7V8G: HOIP RING1 domain

Name: PDB 7V8G: Crystal structure of HOIP RING1 domain bound to IpaH1.4 LRR domain
Published: 2022-03-30
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Crystal structure of HOIP RING1 domain bound to IpaH1.4 LRR domain. Determined by X-ray diffraction at 2.75 Å resolution. Released 30 Mar 2022.

Method: X-ray diffraction
Resolution: 2.75 Å
Organisms: Shigella flexneri serotype 5a (strain M90T), Homo sapiens
Chains: 4
Atoms: 4,800
Mol. weight: 77.52 kDa
Ligands: ZN
Released: 30 Mar 2022

Explore 7V8G in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7V8G contains 31 α-helices and 26 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: 11 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	39-50	12
α-helix	58-70	13
β-strand	75-77	3	1
α-helix	89-90	2
β-strand	95-97	3	1
α-helix	108-110	3
β-strand	115-117	3	1
α-helix	128-130	3
β-strand	135-137	3	1
α-helix	148-150	3
β-strand	155-157	3	1
α-helix	167-170	4
β-strand	175-177	3	1
α-helix	187-190	4
β-strand	195-197	3	1
α-helix	207-210	4
β-strand	215-217	3	1
α-helix	228-232	5
β-strand	238-240	3	1
α-helix	248-258	11
β-strand	267-269	3	1

Chain B: 11 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	41-50	10
α-helix	58-71	14
β-strand	75-77	3	2
α-helix	88-90	3
β-strand	95-97	3	2
α-helix	108-110	3
β-strand	115-117	3	2
α-helix	128-130	3
β-strand	135-137	3	2
α-helix	148-150	3
β-strand	155-157	3	2
α-helix	167-170	4
β-strand	175-177	3	2
α-helix	187-190	4
β-strand	195-197	3	2
α-helix	207-210	4
β-strand	215-217	3	2
α-helix	228-232	5
β-strand	238-240	3	2
α-helix	248-258	11
β-strand	267-269	3	2

Chain C: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	696-698	3	4
β-strand	705-707	3	4
α-helix	708-710	3
β-strand	712-713	2	5
β-strand	720-721	2	5
α-helix	723-736	14
α-helix	739-741	3
α-helix	755-772	18
α-helix	775-786	12

Chain D: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	712-713	2	3
β-strand	720-721	2	3
α-helix	723-736	14
α-helix	739-741	3
α-helix	758-772	15
α-helix	775-785	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RING-type E3 ubiquitin transferase	A, B	protein	240	Shigella flexneri serotype 5a (strain M90T)	A0A0H2USG1 (AlphaFold model)
E3 ubiquitin-protein ligase RNF31	C, D	protein	103	Homo sapiens	Q96EP0 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7V8G_1 RING-type E3 ubiquitin transferase (chains A, B)
GPGSNEFYLKTWSEWEKNGTPGEQRNIAFNRLKICLQNQEAELNLSELDLKTLPDLPPQI
TTLEIRKNLLTHLPDLPPMLKVIHAQFNQLESLPALPETLEELNAGDNKIKELPFLPENL
THLRVHNNRLHILPLLPPELKLLVVSGNRLDSIPPFPDKLEGLALANNFIEQLPELPFSM
NRAVLMNNNLTTLPESVLRLAQNAFVNVAGNPLSGHTMRTLQQITTGPDYSGPRIFFSMG

Sequence of entity 2 (C, D), FASTA

>7V8G_2 E3 ubiquitin-protein ligase RNF31 (chains C, D)
GPGSEFQECAVCGWALPHNRMQALTSCECTICPDCFRQHFTIALKEKHITDMVCPACGRP
DLTDDTQLLSYFSTLDIQLRESLEPDAYALFHKKLTEGVLMRD

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

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 A0A0H2USG1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7YA7 1.4 Å, The crystal structure of IpaH1.4 LRR domain
7V8E 1.9 Å, Crystal structure of IpaH1.4 LRR domain bound to HOIL-1L UBL domain.
7V8H 2.46 Å, Crystal structure of LRR domain from Shigella flexneri IpaH1.4
9G08 3.3 Å, Structure of human RNF213 bound to the secreted effector IpaH1.4 from Shigella flexneri
9JWG 3.47 Å, Cryo-EM Focused Refined Map of Human RNF213 E3 module and IpaH1.4 LRR domain

Browse structure collections

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