculeName: COENZYME A / type: ligand / ID: 3 / Number of copies: 1 / Formula: COA
Molecular weightTheoretical: 767.534 Da
Chemical component information

ChemComp-COA:
COENZYME A

-
Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 16 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 50.25 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

+
Image processing

CTF correctionSoftware - Name: Warp / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 360847
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more