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- EMDB-39697: Tribolium castaneum ABCH-9C in complex with ceramide(d36:1) -

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Basic information

Entry
Database: EMDB / ID: EMD-39697
TitleTribolium castaneum ABCH-9C in complex with ceramide(d36:1)
Map data
Sample
  • Complex: ABCH-9C in complex with ceramide(d36:1)
    • Protein or peptide: ABC transporter G family member 23-like Protein
  • 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: 3.16 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

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Structure visualization

Supplemental images

emd_39697.png

Downloads & links

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Map

FileDownload / File: emd_39697.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: 0.4
Minimum - Maximum-1.5656242 - 2.2755494
Average (Standard dev.)-0.0001872877 (±0.035497256)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Half map: #2

Fileemd_39697_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_39697_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 : ABCH-9C in complex with ceramide(d36:1)

EntireName: ABCH-9C in complex with ceramide(d36:1)
Components
  • Complex: ABCH-9C in complex with ceramide(d36:1)
    • Protein or peptide: ABC transporter G family member 23-like Protein
  • 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

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Supramolecule #1: ABCH-9C in complex with ceramide(d36:1)

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

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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: reference: XP_974932.1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Tribolium castaneum (red flour beetle)
Molecular weightTheoretical: 87.717359 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 LLILDEPTVG 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

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Macromolecule #2: [(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: 2 / Number of copies: 2 / Formula: A1D7S
Molecular weightTheoretical: 752.056 Da

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Macromolecule #3: (~{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: 3 / Number of copies: 1 / Formula: A1D7T
Molecular weightTheoretical: 565.954 Da

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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: 8
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
50.0 mMTristrishydroxymethylaminomethane
2.0 mMDTTDithiothreitol
0.05 %GDNGlyco-diosgenin
GridModel: Quantifoil / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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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: 1.8 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 22500
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 274234
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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