8QZ7

Structure of human ceramide synthase 6 (CerS6) in complex with N-palmitoyl fumonisin B1

PDB DOI: https://doi.org/10.2210/pdb8QZ7/pdb
EM Map EMD-18771: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens, Vicugna pacos
Expression System: Homo sapiens, Escherichia coli
Mutation(s): No

Deposited: 2023-10-26 Released: 2024-11-13
Deposition Author(s): Pascoa, T.C., Pike, A.C.W., Chi, G., Stefanic, S., Quigley, A., Chalk, R., Mukhopadhyay, S.M.M., Venkaya, S., Dix, C., Moreira, T., Tessitore, A., Cole, V., Chu, A., Elkins, J.M., Pautsch, A., Schnapp, G., Carpenter, E.P., Sauer, D.B.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

Structural basis of the mechanism and inhibition of a human ceramide synthase

Pascoa, T.C., Pike, A.C.W., Tautermann, C., Chi, G., Traub, M., Quigley, A., Chalk, R., Stefanic, S., Thamm, S., Pautsch, A., Carpenter, E.P., Schnapp, G., Sauer, D.B.

(2024) Nature Structural & Molecular Biology

DOI: https://doi.org/10.1038/s41594-024-01414-3

Macromolecule Content

Total Structure Weight: 118.92 kDa
Atom Count: 7,366
Modelled Residue Count: 914
Deposited Residue Count: 986
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of Ceramide synthase 6	A, D [auth C]	357	Homo sapiens	Mutation(s): 0 Gene Names: CERS6, LASS6 EC: 2.3.1.291
UniProt & NIH Common Fund Data Resources
Find proteins for Q6ZMG9 (Homo sapiens) Go to UniProtKB: Q6ZMG9
PHAROS: Q6ZMG9 GTEx: ENSG00000172292
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6ZMG9-2
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain D [auth C]	Go to GlyGen: Q6ZMG9-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody-22	B, C [auth D]	136	Vicugna pacos	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XBX (Subject of Investigation/LOI) Query on XBX Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth C] MOL2 format, chain E [auth A] MOL2 format, chain H [auth C] mmCIF format, chain E [auth A] mmCIF format, chain H [auth C]	E [auth A], H [auth C]	(2~{R})-2-[2-[(5~{R},6~{R},7~{S},9~{S},11~{R},16~{R},18~{S},19~{S})-6-[(3~{R})-3-carboxy-5-oxidanyl-5-oxidanylidene-pentanoyl]oxy-19-(hexadecanoylamino)-5,9-dimethyl-11,16,18-tris(oxidanyl)icosan-7-yl]oxy-2-oxidanylidene-ethyl]butanedioic acid C₅₀ H₈₉ N O₁₆ JETFIMCRGHHXJM-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth C] Interactions & Density Focus chain E [auth A] Focus chain H [auth C]
PC1 Query on PC1 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth C] MOL2 format, chain F [auth A] MOL2 format, chain I [auth C] mmCIF format, chain F [auth A] mmCIF format, chain I [auth C]	F [auth A], I [auth C]	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₈ N O₈ P NRJAVPSFFCBXDT-HUESYALOSA-N		Interactions Focus chain F [auth A] Focus chain I [auth C] Interactions & Density Focus chain F [auth A] Focus chain I [auth C]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth C] MOL2 format, chain G [auth A] MOL2 format, chain J [auth C] mmCIF format, chain G [auth A] mmCIF format, chain J [auth C]	G [auth A], J [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth A] Focus chain J [auth C] Interactions & Density Focus chain G [auth A] Focus chain J [auth C]