[English] 日本語
Yorodumi
- EMDB-68536: Cryo-EM structure of CeTECR-CeHACD complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-68536
TitleCryo-EM structure of CeTECR-CeHACD complex
Map datafull map
Sample
  • Complex: Nematode TECR-HACD complex
    • Protein or peptide: Probable very-long-chain enoyl-CoA reductase art-1
    • Protein or peptide: Very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase hpo-8
  • Ligand: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Keywordsvery long chain fatty acids / TECR / HACD / MEMBRANE PROTEIN
Function / homology
Function and homology information


very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase / very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase activity / Synthesis of very long-chain fatty acyl-CoAs / very-long-chain enoyl-CoA reductase / very-long-chain enoyl-CoA reductase activity / very long-chain fatty acid biosynthetic process / 3-hydroxyacyl-CoA dehydratase activity / sphingolipid metabolic process / sphingolipid biosynthetic process / fatty acid elongation ...very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase / very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase activity / Synthesis of very long-chain fatty acyl-CoAs / very-long-chain enoyl-CoA reductase / very-long-chain enoyl-CoA reductase activity / very long-chain fatty acid biosynthetic process / 3-hydroxyacyl-CoA dehydratase activity / sphingolipid metabolic process / sphingolipid biosynthetic process / fatty acid elongation / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
Protein-tyrosine phosphatase-like, PTPLA / Protein tyrosine phosphatase-like protein, PTPLA / : / TECR, ubiquitin-like domain / 3-oxo-5-alpha-steroid 4-dehydrogenase, C-terminal / 3-oxo-5-alpha-steroid 4-dehydrogenase/very-long-chain enoyl-CoA reductase / 3-oxo-5-alpha-steroid 4-dehydrogenase / Steroid 5-alpha reductase C-terminal domain profile. / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase hpo-8 / Probable very-long-chain enoyl-CoA reductase art-1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsYu LY / Ren RB
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of nematode TECR and HACD complex
Authors: Yu LY / Ren RB
History
DepositionJan 18, 2026-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_68536.png

Downloads & links

-
Map

FileDownload / File: emd_68536.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfull map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 300 pix.
= 255. Å		0.85 Å/pix.
x 300 pix.
= 255. Å		0.85 Å/pix.
x 300 pix.
= 255. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.28
Minimum - Maximum-2.3266273 - 2.8145154
Average (Standard dev.)0.000103441904 (±0.048758794)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 255.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: half A map

Fileemd_68536_half_map_1.map
Annotationhalf A map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half B map

Fileemd_68536_half_map_2.map
Annotationhalf B map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Nematode TECR-HACD complex

EntireName: Nematode TECR-HACD complex
Components
  • Complex: Nematode TECR-HACD complex
    • Protein or peptide: Probable very-long-chain enoyl-CoA reductase art-1
    • Protein or peptide: Very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase hpo-8
  • Ligand: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

-
Supramolecule #1: Nematode TECR-HACD complex

SupramoleculeName: Nematode TECR-HACD complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Caenorhabditis elegans (invertebrata)

-
Macromolecule #1: Probable very-long-chain enoyl-CoA reductase art-1

MacromoleculeName: Probable very-long-chain enoyl-CoA reductase art-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: very-long-chain enoyl-CoA reductase
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 35.280988 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MMSGILEVYD AKRTDNLIIT LEGISGSETI KAIKKRIAQK KLKLTEERQA LRVEPKGKPL ADDQKLSDLG LSSQKAVLYV RDLGPQIAW KTVFMAEYAG PLFVYPLFYL RPTFIYGQAA VNATMHPAVQ IAFFAWSFHY AKRLFETQFI HRFGNSTMPQ F NLVKNCSY ...String:
MMSGILEVYD AKRTDNLIIT LEGISGSETI KAIKKRIAQK KLKLTEERQA LRVEPKGKPL ADDQKLSDLG LSSQKAVLYV RDLGPQIAW KTVFMAEYAG PLFVYPLFYL RPTFIYGQAA VNATMHPAVQ IAFFAWSFHY AKRLFETQFI HRFGNSTMPQ F NLVKNCSY YWGFAAFVAY FVNHPLFTPP AFGDLQVYFG LAGFVISEFG NLSIHILLRN LRPAGTRERR IPKPDGNPLS LL FNYVSCP NYTYEVASWI FFSIMVQSLP AIIFTTAGFA QMAIWAQGKH RNYLKEFPDY PKNRKAIVPF VL

UniProtKB: Probable very-long-chain enoyl-CoA reductase art-1

-
Macromolecule #2: Very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase hpo-8

MacromoleculeName: Very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase hpo-8
type: protein_or_peptide / ID: 2
Details: His tag: 2-11 linker:12-13 Drice cutting site:14-18 linker:19-23 Ce-HACD:24-241
Number of copies: 1 / Enantiomer: LEVO
EC number: very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 27.322193 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHHHH HSGDEVDAGS GHMMSVQTYL VAYNVLQILG WSAILVKTVL GLANGLTWPQ LYESVEFELK IFQTAAILEV IHAIVGLVR SPVGTTAMQV TSRVVLVWPI LHLCSTARFS IGVPLLLVAW SVTEVIRYSF YALSVLKQPI PYFLLYLRYT L FYVLYPMG ...String:
MHHHHHHHHH HSGDEVDAGS GHMMSVQTYL VAYNVLQILG WSAILVKTVL GLANGLTWPQ LYESVEFELK IFQTAAILEV IHAIVGLVR SPVGTTAMQV TSRVVLVWPI LHLCSTARFS IGVPLLLVAW SVTEVIRYSF YALSVLKQPI PYFLLYLRYT L FYVLYPMG VSGELLTLFA SLNEVDEKKI LTLEMPNRLN MGISFWWVLI IAALSYIPGF PQLYFYMIGQ RKKILGGGSK KK Q

UniProtKB: Very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase hpo-8

-
Macromolecule #3: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

MacromoleculeName: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
type: ligand / ID: 3 / Number of copies: 1 / Formula: NDP
Molecular weightTheoretical: 745.421 Da
Chemical component information

ChemComp-NDP:
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.76 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 131428
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-22of:
Cryo-EM structure of CeTECR-CeHACD complex

+
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