6N13: E3 ubiquitin-protein ligase parkin

Name: PDB 6N13: UbcH7-Ub Complex with R0RBR Parkin and phosphoubiquitin
Published: 2018-11-28
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

UbcH7-Ub Complex with R0RBR Parkin and phosphoubiquitin. Determined by solution NMR. Released 28 Nov 2018.

Method: Solution NMR
Organism: Homo sapiens
Chains: 4
Atoms: 4,978
Mol. weight: 71.89 kDa
Ligands: ZN
Released: 28 Nov 2018

Explore 6N13 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6N13 contains 22 α-helices and 45 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: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	15
β-strand	12-16	5	15
β-strand	22	1	16
α-helix	23-33	11
β-strand	41-45	5	17
β-strand	48-49	2	17
α-helix	50	1
β-strand	55	1	16
α-helix	56-59	4
β-strand	66-67	2	15
β-strand	68-71	4	17

Chain B: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	147-149	3	1
β-strand	157-159	3	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
α-helix	223	1
β-strand	224-226	3	1
β-strand	230	1	5
β-strand	248-250	3	5
β-strand	258-260	3	5
α-helix	261-274	14
β-strand	278-279	2	6
β-strand	285-286	2	6
α-helix	301-306	6
α-helix	309-327	19
β-strand	350-351	2	7
β-strand	363-364	2	7
β-strand	371	1	7
α-helix	378-383	6
α-helix	395-400	6
β-strand	415-417	3	8
β-strand	424-426	3	8
β-strand	431	1	9
β-strand	433-436	4	10
β-strand	443-446	4	10
β-strand	452	1	10
α-helix	455-460	6
β-strand	463	1	9

Chain C: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	502-517	16
β-strand	522-527	6	13
β-strand	534-539	6	13
β-strand	550	1	14
β-strand	551-556	6	13
α-helix	565-566	2
β-strand	567-570	4	13
α-helix	601-613	13
α-helix	623-631	9
α-helix	633-647	15
β-strand	649	1	14
α-helix	650-651	2

Chain D: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	702-706	5	11
β-strand	713-716	4	11
β-strand	722	1	12
α-helix	723-733	11
α-helix	738-740	3
β-strand	741-744	4	11
β-strand	749	1	11
α-helix	750-751	2
β-strand	755	1	12
α-helix	756-759	4
β-strand	766-771	6	11
α-helix	772	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase parkin	B	protein	322	Homo sapiens	O60260 (AlphaFold model)
ubiquitin	D	protein	76	Homo sapiens	P0CG47 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 L3	C	protein	156	Homo sapiens	P68036 (AlphaFold model)
phosphoubiquitin	A	protein	76	Homo sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>6N13_1 E3 ubiquitin-protein ligase parkin (chains B)
NSFYVYCKGPCQRVQPGKLRVQCSTCRQATLTLTQGPSCWDDVLIPNRMSGECQSPHCPG
TSAEFFFKCGAHPTSDKETSVALHLIATNSRNITCITCTDVRSPVLVFQCNSRHVICLDC
FHLYCVTRLNDRQFVHDPQLGYSLPCVAGCPNSLIKELHHFRILGEEQYNRYQQYGAEEC
VLQMGGVLCPRPGCGAGLLPEPDCRKVTCEGGNGLGCGFAFCRECKEAYHEGECSAVFEA
SGTTTQAYRVDERAAEQARWEAASKETIKKTTKPCPRCHVPVEKNGGCMHMKCPQPQCRL
EWCWNCGCEWNRVCMGDHWFDV

Sequence of entity 2 (D), FASTA

>6N13_2 ubiquitin (chains D)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 3 (C), FASTA

>6N13_3 Ubiquitin-conjugating enzyme E2 L3 (chains C)
GHMAASRRLMKELEEIRKSGMKNFRNIQVDEANLLTWQGLIVPDNPPYDKGAFRIEINFP
AEYPFKPPKITFKTKIYHPNIDEKGQVKLPVISAENWKPATKTDQVIQSLIALVNDPQPE
HPLRADLAEEYSKDRKKFSKNAEEFTKKYGEKRPVD

Sequence of entity 4 (A), FASTA

>6N13_4 phosphoubiquitin (chains A)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8

Primary citation

Synergistic recruitment of UbcH7~Ub and phosphorylated Ubl domain triggers parkin activation. Condos, T.E., Dunkerley, K.M., Freeman, E.A. et al. EMBO J (2018) 37. DOI 10.15252/embj.2018100014 · 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

Browse structure collections

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