6J1Y: Semi-open conformation E3 ligase

Name: PDB 6J1Y: Semi-open conformation E3 ligase
Published: 2019-07-24
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Semi-open conformation E3 ligase. Determined by X-ray diffraction at 2.55 Å resolution. Released 24 Jul 2019.

Method: X-ray diffraction
Resolution: 2.55 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,343
Mol. weight: 122.41 kDa
Released: 24 Jul 2019

Explore 6J1Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6J1Y contains 58 α-helices and 38 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: 29 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	431-443	13
α-helix	445-448	4
α-helix	547-560	14
β-strand	566-571	6	1
α-helix	573-575	3
α-helix	576-586	11
α-helix	590-593	4
β-strand	595-600	6	1
α-helix	610-622	13
α-helix	626-628	3
β-strand	631	1	2
β-strand	640-641	2	3
β-strand	643	1	2
α-helix	645-649	5
α-helix	653-669	17
β-strand	677-678	2	3
α-helix	680-686	7
α-helix	689-691	3
α-helix	693-697	5
α-helix	701-712	12
α-helix	715-718	4
β-strand	723	1	4
β-strand	725-730	6	5
β-strand	733-738	6	5
α-helix	743-745	3
α-helix	746	1
β-strand	747	1	4
α-helix	748	1
α-helix	753-765	13
α-helix	770-783	14
α-helix	786-789	4
α-helix	794-802	9
α-helix	809-814	6
β-strand	816-819	4	6
α-helix	826-837	12
α-helix	840-851	12
α-helix	860-863	4
β-strand	865-866	2	7
β-strand	869-870	2	7
β-strand	873-877	5	6
α-helix	884-885	2
β-strand	886-888	3	6
α-helix	889-891	3
β-strand	893-896	4	6
α-helix	902-914	13

Chain B: 29 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	420-426	7
α-helix	430-443	14
α-helix	444-448	5
β-strand	454	1	8
β-strand	456	1	8
α-helix	458-459	2
β-strand	462-466	5	9
β-strand	472-476	5	9
β-strand	481-483	3	9
α-helix	487-490	4
α-helix	495-499	5
β-strand	502-506	5	10
β-strand	512-516	5	10
β-strand	521-523	3	10
α-helix	547-559	13
β-strand	566-571	6	11
α-helix	573-575	3
α-helix	576-581	6
α-helix	590-593	4
β-strand	595-600	6	11
α-helix	611-622	12
α-helix	626-628	3
β-strand	631	1	12
β-strand	643	1	12
α-helix	647-649	3
α-helix	653-670	18
α-helix	680-686	7
α-helix	689-692	4
α-helix	693-695	3
α-helix	696-699	4
α-helix	701-712	12
β-strand	722	1	13
β-strand	724	1	14
β-strand	740	1	14
β-strand	748	1	13
α-helix	753-766	14
α-helix	770-781	12
α-helix	786-789	4
α-helix	794-802	9
α-helix	809-814	6
β-strand	817-819	3	15
α-helix	826-836	11
α-helix	840-851	12
α-helix	860-863	4
β-strand	865-866	2	16
β-strand	869-870	2	16
β-strand	874-877	4	15
β-strand	886-888	3	15
α-helix	889-891	3
β-strand	893-896	4	15
α-helix	902-914	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NEDD4-like E3 ubiquitin-protein ligase WWP1	A, B	protein	519	Homo sapiens	Q9H0M0 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6J1Y_1 NEDD4-like E3 ubiquitin-protein ligase WWP1 (chains A, B)
GPGSEFQRPTMESVRNFEQWQSQRNQLQGAMQQFNQRYLYSASMLAAENDPYGPLPPGWE
KRVDSTDRVYFVNHNTKTTQWEDPRTQGLQNEEPLPEGWEIRYTREGVRYFVDHNTRTTT
FKDPRNGKSSVTKGGPQIAYERGFRWKLAHFRYLCQSNALPSHVKINVSRQTLFEDSFQQ
IMALKPYDLRRRLYVIFRGEEGLDYGGLAREWFFLLSHEVLNPMYCLFEYAGKNNYCLQI
NPASTINPDHLSYFCFIGRFIAMALFHGKFIDTGFSLPFYKRMLSKKLTIKDLESIDTEF
YNSLIWIRDNNIEECGLEMYFSVDMEILGKVTSHDLKLGGSNILVTEENKDEYIGLMTEW
RFSRGVQEQTKAFLDGFNEVVPLQWLQYFDEKELEVMLCGMQEVDLADWQRNTVYRHYTR
NSKQIIWFWQFVKETDNEVRMRLLQFVTGTCRLPLGGFAELMGSNGPQKFCIEKVGKDTW
LPRSHTCFNRLDLPPYKSYEQLKEKLLFAIEETEGFGQE

Primary citation

A multi-lock inhibitory mechanism for fine-tuning enzyme activities of the HECT family E3 ligases. Wang, Z., Liu, Z., Chen, X. et al. Nat Commun (2019) 10:3162-3162. DOI 10.1038/s41467-019-11224-7 · PubMed

Other PDB entries of the same protein (UniProt Q9H0M0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5HPS 2.05 Å, System-wide modulation of HECT E3 ligases with selective ubiquitin variant probes: WWP1…
1ND7 2.1 Å, Conformational Flexibility Underlies Ubiquitin Ligation Mediated by the WWP1 HECT domain…
6J1X 2.3 Å, WWP1 close conformation
8EI4 2.43 Å, Crystal structure of the WWP1 HECT domain in complex with H302, a Helicon Polypeptide
5HPT 2.84 Å, System-wide modulation of HECT E3 ligases with selective ubiquitin variant probes: WWP1,…
9EQK 3.0 Å, WWP1 WW2-2,3-linker-WW3-WW4-HECT (WWP1-2L34H) with ordered WW2 domain
2OP7 WW4

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