7V8F: UBE2L3

Name: PDB 7V8F: Crystal structure of UBE2L3 bound to HOIP RING1 domain.
Published: 2022-03-30
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Crystal structure of UBE2L3 bound to HOIP RING1 domain. Determined by X-ray diffraction at 1.66 Å resolution. Released 30 Mar 2022.

Method: X-ray diffraction
Resolution: 1.66 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,160
Mol. weight: 29.96 kDa
Ligands: ZN
Released: 30 Mar 2022

Explore 7V8F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7V8F contains 13 α-helices and 13 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: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	2-16	15
β-strand	22-27	6	3
β-strand	34-39	6	3
β-strand	50	1	4
β-strand	51-56	6	3
β-strand	67-70	4	3
β-strand	79	1	5
β-strand	84	1	3
β-strand	85	1	5
α-helix	88-90	3
α-helix	101-113	13
α-helix	123-131	9
α-helix	133-147	15
α-helix	148	1
β-strand	149	1	4
α-helix	150-151	2

Chain B: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	696-698	3	1
β-strand	705-707	3	1
α-helix	708-710	3
β-strand	712-713	2	2
β-strand	720-721	2	2
α-helix	723-736	14
α-helix	739-741	3
α-helix	755-757	3
α-helix	758-772	15
α-helix	775-787	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase RNF31	B	protein	103	Homo sapiens	Q96EP0 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 L3	A	protein	158	Homo sapiens	P68036 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>7V8F_1 E3 ubiquitin-protein ligase RNF31 (chains B)
GPGSEFQECAVCGWALPHNRMQALTSCECTICPDCFRQHFTIALKEKHITDMVCPACGRP
DLTDDTQLLSYFSTLDIQLRESLEPDAYALFHKKLTEGVLMRD

Sequence of entity 2 (A), FASTA

>7V8F_2 Ubiquitin-conjugating enzyme E2 L3 (chains A)
GPGSMAASRRLMKELEEIRKCGMKNFRNIQVDEANLLTWQGLIVPDNPPYDKGAFRIEIN
FPAEYPFKPPKITFKTKIYHPNIDEKGQVCLPVISAENWKPATKTDQVIQSLIALVNDPQ
PEHPLRADLAEEYSKDRKKFCKNAEEFTKKYGEKRPVD

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

Mechanistic insights into the subversion of the linear ubiquitin chain assembly complex by the E3 ligase IpaH1.4 of Shigella flexneri. Liu, J., Wang, Y., Wang, D. et al. Proc Natl Acad Sci U S A (2022) 119:e2116776119-e2116776119. DOI 10.1073/pnas.2116776119 · PubMed

Other PDB entries of the same protein (UniProt Q96EP0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6KC5 1.54 Å, HOIP-HOIPIN1 complex
4LJO 1.56 Å, Structure of an active ligase (HOIP)/ubiquitin transfer complex
4P09 1.7 Å, Crystal structure of HOIP PUB domain
9B0B 1.7 Å, Structure of Optineurin bound to HOIP NZF1 domain
9B12 1.81 Å, Structure of Optineurin bound to HOIP NZF1 domain and M1-linked diubiquitin, crystal…
4OWF 2.0 Å, Crystal structure of the NEMO CoZi in complex with HOIP NZF1 domain
4OYK 2.0 Å, Structure of HOIP PUB domain bound to OTULIN PIM
6SC5 2.1 Å, dAb3/HOIP-RBR-Ligand2
6SC8 2.11 Å, dAb3/HOIP-RBR-Ligand4
6KC6 2.12 Å, HOIP-HOIPIN8 complex
4LJP 2.15 Å, Structure of an active ligase (HOIP-H889A)/ubiquitin transfer complex
6GZY 2.15 Å, HOIP-fragment5 complex

Browse structure collections

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