[English] 日本語
Yorodumi
- EMDB-65676: Cryo-EM structure of CHS bound state human ABCD3 in inward-facing... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-65676
TitleCryo-EM structure of CHS bound state human ABCD3 in inward-facing conformation
Map data
Sample
  • Complex: CHS bound ABCD3
    • Protein or peptide: ATP-binding cassette sub-family D member 3,Green fluorescent protein
  • Ligand: CHOLESTEROL HEMISUCCINATE
KeywordsABC transporter / TRANSPORT PROTEIN
Function / homology
Function and homology information


phytanic acid metabolic process / long-chain fatty acid import into peroxisome / very long-chain fatty acid catabolic process / very long-chain fatty acid metabolic process / Class I peroxisomal membrane protein import / peroxisome organization / fatty acyl-CoA hydrolase activity / ABC transporters in lipid homeostasis / bile acid biosynthetic process / Hydrolases; Acting on ester bonds; Thioester hydrolases ...phytanic acid metabolic process / long-chain fatty acid import into peroxisome / very long-chain fatty acid catabolic process / very long-chain fatty acid metabolic process / Class I peroxisomal membrane protein import / peroxisome organization / fatty acyl-CoA hydrolase activity / ABC transporters in lipid homeostasis / bile acid biosynthetic process / Hydrolases; Acting on ester bonds; Thioester hydrolases / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / peroxisomal membrane / long-chain fatty acid transmembrane transporter activity / bile acid and bile salt transport / fatty acid beta-oxidation / RHOC GTPase cycle / peroxisomal matrix / ATPase-coupled transmembrane transporter activity / RHOA GTPase cycle / ABC-type transporter activity / bioluminescence / generation of precursor metabolites and energy / fatty acid biosynthetic process / peroxisome / response to xenobiotic stimulus / protein homodimerization activity / ATP hydrolysis activity / mitochondrion / ATP binding / membrane / cytosol
Similarity search - Function
Peroxysomal long chain fatty acyl transporter / ABC transporter transmembrane region 2 / : / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein ...Peroxysomal long chain fatty acyl transporter / ABC transporter transmembrane region 2 / : / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP-binding cassette sub-family D member 3 / Green fluorescent protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.81 Å
AuthorsAiba S / Okamoto HH / Kusakizako T / Nureki O
Funding support Japan, 3 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP16H06294 Japan
Japan Society for the Promotion of Science (JSPS)JP20K15754 Japan
Japan Society for the Promotion of Science (JSPS)JP25KJ1114 Japan
CitationJournal: To Be Published
Title: Structural Insights into the Broad Substrate Recognition Mechanism of Human ABCD3
Authors: Aiba S / Okamoto HH / Tomita A / Sano F / Kusakizako T / Nureki O
History
DepositionAug 3, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_65676.png

Downloads & links

-
Map

FileDownload / File: emd_65676.map.gz / Format: CCP4 / Size: 10.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 144 pix.
= 159.36 Å		1.11 Å/pix.
x 144 pix.
= 159.36 Å		1.11 Å/pix.
x 138 pix.
= 152.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.10667 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.2
Minimum - Maximum-8.965626 - 12.357991
Average (Standard dev.)0.00074713916 (±0.57764715)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin788191
Dimensions144138144
Spacing138144144
CellA: 152.72046 Å / B: 159.36049 Å / C: 159.36049 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_65676_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_65676_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_65676_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : CHS bound ABCD3

EntireName: CHS bound ABCD3
Components
  • Complex: CHS bound ABCD3
    • Protein or peptide: ATP-binding cassette sub-family D member 3,Green fluorescent protein
  • Ligand: CHOLESTEROL HEMISUCCINATE

-
Supramolecule #1: CHS bound ABCD3

SupramoleculeName: CHS bound ABCD3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: ATP-binding cassette sub-family D member 3,Green fluorescent protein

MacromoleculeName: ATP-binding cassette sub-family D member 3,Green fluorescent protein
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on ester bonds; Thioester hydrolases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 104.527633 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAAFSKYLTA RNSSLAGAAF LLLCLLHKRR RALGLHGKKS GKPPLQNNEK EGKKERAVVD KVFFSRLIQI LKIMVPRTFC KETGYLVLI AVMLVSRTYC DVWMIQNGTL IESGIIGRSR KDFKRYLLNF IAAMPLISLV NNFLKYGLNE LKLCFRVRLT K YLYEEYLQ ...String:
MAAFSKYLTA RNSSLAGAAF LLLCLLHKRR RALGLHGKKS GKPPLQNNEK EGKKERAVVD KVFFSRLIQI LKIMVPRTFC KETGYLVLI AVMLVSRTYC DVWMIQNGTL IESGIIGRSR KDFKRYLLNF IAAMPLISLV NNFLKYGLNE LKLCFRVRLT K YLYEEYLQ AFTYYKMGNL DNRIANPDQL LTQDVEKFCN SVVDLYSNLS KPFLDIVLYI FKLTSAIGAQ GPASMMAYLV VS GLFLTRL RRPIGKMTIT EQKYEGEYRY VNSRLITNSE EIAFYNGNKR EKQTVHSVFR KLVEHLHNFI LFRFSMGFID SII AKYLAT VVGYLVVSRP FLDLSHPRHL KSTHSELLED YYQSGRMLLR MSQALGRIVL AGREMTRLAG FTARITELMQ VLKD LNHGK YERTMVSQQE KGIEGVQVIP LIPGAGEIII ADNIIKFDHV PLATPNGDVL IRDLNFEVRS GANVLICGPN GCGKS SLFR VLGELWPLFG GRLTKPERGK LFYVPQRPYM TLGTLRDQVI YPDGREDQKR KGISDLVLKE YLDNVQLGHI LEREGG WDS VQDWMDVLSG GEKQRMAMAR LFYHKPQFAI LDECTSAVSV DVEGYIYSHC RKVGITLFTV SHRKSLWKHH EYYLHMD GR GNYEFKQITE DTVEFGSLEV LFQGPAVSKG EELFTGVVPI LVELDGDVNG HKFSVSGEGE GDATYGKLTL KFICTTGK L PVPWPTLVTT LTYGVQCFSR YPDHMKQHDF FKSAMPEGYV QERTIFFKDD GNYKTRAEVK FEGDTLVNRI ELKGIDFKE DGNILGHKLE YNYNSHNVYI MADKQKNGIK VNFKIRHNIE DGSVQLADHY QQNTPIGDGP VLLPDNHYLS TQSKLSKDPN EKRDHMVLL EFVTAAGITL GMDELYKHHH HHHHH

UniProtKB: ATP-binding cassette sub-family D member 3, Green fluorescent protein

-
Macromolecule #2: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMTris-HClTris(hydroxymethyl)aminomethane hydrochloride
150.0 mMNaClSodium chloride
0.3 g/LGDNGlyco-diosgenin
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.81 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 44696
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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