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- PDB-8yzp: Tribolium castaneum ABCH-9C in complex with ceramide(d36:1) -

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Basic information

Entry
Database: PDB / ID: 8yzp
TitleTribolium castaneum ABCH-9C in complex with ceramide(d36:1)
ComponentsABC transporter G family member 23-like Protein
KeywordsTRANSPORT PROTEIN / ATP-binding cassette (ABC) transporter / ABCH
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsYang, Q. / Chen, J. / Zhou, Y.
Funding support China, 1items
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, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ABC transporter G family member 23-like Protein
B: ABC transporter G family member 23-like Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,5055
Polymers175,4352
Non-polymers2,0703
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ABC transporter G family member 23-like Protein / ABCH-9C


Mass: 87717.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: reference: XP_974932.1 / Source: (gene. exp.) Tribolium castaneum (red flour beetle) / Gene: AUGUSTUS-3.0.2_34444, TcasGA2_TC034444 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: A0A139WBS7
#2: Chemical ChemComp-A1D7S / [(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


Mass: 752.056 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C43H78NO7P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1D7T / (~{E})-~{N}-[(2~{S},3~{R})-1,3-bis(oxidanyl)octadecan-2-yl]octadec-9-enamide


Mass: 565.954 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H71NO3
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: ABCH-9C in complex with ceramide(d36:1) / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Tribolium castaneum (red flour beetle)
Source (recombinant)Organism: Homo sapiens (human) / Strain: HEK293F
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaCl1
250 mMtrishydroxymethylaminomethaneTris1
32 mMDithiothreitolDTT1
40.05 %Glyco-diosgeninGDN1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 22500 X / Nominal defocus max: 1800 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 274234 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00210409
ELECTRON MICROSCOPYf_angle_d0.40914091
ELECTRON MICROSCOPYf_dihedral_angle_d4.7391444
ELECTRON MICROSCOPYf_chiral_restr0.0381614
ELECTRON MICROSCOPYf_plane_restr0.0041760

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