2XBB: Nedd4 HECT:Ub complex

Nedd4 HECT:Ub complex. Determined by X-ray diffraction at 2.68 Å resolution. Released 23 Mar 2011.

Method: X-ray diffraction
Resolution: 2.68 Å
Organisms: HOMO SAPIENS, BOS TAURUS
Chains: 4
Atoms: 7,659
Mol. weight: 108.9 kDa
Released: 23 Mar 2011

Explore 2XBB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2XBB contains 67 α-helices and 46 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: 29 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	522-532	11
α-helix	534-536	3
β-strand	543-547	5	1
α-helix	549-551	3
α-helix	552-562	11
α-helix	566-570	5
α-helix	572	1
β-strand	573-577	5	1
α-helix	585-600	16
α-helix	603-605	3
β-strand	608-610	3	2
β-strand	618-620	3	2
α-helix	624-627	4
α-helix	631-647	17
β-strand	652	1	3
β-strand	656	1	2
α-helix	658-664	7
α-helix	671-674	4
α-helix	679-690	12
α-helix	694-696	3
β-strand	699	1	4
β-strand	701-705	5	5
β-strand	710-714	5	5
α-helix	722	1
β-strand	723	1	4
α-helix	724	1
α-helix	729-741	13
α-helix	743-745	3
α-helix	746-757	12
α-helix	764-767	4
α-helix	770-777	8
β-strand	778	1	3
α-helix	785-790	6
β-strand	792-795	4	6
α-helix	803-813	11
α-helix	817-828	12
α-helix	833-834	2
α-helix	838-840	3
β-strand	850-854	5	6
α-helix	861-862	2
β-strand	863-865	3	6
α-helix	866-868	3
β-strand	870-873	4	6
α-helix	879-892	14

Chain B: 27 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	522-532	11
α-helix	534-536	3
β-strand	542-547	6	7
α-helix	549-551	3
α-helix	552-562	11
α-helix	566-570	5
β-strand	572-577	6	7
α-helix	585-600	16
α-helix	603-605	3
β-strand	608-610	3	8
β-strand	618-620	3	8
α-helix	624-627	4
α-helix	631-647	17
β-strand	652-653	2	9
β-strand	656	1	8
α-helix	658-664	7
α-helix	673-677	5
α-helix	679-690	12
α-helix	694-696	3
β-strand	699	1	10
β-strand	701-705	5	11
β-strand	710-714	5	11
α-helix	719-721	3
β-strand	723	1	10
α-helix	729-741	13
α-helix	743-745	3
α-helix	746-757	12
α-helix	762-765	4
α-helix	770-777	8
β-strand	778-779	2	9
α-helix	785-790	6
β-strand	792-795	4	12
α-helix	803-813	11
α-helix	817-827	11
α-helix	833-834	2
α-helix	838-840	3
β-strand	842	1	13
β-strand	847	1	13
β-strand	850-854	5	12
α-helix	861-862	2
β-strand	863-865	3	12
α-helix	866-868	3
β-strand	870-873	4	12
α-helix	879-892	14

Chain C: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	14
α-helix	11	1
β-strand	12-16	5	14
β-strand	22	1	15
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	14
β-strand	48-49	2	14
α-helix	50-51	2
β-strand	55	1	15
α-helix	57-59	3
β-strand	66-71	6	14
α-helix	72-73	2

Chain D: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	16
β-strand	12-16	5	16
β-strand	22	1	17
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	16
β-strand	48-49	2	16
β-strand	55	1	17
α-helix	57-59	3
α-helix	65	1
β-strand	66-71	6	16
α-helix	72-73	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase NEDD4	A, B	protein	386	HOMO SAPIENS	P46934 (AlphaFold model)
Ubiquitin	C, D	protein	76	BOS TAURUS	P63048 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2XBB_1 E3 UBIQUITIN-PROTEIN LIGASE NEDD4 (chains A, B)
GPLGSRDYKRKYEFFRRKLKKQNDIPNKFEMKLRRATVLEDSYRRIMGVKRADFLKARLW
IEFDGEKGLDYGGVAREWFFLISKEMFNPYYGLFEYSATDNYTLQINPNSGLCNEDHLSY
FKFIGRVAGMAVYHGKLLDGFFIRPFYKMMLHKPITLHDMESVDSEYYNSLRWILENDPT
ELDLRFIIDEELFGQTHQHELKNGGSEIVVTNKNKKEYIYLVIQWRFVNRIQKQMAAFKE
GFFELIPQDLIKIFDENELELLMCGLGDVDVNDWREHTKYKNGYSANHQVIQWFWKAVLM
MDSEKRIRLLQFVTGTSRVPMNGFAELYGSNGPQSFTVEQWGTPEKLPRAHTCFNRLDLP
PYESFEELWDKLQMAIENTQGFDGVD

Sequence of entity 2 (C, D), FASTA

>2XBB_2 UBIQUITIN (chains C, D)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Primary citation

Structure of the Hect:Ubiquitin Complex and its Role in Ubiquitin Chain Elongation. Maspero, E., Mari, S., Valentini, E. et al. EMBO Rep (2011) 12:342. DOI 10.1038/EMBOR.2011.21 · PubMed

Other PDB entries of the same protein (UniProt P46934 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4N7F 1.1 Å, Crystal structure of 3rd WW domain of human Nedd4-1
4N7H 1.7 Å, Crystal Structure of the Complex of 3rd WW domain of Human Nedd4 and 1st PPXY Motif of…
3B7Y 1.8 Å, Crystal structure of the C2 Domain of the E3 Ubiquitin-Protein Ligase NEDD4
9H9O 2.12 Å, Crystal structure of NEDD4 HECT domain in complex with norclomipramine
9H9T 2.17 Å, Crystal structure of NEDD4 HECT domain in complex with covalent inhibitor
5C91 2.44 Å, NEDD4 HECT with covalently bound indole-based inhibitor
2XBF 2.5 Å, Nedd4 HECT structure
4BBN 2.51 Å, NEDD4 HECT-Ub:Ub complex
4BE8 3.0 Å, NEDD4 HECT A889F structure
5C7J 3.0 Å, Crystal structure of NEDD4 with a ub variant
2KPZ Human NEDD4 3RD WW Domain Complex with The Human T-cell Leukemia virus 1 GAG-Pro…
2KQ0 Human NEDD4 3rd WW Domain Complex with Ebola Zaire Virus Matrix Protein VP40 Derived…

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