8IK6: PUbl depleted Parkin complex with pUbiquitin

pUbl depleted Parkin complex with pUbiquitin. Determined by X-ray diffraction at 3.3 Å resolution. Released 11 Sept 2024.

Method: X-ray diffraction
Resolution: 3.3 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,518
Mol. weight: 92.58 kDa
Ligands: ZN
Released: 11 Sept 2024

Explore 8IK6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8IK6 contains 20 α-helices and 66 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: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	147-150	4	15
β-strand	156-159	4	15
β-strand	160-166	7	16
β-strand	175-176	2	17
α-helix	184-187	4
β-strand	193	1	18
β-strand	194-195	2	17
β-strand	205	1	18
β-strand	206-212	7	16
β-strand	224-225	2	15
β-strand	229-230	2	19
α-helix	236-238	3
β-strand	248-250	3	19
β-strand	257	1	20
β-strand	258-260	3	19
α-helix	261-273	13
β-strand	278-280	3	21
β-strand	284-286	3	21
α-helix	301-307	7
α-helix	309-321	13
α-helix	395-399	5
β-strand	402	1	20
β-strand	415-417	3	22
β-strand	424-426	3	22
β-strand	431	1	23
β-strand	433-435	3	24
β-strand	444-446	3	24
β-strand	452	1	24
α-helix	455-461	7
β-strand	463	1	23

Chain B: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	25
β-strand	13-16	4	25
β-strand	22	1	26
α-helix	23-34	12
β-strand	42-45	4	25
β-strand	48-49	2	25
β-strand	55	1	26
α-helix	61-62	2
β-strand	66-70	5	25

Chain C: 7 helices, 29 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	184-187	4
β-strand	193	1	4
β-strand	194-196	3	3
β-strand	205	1	4
β-strand	206-212	7	2
α-helix	222-223	2
β-strand	224-225	2	1
β-strand	229-230	2	5
β-strand	237	1	6
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	309-326	18
β-strand	330-331	2	9
β-strand	340-342	3	9
β-strand	349-351	3	10
β-strand	363-365	3	10
α-helix	395-399	5
β-strand	402	1	7
β-strand	417	1	11
β-strand	424	1	11
β-strand	431	1	12
β-strand	433-435	3	13
β-strand	444-446	3	13
β-strand	452	1	13
α-helix	455-461	7
β-strand	463	1	12

Chain D: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	9
β-strand	12-16	5	9
β-strand	22	1	14
α-helix	23-33	11
α-helix	38-40	3
β-strand	41-45	5	9
β-strand	48-49	2	9
α-helix	50-51	2
β-strand	55	1	14
α-helix	61-62	2
β-strand	66-72	7	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase parkin	A, C	protein	327	Homo sapiens	O60260 (AlphaFold model)
Ubiquitin	B, D	protein	75	Homo sapiens	P62987 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>8IK6_1 E3 ubiquitin-protein ligase parkin (chains A, C)
GPSIYNSFYVYCKGPCQRVQPGKLRVQCSTCRQATLTLTQGPSCWDDVLIPNRMSGECQS
PHCPGTSAEFFFKCGAHPTSDKETSVALHLIATNSRNITCITCTDVRSPVLVFQCNSRHV
ICLDCFHLYCVTRLNDRQFVHDPQLGYSLPCVAGCPNSLIKELHHFRILGEEQYNRYQQY
GAEECVLQMGGVLCPRPGCGAGLLPEPDCRKVTCEGGNGLGCGFAFCRECKEAYHEGECS
AVFENLYFQSQAYRVDERAAEQARWEAASKETIKKTTKPCPRCHVPVEKNGGCMHMKCPQ
PQCRLEWCWNCGCEWNRVCMGDHWFDV

Sequence of entity 2 (B, D), FASTA

>8IK6_2 Ubiquitin (chains B, D)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	14

Water and common crystallization additives (SO4) 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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