8Z00 | pdb_00008z00

Tribolium castaneum ABCH-9C in complex with LMNG and ceramide(d36:1)

PDB DOI: https://doi.org/10.2210/pdb8Z00/pdb
EM Map EMD-39698: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Tribolium castaneum
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-04-08 Released: 2025-04-16
Deposition Author(s): Yang, Q., Chen, J., Zhou, Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.76 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8Z00

This is version 1.0 of the entry. See complete history.

Literature

Structural basis of ceramide transportation and its regulation by ABCH transporter

Chen, J., Zhou, Y., Yang, Q.

To be published.

Macromolecule Content

Total Structure Weight: 179.52 kDa
Atom Count: 10,350
Modeled Residue Count: 1,284
Deposited Residue Count: 1,582
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC transporter G family member 23-like Protein	A, B	791	Tribolium castaneum	Mutation(s): 0 Gene Names: AUGUSTUS-3.0.2_34444, TcasGA2_TC034444
UniProt
Find proteins for A0A139WBS7 (Tribolium castaneum) Explore A0A139WBS7 Go to UniProtKB: A0A139WBS7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A139WBS7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AV0 (Subject of Investigation/LOI) Query on AV0 Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	Lauryl Maltose Neopentyl Glycol C₄₇ H₈₈ O₂₂ MADJBYLAYPCCOO-VWHTXWAPSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
A1D7S (Subject of Investigation/LOI) Query on A1D7S Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	[(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 C₄₃ H₇₈ N O₇ P BCVRSQNGADAZKS-GZACMAKJSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
A1D7T Query on A1D7T Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	(~{E})-~{N}-[(2~{S},3~{R})-1,3-bis(oxidanyl)octadecan-2-yl]octadec-9-enamide C₃₆ H₇₁ N O₃ MJQIARGPQMNBGT-CJDDIQBSSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.76 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-04-16

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32161133010

Revision History (Full details and data files)

Version 1.0: 2025-04-16
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.