8JWV: Untethered R0RBR

Untethered R0RBR. Determined by X-ray diffraction at 2.9 Å resolution. Released 3 Jul 2024.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,435
Mol. weight: 37.49 kDa
Ligands: ZN, BA
Released: 3 Jul 2024

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

Secondary structure: helices and β-sheets

8JWV contains 9 α-helices and 31 β-strands across 1 chain. 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: 9 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	147-150	4	1
β-strand	156-159	4	1
β-strand	160-166	7	2
β-strand	174-176	3	3
α-helix	183-187	5
β-strand	193	1	4
β-strand	194-196	3	3
β-strand	205	1	4
β-strand	206-212	7	2
β-strand	223	1	2
β-strand	224-225	2	1
β-strand	229-230	2	5
α-helix	236	1
β-strand	237	1	6
α-helix	238	1
β-strand	244	1	6
β-strand	248-250	3	5
β-strand	257	1	7
β-strand	258-260	3	5
α-helix	261-273	13
β-strand	278-280	3	8
β-strand	284-286	3	8
α-helix	301-307	7
α-helix	308-326	19
β-strand	330-331	2	9
β-strand	340-341	2	9
β-strand	349-351	3	10
β-strand	363-365	3	10
β-strand	371	1	10
α-helix	372-373	2
α-helix	395-400	6
β-strand	402	1	7
β-strand	415-417	3	11
β-strand	424-426	3	11
β-strand	431	1	12
β-strand	433-435	3	13
β-strand	444-446	3	13
β-strand	451-452	2	13
α-helix	455-461	7
β-strand	463	1	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase parkin	A	protein	325	Homo sapiens	O60260 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8JWV_1 E3 ubiquitin-protein ligase parkin (chains A)
SIYNSFYVYCKGPCQRVQPGKLRVQCSTCRQATLTLTQGPSCWDDVLIPNRMSGECQSPH
CPGTSAEFFFKCGAHPTSDKETSVALHLIATNSRNITCITCTDVRSPVLVFQCNSRHVIC
LDCFHLYCVTRLNDRQFVHDPQLGYSLPCVAGCPNSLIKELHHFRILGEEQYNRYQQYGA
EECVLQMGGVLCPRPGCGAGLLPEPDCRKVTCEGGNGLGCGFAFCRECKEAYHEGECSAV
FENLYFQSQAYRVDERAAEQARWEAASKETIKKTTKPCPRCHVPVEKNGGCMHMKCPQPQ
CRLEWCWNCGCEWNRVCMGDHWFDV

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8
BA	Barium ion	Ba	1

Water and common crystallization additives (GOL) are not listed.

Primary citation

Additional feedforward mechanism of Parkin activation via binding of phospho-UBL and RING0 in trans. Lenka, D.R., Dahe, S.V., Antico, O. et al. Elife (2024) 13. DOI 10.7554/eLife.96699 · PubMed

Other PDB entries of the same protein (UniProt O60260 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4I1F 1.58 Å, Structure of Parkin-S223P E3 ligase
5C1Z 1.79 Å, Parkin (UblR0RBR)
6GLC 1.8 Å, Structure of phospho-Parkin bound to phospho-ubiquitin
8WZN 1.8 Å, ParkinK211N in complex with phospho NEDD8
8IKM 1.92 Å, Trans complex of phospho parkin
4I1H 2.0 Å, Structure of Parkin E3 ligase
4BM9 2.25 Å, Structure of the autoinhibited Parkin catalytic domain
8WZO 2.25 Å, Parkin in complex with phospho NEDD8
5C9V 2.35 Å, Structure of human Parkin G319A
8IKV 2.35 Å, pUbl depleted phospho-Parkin(K211N,R163D) in complex with pUb
5C23 2.37 Å, Parkin (S65DUblR0RBR)
5N38 2.6 Å, S65DParkin and pUB complex

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