8EI4: WWP1 HECT domain

Name: PDB 8EI4: Crystal structure of the WWP1 HECT domain in complex with H302, a Helicon Polypeptide
Published: 2023-10-25
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Crystal structure of the WWP1 HECT domain in complex with H302, a Helicon Polypeptide. Determined by X-ray diffraction at 2.43 Å resolution. Released 25 Oct 2023.

Method: X-ray diffraction
Resolution: 2.43 Å
Organisms: Homo sapiens, synthetic construct
Chains: 2
Atoms: 3,210
Mol. weight: 46.77 kDa
Ligands: WHL
Released: 25 Oct 2023

Explore 8EI4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8EI4 contains 22 α-helices and 16 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: 21 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	547-560	14
β-strand	566-570	5	1
α-helix	576-585	10
α-helix	589-593	5
β-strand	595-599	5	1
α-helix	610-623	14
β-strand	631-632	2	2
β-strand	642-643	2	2
α-helix	645-649	5
α-helix	653-669	17
α-helix	680-686	7
α-helix	689-691	3
α-helix	693-699	7
α-helix	701-711	11
β-strand	723	1	3
β-strand	725	1	4
β-strand	728	1	5
β-strand	735	1	5
β-strand	738	1	4
α-helix	743-745	3
β-strand	747	1	3
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	861-863	3
β-strand	865	1	7
β-strand	870	1	7
β-strand	873-876	4	6
α-helix	884-885	2
β-strand	886-888	3	6
β-strand	893-895	3	6
α-helix	902-915	14

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	7-16	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NEDD4-like E3 ubiquitin-protein ligase WWP1	A	protein	376	Homo sapiens	Q9H0M0 (AlphaFold model)
H302	B	protein	19	synthetic construct

Sequence of entity 1 (A), FASTA

>8EI4_1 NEDD4-like E3 ubiquitin-protein ligase WWP1 (chains A)
GSHMGFRWKLAHFRYLCQSNALPSHVKINVSRQTLFEDSFQQIMALKPYDLRRRLYVIFR
GEEGLDYGGLAREWFFLLSHEVLNPMYCLFEYAGKNNYCLQINPASTINPDHLSYFCFIG
RFIAMALFHGKFIDTGFSLPFYKRMLSKKLTIKDLESIDTEFYNSLIWIRDNNIEECGLE
MYFSVDMEILGKVTSHDLKLGGSNILVTEENKDEYIGLMTEWRFSRGVQEQTKAFLDGFN
EVVPLQWLQYFDEKELEVMLCGMQEVDLADWQRNTVYRHYTRNSKQIIWFWQFVKETDNE
VRMRLLQFVTGTCRLPLGGFAELMGSNGPQKFCIEKVGKDTWLPRSHTCFNRLDLPPYKS
YEQLKEKLLFAIEETE

Sequence of entity 2 (B), FASTA

>8EI4_2 H302 (chains B)
XDPASMRCHRAAHICSVLX

Ligands and cofactors

ID	Name	Formula	Copies
WHL	N,N'-(1,4-phenylene)diacetamide	C10 H12 N2 O2	1

Water and common crystallization additives (EDO) are not listed.

Primary citation

Recognition and reprogramming of E3 ubiquitin ligase surfaces by alpha-helical peptides. Tokareva, O.S., Li, K., Travaline, T.L. et al. Nat Commun (2023) 14:6992-6992. DOI 10.1038/s41467-023-42395-z · 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
6J1Y 2.55 Å, Semi-open conformation E3 ligase
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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