8HTC: NAD--protein-threonine ADP-ribosyltransferase

Name: PDB 8HTC: Crystal structure of a SeMet-labeled effector from Chromobacterium violaceum in complex with Ubiquitin
Published: 2023-11-22
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Crystal structure of a SeMet-labeled effector from Chromobacterium violaceum in complex with Ubiquitin. Determined by X-ray diffraction at 2.2 Å resolution. Released 22 Nov 2023.

Method: X-ray diffraction
Resolution: 2.2 Å
Organisms: Chromobacterium violaceum ATCC 12472, Homo sapiens
Chains: 2
Atoms: 2,416
Mol. weight: 35.4 kDa
Released: 22 Nov 2023

Explore 8HTC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8HTC contains 16 α-helices and 21 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 12 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	46-57	12
β-strand	62-67	6	1
α-helix	70-73	4
α-helix	74-78	5
α-helix	79-86	8
β-strand	96-98	3	2
β-strand	99-101	3	1
β-strand	107	1	3
β-strand	117-121	5	1
β-strand	126-131	6	2
β-strand	157	1	4
α-helix	159-166	8
α-helix	169-173	5
α-helix	181-187	7
α-helix	191-193	3
β-strand	194	1	4
β-strand	196	1	2
α-helix	199-212	14
β-strand	216	1	3
α-helix	217-219	3
β-strand	220-224	5	2
α-helix	227-229	3
β-strand	230-234	5	1
α-helix	240-254	15
β-strand	262-266	5	1
β-strand	269-273	5	1

Chain B: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	5
β-strand	12-17	6	5
β-strand	22	1	6
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-44	4	5
β-strand	49	1	5
α-helix	50-51	2
β-strand	55	1	6
α-helix	57-59	3
β-strand	66-71	6	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NAD(+)--protein-threonine ADP-ribosyltransferase	A	protein	233	Chromobacterium violaceum ATCC 12472	Q7NY09 (AlphaFold model)
Ubiquitin-40S ribosomal protein S27a (Fragment)	B	protein	81	Homo sapiens	P62979 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8HTC_1 NAD(+)--protein-threonine ADP-ribosyltransferase (chains A)
SNRQEKLAQLMRQFESGGLYLRTVSDHRDEFENTFMPKLDACLGHGCDERYWSSATFIQQ
GLNGKVHDPHADRTGLIISADARLGGFSTFDAATANVPSGLEPSQYFPGQFPKFDMMGAY
QATWNEDIFSVDATAVSEQQMDELGIPDEYRSVFDFDRIQEKMAQPRLAGREVEPTEAKI
CYQPKDVLGIYVDVDSPASQSKARELQQAMREQGFDLPFIAYRGGAAQELASV

Sequence of entity 2 (B), FASTA

>8HTC_2 Ubiquitin-40S ribosomal protein S27a (Fragment) (chains B)
GPLGSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRT
LSDYNIQKESTLHLVLRLRGG

Primary citation

Molecular basis of threonine ADP-ribosylation of ubiquitin by bacterial ARTs. Tan, J., Xu, Y., Wang, X. et al. Nat Chem Biol (2024) 20:463-472. DOI 10.1038/s41589-023-01475-3 · PubMed

Other PDB entries of the same protein (UniProt Q7NY09 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8HTD 1.85 Å, Crystal structure of an effector from Chromobacterium violaceum in complex with ubiquitin
8UX2 1.87 Å, Chromobacterium violaceum mono-ADP-ribosyltransferase CteC in complex with NAD+
8HTF 2.15 Å, Crystal structure of an effector in complex with ubiquitin
8HTE 2.31 Å, Crystal structure of an effector mutant in complex with ubiquitin

Browse structure collections

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