7OD1: RBR ubiquitin ligase ARIH2

Name: PDB 7OD1: Crystal structure of RBR ubiquitin ligase ARIH2
Published: 2021-09-15
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Crystal structure of RBR ubiquitin ligase ARIH2. Determined by X-ray diffraction at 2.45 Å resolution. Released 15 Sept 2021.

Method: X-ray diffraction
Resolution: 2.45 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,972
Mol. weight: 116.57 kDa
Ligands: ZN
Released: 15 Sept 2021

Explore 7OD1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7OD1 contains 38 α-helices and 28 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: 17 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	61-65	5	1
α-helix	66-84	19
α-helix	88-97	10
α-helix	102-111	10
α-helix	113-119	7
β-strand	151-152	2	2
β-strand	160-161	2	2
α-helix	162-174	13
β-strand	182	1	3
β-strand	191	1	3
α-helix	194-197	4
α-helix	198-200	3
α-helix	204-221	18
β-strand	225-227	3	1
β-strand	235-239	5	1
β-strand	246-248	3	4
β-strand	255-257	3	4
α-helix	270-282	13
α-helix	284-287	4
β-strand	294-296	3	5
β-strand	303-305	3	5
β-strand	312-314	3	6
β-strand	321-323	3	6
β-strand	329	1	6
α-helix	330-332	3
α-helix	354-398	45
α-helix	404-432	29
α-helix	434-435	2
α-helix	438-462	25
α-helix	464-466	3
α-helix	469-490	22

Chain B: 21 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	61-65	5	7
α-helix	66-84	19
α-helix	88-97	10
α-helix	102-111	10
α-helix	114-119	6
α-helix	148-150	3
β-strand	151-152	2	8
β-strand	160-161	2	8
α-helix	162-174	13
β-strand	182	1	9
α-helix	190	1
β-strand	191	1	9
α-helix	192-193	2
α-helix	194-197	4
α-helix	198-200	3
α-helix	204-221	18
β-strand	225-227	3	7
β-strand	235-239	5	7
β-strand	246-248	3	10
β-strand	255-257	3	10
α-helix	270-282	13
α-helix	284-287	4
β-strand	294-296	3	11
β-strand	303-305	3	11
β-strand	312-314	3	12
β-strand	321-323	3	12
β-strand	329	1	12
α-helix	330-333	4
α-helix	345-346	2
α-helix	354-398	45
α-helix	404-433	30
α-helix	435	1
α-helix	438-462	25
α-helix	464-466	3
α-helix	469-490	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase ARIH2	A, B	protein	493	Homo sapiens	O95376 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7OD1_1 E3 ubiquitin-protein ligase ARIH2 (chains A, B)
MSVDMNSQGSDSNEEDYDPNCEEEEEEEEDDPGDIEDYYVGVASDVEQQGADAFDPEEYQ
FTCLTYKESEGALNEHMTSLASVLKVSHSVAKLILVNFHWQVSEILDRYKSNSAQLLVEA
RVQPNPSKHVPTSHPPHHCAVCMQFVRKENLLSLACQHQFCRSCWEQHCSVLVKDGVGVG
VSCMAQDCPLRTPEDFVFPLLPNEELREKYRRYLFRDYVESHYQLQLCPGADCPMVIRVQ
EPRARRVQCNRCNEVFCFKCRQMYHAPTDCATIRKWLTKCADDSETANYISAHTKDCPKC
NICIEKNGGCNHMQCSKCKHDFCWMCLGDWKTHGSEYYECSRYKENPDIVNQSQQAQARE
ALKKYLFYFERWENHNKSLQLEAQTYQRIHEKIQERVMNNLGTWIDWQYLQNAAKLLAKC
RYTLQYTYPYAYYMESGPRKKLFEYQQAQLEAEIENLSWKVERADSYDRGDLENQMHIAE
QRRRTLLKDFHDT

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	12

Primary citation

CUL5-ARIH2 E3-E3 ubiquitin ligase structure reveals cullin-specific NEDD8 activation. Kostrhon, S., Prabu, J.R., Baek, K. et al. Nat Chem Biol (2021) 17:1075-1083. DOI 10.1038/s41589-021-00858-8 · PubMed

Other PDB entries of the same protein (UniProt O95376 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9T7V 2.95 Å, Structure of LRRC58-EloB/C-CDO1 in complex with NEDD8-CUL5-RBX2-ARIH2-Ub
9SDX 2.97 Å, Structure of RBR binding E2 variant crosslinked with NEDD8-CUL5-RBX2 bound ARIH2 and Ub
9SDY 3.06 Å, Structure of RBR E2 variant binding to CUL5-RBX2 bound ARIH2
7ONI 3.4 Å, Structure of Neddylated CUL5 C-terminal region-RBX2-ARIH2*

Browse structure collections

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