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- EMDB-39704: Tribolium castaneum ABCH-9C(E224Q) mutant in complex with ATP -

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Basic information

Entry
Database: EMDB / ID: EMD-39704
TitleTribolium castaneum ABCH-9C(E224Q) mutant in complex with ATP
Map data
Sample
  • Complex: ABCH-9C(E224Q) mutant in complex with ATP
    • Protein or peptide: ABC transporter G family member 23-like Protein
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
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: 3.45 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 9, 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_39704.png

Downloads & links

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Map

FileDownload / File: emd_39704.map.gz / Format: CCP4 / Size: 209.3 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 380 pix.
= 408.12 Å		1.07 Å/pix.
x 380 pix.
= 408.12 Å		1.07 Å/pix.
x 380 pix.
= 408.12 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: 0.3
Minimum - Maximum-1.1164058 - 1.8036004
Average (Standard dev.)0.0000009832529 (±0.0254433)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 408.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39704_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_39704_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(E224Q) mutant in complex with ATP

EntireName: ABCH-9C(E224Q) mutant in complex with ATP
Components
  • Complex: ABCH-9C(E224Q) mutant in complex with ATP
    • Protein or peptide: ABC transporter G family member 23-like Protein
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: ABCH-9C(E224Q) mutant in complex with ATP

SupramoleculeName: ABCH-9C(E224Q) mutant in complex with ATP / 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: 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

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 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
50.0 mMC4H11NO3trishydroxymethylaminomethane
150.0 mMNaClsodium chloride
2.0 mMC4H10O2S2dithiothreitol
0.05 %C4H10O2S2Glyco-diosgenin
2.0 mMMgMagnesium ion
5.0 mMC10H16N5O13P3Adenosinetriphosphate
GridModel: Quantifoil / Support film - Material: CARBON / Support film - topology: HOLEY
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: 2.0 µm / Nominal defocus min: 1.0 µm
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: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 242140
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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