5HPT: NEDD4-like E3 ubiquitin-protein ligase WWP1

System-wide modulation of HECT E3 ligases with selective ubiquitin variant probes: WWP1, Ubv P2.3 and UBCH7. Determined by X-ray diffraction at 2.84 Å resolution. Released 16 Mar 2016.

Method: X-ray diffraction
Resolution: 2.84 Å
Organism: Homo sapiens
Chains: 8
Atoms: 13,529
Mol. weight: 200.91 kDa
Released: 16 Mar 2016

Explore 5HPT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5HPT contains 94 α-helices and 82 β-strands across 8 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: 24 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	547-559	13
β-strand	566-571	6	1
α-helix	573-575	3
α-helix	576-585	10
α-helix	589-593	5
β-strand	595-600	6	1
α-helix	614-623	10
α-helix	626-628	3
β-strand	631-633	3	2
β-strand	641-643	3	2
α-helix	645-649	5
α-helix	653-670	18
β-strand	678	1	2
α-helix	680-686	7
α-helix	689-691	3
α-helix	693-699	7
α-helix	701-712	12
β-strand	723	1	3
β-strand	725-730	6	4
β-strand	733-738	6	4
α-helix	743-745	3
β-strand	747	1	3
α-helix	748	1
α-helix	753-766	14
α-helix	770-783	14
α-helix	786-789	4
α-helix	794-801	8
α-helix	804-806	3
α-helix	809-814	6
β-strand	817-819	3	5
α-helix	826-837	12
α-helix	840-851	12
α-helix	861-863	3
β-strand	865	1	6
β-strand	870	1	6
β-strand	874-876	3	5
β-strand	886-888	3	5
β-strand	893-895	3	5
α-helix	902-914	13

Chain B: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	7
β-strand	12-16	5	7
β-strand	22	1	8
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	7
β-strand	48-49	2	7
β-strand	55	1	8
β-strand	66-71	6	7
α-helix	72-73	2

Chain C: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	5-15	11
β-strand	22-27	6	9
β-strand	34-39	6	9
β-strand	51-56	6	9
β-strand	67-70	4	9
β-strand	79	1	10
β-strand	84	1	9
β-strand	85	1	10
α-helix	88-90	3
α-helix	101-113	13
α-helix	123-130	8
α-helix	133-147	15

Chain D: 23 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	547-560	14
β-strand	566-571	6	11
α-helix	573-575	3
α-helix	576-584	9
α-helix	589-593	5
β-strand	595-600	6	11
α-helix	605-607	3
α-helix	614-623	10
α-helix	626-628	3
β-strand	631-633	3	12
β-strand	641-643	3	12
α-helix	647-649	3
α-helix	653-669	17
β-strand	678	1	12
α-helix	680-686	7
α-helix	689-691	3
α-helix	696-699	4
α-helix	701-712	12
β-strand	723	1	13
β-strand	725-730	6	14
β-strand	733-738	6	14
α-helix	743-745	3
β-strand	747	1	13
α-helix	753-766	14
α-helix	770-783	14
α-helix	786-789	4
α-helix	794-801	8
α-helix	811-814	4
β-strand	817-818	2	15
α-helix	826-837	12
α-helix	841-851	11
α-helix	861-863	3
β-strand	865	1	16
β-strand	870	1	16
β-strand	874-875	2	15
β-strand	886-888	3	15
β-strand	893-895	3	15
α-helix	902-912	11

Chain E: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	17
β-strand	12-16	5	17
β-strand	22	1	18
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	17
β-strand	48-50	3	17
β-strand	55	1	18
β-strand	66-71	6	17
α-helix	72-73	2

Chain F: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	4-15	12
β-strand	22	1	19
β-strand	26-27	2	19
β-strand	34-39	6	19
β-strand	51-56	6	19
β-strand	67-70	4	19
β-strand	76	1	20
β-strand	79	1	20
β-strand	84	1	19
β-strand	85	1	20
α-helix	88-90	3
α-helix	101-113	13
α-helix	123-130	8
α-helix	133-146	14

Chain G: 27 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	547-560	14
β-strand	566-571	6	21
α-helix	573-575	3
α-helix	576-585	10
α-helix	589-593	5
β-strand	595-600	6	21
α-helix	613-623	11
α-helix	626-628	3
β-strand	631-633	3	22
β-strand	641-643	3	22
α-helix	645-649	5
α-helix	653-670	18
β-strand	678	1	22
α-helix	680-686	7
α-helix	689-692	4
α-helix	693-699	7
α-helix	701-712	12
β-strand	723	1	23
β-strand	725-730	6	24
β-strand	733-738	6	24
α-helix	743-745	3
α-helix	746	1
β-strand	747	1	23
α-helix	748	1
α-helix	753-766	14
α-helix	770-783	14
α-helix	786-789	4
α-helix	794-801	8
α-helix	805-807	3
α-helix	809-814	6
β-strand	816-818	3	25
α-helix	826-836	11
α-helix	840-851	12
α-helix	861-863	3
β-strand	865	1	26
β-strand	870	1	26
β-strand	873-876	4	25
α-helix	884-885	2
β-strand	886-888	3	25
β-strand	893-895	3	25
α-helix	902-904	3
α-helix	905-914	10

Chain H: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	27
β-strand	12-16	5	27
β-strand	22	1	28
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	27
β-strand	48-49	2	27
α-helix	50-51	2
β-strand	55	1	28
β-strand	66-71	6	27
α-helix	72-73	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NEDD4-like E3 ubiquitin-protein ligase WWP1	A, D, G	protein	383	Homo sapiens	Q9H0M0 (AlphaFold model)
Ubiquitin variant P2.3	B, E, H	protein	83	Homo sapiens	P62987 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 L3	C, F	protein	161	Homo sapiens	P68036 (AlphaFold model)

Sequence of entity 1 (A, D, G), FASTA

>5HPT_1 NEDD4-like E3 ubiquitin-protein ligase WWP1 (chains A, D, G)
GSGGPQIAYERGFRWKLAHFRYLCQSNALPSHVKINVSRQTLFEDSFQQIMALKPYDLRR
RLYVIFRGEEGLDYGGLAREWFFLLSHEVLNPMYCLFEYAGKNNYCLQINPASTINPDHL
SYFCFIGRFIAMALFHGKFIDTGFSLPFYKRMLSKKLTIKDLESIDTEFYNSLIWIRDNN
IEECGLEMYFSVDMEILGKVTSHDLKLGGSNILVTEENKDEYIGLMTEWRFSRGVQEQTK
AFLDGFNEVVPLQWLQYFDEKELEVMLCGMQEVDLADWQRNTVYRHYTRNSKQIIWFWQF
VKETDNEVRMRLLQFVTGTCRLPLGGFAELMGSNGPQKFCIEKVGKDTWLPRSHTCFNRL
DLPPYKSYEQLKEKLLFAIEETE

Sequence of entity 2 (B, E, H), FASTA

>5HPT_2 Ubiquitin variant  P2.3 (chains B, E, H)
GSGGSMQILVKTFTWKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRT
LSDYNIKMGSSLYLVLRLPGQRI

Sequence of entity 3 (C, F), FASTA

>5HPT_3 Ubiquitin-conjugating enzyme E2 L3 (chains C, F)
AASRRLMKELEEIRKCGMKNFRNIQVDEANLLTWQGLIVPDNPPYDKGAFRIEINFPAEY
PFKPPKITFKTKIYHPNIDEKGQVCLPVISAENWKPATKTDQVIQSLIALVNDPQPEHPL
RADLAEEYSKDRKKFCKNAEEFTKKYGEKRPVDGGHHHHHH

Primary citation

System-Wide Modulation of HECT E3 Ligases with Selective Ubiquitin Variant Probes. Zhang, W., Wu, K.P., Sartori, M.A. et al. Mol Cell (2016) 62:121-136. DOI 10.1016/j.molcel.2016.02.005 · 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
6J1Y 2.55 Å, Semi-open conformation E3 ligase
9EQK 3.0 Å, WWP1 WW2-2,3-linker-WW3-WW4-HECT (WWP1-2L34H) with ordered WW2 domain
2OP7 WW4

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