8ST7: E3 ligase VsHECT

Structure of E3 ligase VsHECT bound to ubiquitin. Determined by X-ray diffraction at 1.44 Å resolution. Released 12 Jul 2023.

Method: X-ray diffraction
Resolution: 1.44 Å
Organisms: Homo sapiens, Verrucomicrobiota
Chains: 4
Atoms: 5,185
Mol. weight: 69.38 kDa
Ligands: AYE
Released: 12 Jul 2023

Explore 8ST7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8ST7 contains 31 α-helices and 28 β-strands across 4 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, 6 β-strands

Element	Residues	Length	Sheet
α-helix	630-648	19
α-helix	656-663	8
α-helix	664-666	3
β-strand	672	1	6
β-strand	689	1	6
α-helix	694-702	9
α-helix	703-705	3
β-strand	706	1	7
β-strand	720	1	7
α-helix	722-730	9
α-helix	739-756	18
α-helix	770-786	17
β-strand	788	1	8
β-strand	791	1	8
α-helix	793-804	12
α-helix	813-828	16
α-helix	832-841	10
α-helix	844-846	3

Chain B: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	3
β-strand	12-16	5	3
β-strand	22	1	4
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	3
β-strand	48-49	2	3
α-helix	50-51	2
β-strand	52	1	5
β-strand	54	1	5
β-strand	55	1	4
α-helix	57-59	3
β-strand	66-71	6	3

Chain C: 11 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	633-648	16
α-helix	656-663	8
α-helix	664-666	3
β-strand	672	1	9
β-strand	689	1	9
α-helix	694-703	10
β-strand	706	1	10
β-strand	720	1	10
α-helix	722-730	9
α-helix	739-757	19
α-helix	770-786	17
β-strand	788	1	11
β-strand	791	1	11
α-helix	793-804	12
α-helix	813-828	16
α-helix	832-841	10
α-helix	844-846	3

Chain D: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
β-strand	12-16	5	1
β-strand	22	1	2
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	1
β-strand	48-49	2	1
α-helix	50-51	2
β-strand	55	1	2
α-helix	57-59	3
β-strand	66-71	6	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin	B, D	protein	75	Homo sapiens	F5H388 (AlphaFold model)
E3 ubiquitin-protein ligase SopA-like catalytic domain-containing protein	A, C	protein	226	Verrucomicrobiota	A0A2V2RSR1 (AlphaFold model)

Sequence of entity 1 (B, D), FASTA

>8ST7_1 Ubiquitin (chains B, D)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRG

Sequence of entity 2 (A, C), FASTA

>8ST7_2 E3 ubiquitin-protein ligase SopA-like catalytic domain-containing protein (chains A, C)
HHHHHHSSGLEVLFQGPQNISNLLDQIFQHDEQGAYRTLFKEVVRKKDTNRKLTGIKETS
ASEREPYSIDETDPEKLKKIFLRLYISPPKLYISRNDRISKEHIKQILEAYGLQEAAPEE
QSYALLAISALFCKYSSSGIFGTEENSPPELRRYACSLLSEVGDMRLEGVSQNEIVDYQN
RLRGAKNAFTCTAVLFSTIQKKLQLLHKDQKNLKKIYDQIIPLVWQ

Ligands and cofactors

ID	Name	Formula	Copies
AYE	prop-2-en-1-amine	C3 H7 N	2

Primary citation

Bacterial ligases reveal fundamental principles of polyubiquitin specificity. Franklin, T.G., Brzovic, P.S., Pruneda, J.N. Mol Cell (2023) 83:4538-4554.e4. DOI 10.1016/j.molcel.2023.11.017 · PubMed

Other PDB entries of the same protein (UniProt F5H388 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4I6N 1.7 Å, Crystal structure of Trichinella spiralis UCH37 catalytic domain bound to Ubiquitin…
6W9R 1.82 Å, Crystal structure of an OTU deubiquitinase from Wolbachia pipientis wMel bound to…
8RQI 1.94 Å, Structure of Rhizobium NopD with ubiquitin
4IG7 2.0 Å, Crystal structure of Trichinella spiralis UCH37 bound to Ubiquitin vinyl methyl ester
4PQT 2.05 Å, Insights into the mechanism of deubiquitination by JAMM deubiquitinases from co-crystal…
6W9S 2.1 Å, Crystal structure of an OTU deubiquitinase from Escherichia albertii bound to ubiquitin
9FN4 2.15 Å, DUBS Parachlamydia sp. PcJOS
9FPA 2.18 Å, DUBS Parachlamydia sp. PcJOS orthorhombic crystal form
6NN6 3.9 Å, Structure of Dot1L-H2BK120ub nucleosome complex

Browse structure collections

About this viewer

MolViewer shows 8ST7 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.