8IKM: Trans complex of phospho parkin

Trans complex of phospho parkin. Determined by X-ray diffraction at 1.92 Å resolution. Released 11 Sept 2024.

Method: X-ray diffraction
Resolution: 1.92 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,052
Mol. weight: 52.79 kDa
Ligands: ZN
Released: 11 Sept 2024

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

Secondary structure: helices and β-sheets

8IKM contains 17 α-helices and 34 β-strands across 3 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: 5 helices, 19 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	224-225	2	1
β-strand	229-230	2	5
α-helix	236-238	3
β-strand	248-250	3	5
β-strand	258-260	3	5
α-helix	261-273	13
β-strand	278-280	3	6
β-strand	284-286	3	6
α-helix	301-307	7
α-helix	309-326	18
β-strand	330-331	2	7
β-strand	340-342	3	7
β-strand	349-351	3	8
β-strand	363-365	3	8
β-strand	371	1	8

Chain B: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	7
β-strand	12-16	5	7
β-strand	22	1	9
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	7
β-strand	48-49	2	7
α-helix	50-51	2
β-strand	55	1	9
α-helix	56-59	4
α-helix	61-62	2
β-strand	66-72	7	7

Chain C: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	10
α-helix	7-9	3
α-helix	10-12	3
β-strand	13-16	4	10
β-strand	22	1	11
α-helix	23-34	12
α-helix	38-40	3
β-strand	43-45	3	12
β-strand	48-50	3	12
α-helix	51	1
β-strand	55	1	11
α-helix	56-59	4
α-helix	61-62	2
β-strand	66-67	2	10
β-strand	68	1	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase parkin	A	protein	247	Homo sapiens	O60260 (AlphaFold model)
Ubiquitin	B	protein	75	Homo sapiens	P62987 (AlphaFold model)
E3 ubiquitin-protein ligase parkin	C	protein	146	Homo sapiens	O60260 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8IKM_1 E3 ubiquitin-protein ligase parkin (chains A)
SIYNSFYVYCKGPCQRVQPGKLRVQCSTCRQATLTLTQGPSCWDDVLIPNRMSGECQSPH
CPGTSAEFFFKCGAHPTSDKETSVALHLIATNSRNITCITCTDVRSPVLVFQCNSRHVIC
LDCFHLYCVTRLNDRQFVHDPQLGYSLPCVAGCPNSLIKELHHFRILGEEQYNRYQQYGA
EECVLQMGGVLCPRPGCGAGLLPEPDCRKVTCEGGNGLGCGFAFCRECKEAYHEGECSAV
FENLYFQ

Sequence of entity 2 (B), FASTA

>8IKM_2 Ubiquitin (chains B)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRG

Sequence of entity 3 (C), FASTA

>8IKM_3 E3 ubiquitin-protein ligase parkin (chains C)
MIVFVRFNSSHGFPVEVDSDTSIFQLKEVVAKRQGVPADQLRVIFAGKELRNDWTVQNCD
LDQQSIVHIVQRPWRKGQEMNATGGDDPRNAAGGCEREPQSLTRVDLSSSVLPGDSVGLA
VILHTDSRKDSPPAGSPAGRLEVLFQ

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	6

Water and common crystallization additives (PEG, 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
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
8IKT 2.6 Å, Ternary trans-complex of phospho-parkin with cis ACT and pUb

Browse structure collections

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