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- EMDB-61821: Tribolium castaneum ABCH-9C in complex with NBD-ceramide(d36:1) -

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Basic information

Entry
Database: EMDB / ID: EMD-61821
TitleTribolium castaneum ABCH-9C in complex with NBD-ceramide(d36:1)
Map data
Sample
  • Complex: ABCH-9C in complex with NBD-ceramide(d36:1)
    • Protein or peptide: ABC transporter G family member 23-like Protein
  • Ligand: ~{N}-[(~{E},2~{S},3~{R})-18-[(4-nitro-2,1,3-benzoxadiazol-7-yl)amino]-1,3-bis(oxidanyl)octadec-4-en-2-yl]octadecanamide
  • 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
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: 3.02 Å
AuthorsChen J / Duan Y / Zhou Y / Yang Q
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 / Duan Y / Zhou Y / Yang Q
History
DepositionOct 7, 2024-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61821.png

Downloads & links

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Map

FileDownload / File: emd_61821.map.gz / Format: CCP4 / Size: 103 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 300 pix.
= 322.2 Å		1.07 Å/pix.
x 300 pix.
= 322.2 Å		1.07 Å/pix.
x 300 pix.
= 322.2 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: 0.33
Minimum - Maximum-1.5389044 - 2.2561672
Average (Standard dev.)-0.00055454334 (±0.045055386)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 322.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61821_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_61821_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 NBD-ceramide(d36:1)

EntireName: ABCH-9C in complex with NBD-ceramide(d36:1)
Components
  • Complex: ABCH-9C in complex with NBD-ceramide(d36:1)
    • Protein or peptide: ABC transporter G family member 23-like Protein
  • Ligand: ~{N}-[(~{E},2~{S},3~{R})-18-[(4-nitro-2,1,3-benzoxadiazol-7-yl)amino]-1,3-bis(oxidanyl)octadec-4-en-2-yl]octadecanamide
  • 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

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

SupramoleculeName: ABCH-9C in complex with NBD-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: 87.774414 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 G

UniProtKB: ABC transporter G family member 23-like Protein

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Macromolecule #2: ~{N}-[(~{E},2~{S},3~{R})-18-[(4-nitro-2,1,3-benzoxadiazol-7-yl)am...

MacromoleculeName: ~{N}-[(~{E},2~{S},3~{R})-18-[(4-nitro-2,1,3-benzoxadiazol-7-yl)amino]-1,3-bis(oxidanyl)octadec-4-en-2-yl]octadecanamide
type: ligand / ID: 2 / Number of copies: 1 / Formula: A1EC8
Molecular weightTheoretical: 744.059 Da

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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

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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
1.0 mMDTTDithiothreitol
0.05 %GDNGlyco-diosgenin
GridModel: Quantifoil / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS 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 opticsCalibrated magnification: 22500 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 241308
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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