7YA7: IpaH1.4 LRR domain

Name: PDB 7YA7: The crystal structure of IpaH1.4 LRR domain
Published: 2023-02-08
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

The crystal structure of IpaH1.4 LRR domain. Determined by X-ray diffraction at 1.4 Å resolution. Released 8 Feb 2023.

Method: X-ray diffraction
Resolution: 1.4 Å
Organism: Shigella flexneri 5a
Chains: 2
Atoms: 4,150
Mol. weight: 54.64 kDa
Released: 8 Feb 2023

Explore 7YA7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7YA7 contains 22 α-helices and 20 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: 11 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	45-56	12
α-helix	65-77	13
β-strand	82-84	3	1
α-helix	96-97	2
β-strand	102-104	3	1
α-helix	114-117	4
β-strand	122-124	3	1
α-helix	134-137	4
β-strand	142-144	3	1
α-helix	153-157	5
β-strand	162-164	3	1
α-helix	174-177	4
β-strand	182-184	3	1
α-helix	194-197	4
β-strand	202-204	3	1
α-helix	213-217	5
β-strand	222-224	3	1
α-helix	235-239	5
β-strand	245-247	3	1
α-helix	255-265	11
β-strand	274-276	3	1

Chain B: 11 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	48-57	10
α-helix	65-78	14
β-strand	82-84	3	2
α-helix	95-97	3
β-strand	102-104	3	2
α-helix	115-117	3
β-strand	122-124	3	2
α-helix	135-137	3
β-strand	142-144	3	2
α-helix	153-157	5
β-strand	162-164	3	2
α-helix	174-177	4
β-strand	182-184	3	2
α-helix	195-197	3
β-strand	202-204	3	2
α-helix	213-217	5
β-strand	222-224	3	2
α-helix	235-239	5
β-strand	245-247	3	2
α-helix	255-259	5
β-strand	274-275	2	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RING-type E3 ubiquitin transferase	A, B	protein	243	Shigella flexneri 5a	A0A0H2USG1 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7YA7_1 RING-type E3 ubiquitin transferase (chains A, B)
GPLGSCNEFYLKTWSEWEKNGTPGEQRNIAFNRLKICLQNQEAELNLSELDLKTLPDLPP
QITTLEIRKNLLTHLPDLPPMLKVIHAQFNQLESLPALPETLEELNAGDNKIKELPFLPE
NLTHLRVHNNRLHILPLLPPELKLLVVSGNRLDSIPPFPDKLEGLALANNFIEQLPELPF
SMNRAVLMNNNLTTLPESVLRLAQNAFVNVAGNPLSGHTMRTLQQITTGPDYSGPRIFFS
MGN

Primary citation

Structural insight into the recognition of the linear ubiquitin assembly complex by Shigella E3 ligase IpaH1.4/2.5. Hiragi, K., Nishide, A., Takagi, K. et al. J Biochem (2023) 173:317-326. DOI 10.1093/jb/mvac109 · PubMed

Other PDB entries of the same protein (UniProt A0A0H2USG1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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
7V8G 2.75 Å, Crystal structure of HOIP RING1 domain bound to IpaH1.4 LRR domain
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

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