[English] 日本語
Yorodumi
- EMDB-39699: Tribolium castaneum ABCH-9C(E224Q) mutant in complex with LMNG an... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-39699
TitleTribolium castaneum ABCH-9C(E224Q) mutant in complex with LMNG and ceramide(d36:1)
Map data
Sample
  • Complex: ABCH-9C(E224Q) mutant in complex with LMNG and ceramide(d36:1)
    • Protein or peptide: ABC transporter G family member 23-like Protein
  • Ligand: Lauryl Maltose Neopentyl Glycol
  • Ligand: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-[(5~{Z},8~{Z},11~{E},14~{E},17~{Z})-icosa-5,8,11,14,17-pentaenoxy]propan-2-yl] octadecanoate
  • Ligand: (~{E})-~{N}-[(2~{S},3~{R})-1,3-bis(oxidanyl)octadecan-2-yl]octadec-9-enamide
KeywordsATP-binding cassette (ABC) transporter / ABCH / TRANSPORT PROTEIN
Function / homology
Function and homology information


ABC-type transporter activity / ATP-binding cassette (ABC) transporter complex / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
ABC-2 transporter / : / ABC transporter integral membrane type-2 domain profile. / ABC-2 family transporter protein / ABC-2 type transporter / 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. ...ABC-2 transporter / : / ABC transporter integral membrane type-2 domain profile. / ABC-2 family transporter protein / ABC-2 type transporter / 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
ABC transporter G family member 23-like Protein
Similarity search - Component
Biological speciesTribolium castaneum (red flour beetle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsYang Q / Chen J / Zhou Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32161133010 China
CitationJournal: To Be Published
Title: Structural basis of ceramide transportation and its regulation by ABCH transporter
Authors: Chen J / Zhou Y / Yang Q
History
DepositionApr 8, 2024-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_39699.png

Downloads & links

-
Map

FileDownload / File: emd_39699.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.)
1.07 Å/pix.
x 360 pix.
= 386.64 Å		1.07 Å/pix.
x 360 pix.
= 386.64 Å		1.07 Å/pix.
x 360 pix.
= 386.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.074 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.32
Minimum - Maximum-1.9426341 - 2.593552
Average (Standard dev.)-0.00017757861 (±0.036177292)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 386.64 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_39699_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_39699_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : ABCH-9C(E224Q) mutant in complex with LMNG and ceramide(d36:1)

EntireName: ABCH-9C(E224Q) mutant in complex with LMNG and ceramide(d36:1)
Components
  • Complex: ABCH-9C(E224Q) mutant in complex with LMNG and ceramide(d36:1)
    • Protein or peptide: ABC transporter G family member 23-like Protein
  • Ligand: Lauryl Maltose Neopentyl Glycol
  • Ligand: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-[(5~{Z},8~{Z},11~{E},14~{E},17~{Z})-icosa-5,8,11,14,17-pentaenoxy]propan-2-yl] octadecanoate
  • Ligand: (~{E})-~{N}-[(2~{S},3~{R})-1,3-bis(oxidanyl)octadecan-2-yl]octadec-9-enamide

-
Supramolecule #1: ABCH-9C(E224Q) mutant in complex with LMNG and ceramide(d36:1)

SupramoleculeName: ABCH-9C(E224Q) mutant in complex with LMNG and ceramide(d36:1)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Tribolium castaneum (red flour beetle)

-
Macromolecule #1: ABC transporter G family member 23-like Protein

MacromoleculeName: ABC transporter G family member 23-like Protein / type: protein_or_peptide / ID: 1 / Details: Sequence reference NCBI XP_974932.1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Tribolium castaneum (red flour beetle)
Molecular weightTheoretical: 87.716375 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGEDDKLKRM FSWSSNALSE GSAMGERVEP VVPGPDLVGV NVERPPAPLV HQQSTVWSKR QHAVCVRHAF KQYGSKKNPN HVLSDLNMT VAKGTIYGLL GASGCGKTTL LSCIVGRRRL NTGEIWVLGG KPGTKGSGVP GKRVGYMPQE IALYGEFSIK E TMMYFGWI ...String:
MGEDDKLKRM FSWSSNALSE GSAMGERVEP VVPGPDLVGV NVERPPAPLV HQQSTVWSKR QHAVCVRHAF KQYGSKKNPN HVLSDLNMT VAKGTIYGLL GASGCGKTTL LSCIVGRRRL NTGEIWVLGG KPGTKGSGVP GKRVGYMPQE IALYGEFSIK E TMMYFGWI FGMESSEINE RLQFLLNFLD LPSQNRLVKN LSGGQQRRVS FAVALMHDPE LLILDQPTVG VDPLLRQSIW NH LVQITKD GNKTVIITTH YIEEARQAHT IGLMRSGKLL AEESPHVLLS MYGCQSLEEV FLKLSRKQGQ ANQNDINISN NIS LATLNW GKKDSISVTE ESGVVGLNFH QSKEILIADS TNGHIDLNGL GKPSSSKSSM ADACDDCSCS DMTSWGKIKA LLQK NFLRM WRNVGVMLFI FALPVMQVIL FCLAIGRDPT GLKLAIVNHE KNYTNQSYQE CSFDYGCKFS YLSCRYLNNL RNSTI LKEY YPDPESAVDA VKQGHAWGAL YFTENFTDAL VARMALGKDA DPETLDQSEV RVWLDMSNQQ IGIILQRDLQ LSYQDF AKD LLGACEQNPD LAEIPISFKE PIYGSNKPSF TDFVAPGVIL TIVFFLAVAL TSSALIIERM EGLLDRSWVA GVTPGEI LF SHVVTQFVVM CGQTALVLIF MILVFGVQCK GDIGWVIVLT ILQGLCGMCF GFVISAICEL ERNAIQLALG SFYPTLLL S GVIWPIEGMP TVLRYVSTFL PLTLATTSLR AMLTRGWSIA EPAVYYGFLA TIIWIVAFLT ISMLVLRFKR

UniProtKB: ABC transporter G family member 23-like Protein

-
Macromolecule #2: Lauryl Maltose Neopentyl Glycol

MacromoleculeName: Lauryl Maltose Neopentyl Glycol / type: ligand / ID: 2 / Number of copies: 2 / Formula: AV0
Molecular weightTheoretical: 1.005188 KDa
Chemical component information

ChemComp-AV0:
Lauryl Maltose Neopentyl Glycol

-
Macromolecule #3: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-[(5~{Z},8~{Z...

MacromoleculeName: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-[(5~{Z},8~{Z},11~{E},14~{E},17~{Z})-icosa-5,8,11,14,17-pentaenoxy]propan-2-yl] octadecanoate
type: ligand / ID: 3 / Number of copies: 2 / Formula: A1D7S
Molecular weightTheoretical: 752.056 Da

-
Macromolecule #4: (~{E})-~{N}-[(2~{S},3~{R})-1,3-bis(oxidanyl)octadecan-2-yl]octade...

MacromoleculeName: (~{E})-~{N}-[(2~{S},3~{R})-1,3-bis(oxidanyl)octadecan-2-yl]octadec-9-enamide
type: ligand / ID: 4 / Number of copies: 1 / Formula: A1D7T
Molecular weightTheoretical: 565.954 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMTristrishydroxymethylaminomethane
150.0 mMNaClsodium chloride
2.0 mMDTTdithiothreitol
0.05 %GDNGlyco-diosgenin
GridModel: Quantifoil / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 479663
Initial angle assignmentType: MAXIMUM LIKELIHOOD
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