4BBN: NEDD4 HECT-Ub:Ub complex

NEDD4 HECT-Ub:Ub complex. Determined by X-ray diffraction at 2.51 Å resolution. Released 1 May 2013.

Method: X-ray diffraction
Resolution: 2.51 Å
Organisms: HOMO SAPIENS, BOS TAURUS
Chains: 3
Atoms: 4,492
Mol. weight: 62.83 kDa
Released: 1 May 2013

Explore 4BBN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4BBN contains 31 α-helices and 28 β-strands across 3 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	521-532	12
β-strand	542-547	6	1
α-helix	549-551	3
α-helix	552-562	11
α-helix	566-570	5
β-strand	572-577	6	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	624-626	3
α-helix	630-646	17
β-strand	655	1	2
α-helix	657-663	7
α-helix	670-676	7
α-helix	678-689	12
α-helix	693-695	3
β-strand	698	1	3
β-strand	700-705	6	4
β-strand	708-713	6	4
β-strand	722	1	3
α-helix	728-740	13
α-helix	742-744	3
α-helix	745-756	12
α-helix	761-764	4
α-helix	769-777	9
α-helix	784-789	6
β-strand	791-794	4	5
α-helix	802-813	12
α-helix	816-827	12
α-helix	836-839	4
β-strand	841-843	3	6
β-strand	845-846	2	6
β-strand	849-853	5	5
α-helix	860-861	2
β-strand	862-864	3	5
α-helix	865-867	3
β-strand	869-872	4	5
α-helix	878-890	13

Chain C: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	7
β-strand	12-16	5	7
α-helix	23-33	11
α-helix	38-40	3
β-strand	41-45	5	7
β-strand	48-49	2	7
α-helix	50-51	2
β-strand	66-71	6	7
α-helix	72-73	2

Chain F: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	8
β-strand	12-16	5	8
β-strand	22	1	9
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	8
β-strand	48-49	2	8
α-helix	50-51	2
β-strand	55	1	9
β-strand	66-71	6	8
β-strand	74-75	2	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase NEDD4	A	protein	385	HOMO SAPIENS	P46934 (AlphaFold model)
Polyubiquitin-B	C	protein	76	BOS TAURUS	P0CG53 (AlphaFold model)
Polyubiquitin-B	F	protein	76	BOS TAURUS	P0CG53 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4BBN_1 E3 UBIQUITIN-PROTEIN LIGASE NEDD4 (chains A)
GPLGSRDYKRKYEFFRRKLKKQNDIPNKFEMKLRRATVLEDSYRRIMGVKRADFLKARLW
IEFDGEKGLDYGGVAREWFFLISKEMFNPYYGLFEYSATDNYTLQINPNSGINPDHLSYF
KFIGRVAGMAVYHGKLLDGFFIRPFYKMMLHKPITLHDMESVDSEYYNSLRWILENDPTE
LDLRFIIDEELFGQTHQHELKNGGSEIVVTNKNKKEYIYLVIQWRFVNRIQKQMAAFKEG
FFELIPQDLIKIFDENELELLMSGLGDVDVNDWREHTKYKNGYSANHQVIQWFWKAVLMM
DSEKRIRLLQFVTGTSRVPMNGFAELYGSNGPQSFTVEQWGTPEKLPRAHTCFNRLDLPP
YESFEELWDKLQMAIENTQGFDGVD

Sequence of entity 2 (C), FASTA

>4BBN_2 POLYUBIQUITIN-B (chains C)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 3 (F), FASTA

>4BBN_3 POLYUBIQUITIN-B (chains F)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGC

Primary citation

Structure of a Ubiquitin-Loaded Hect Ligase Reveals the Molecular Basis for Catalytic Priming. Maspero, E., Valentini, E., Mari, S. et al. Nat Struct Mol Biol (2013) 20:696. DOI 10.1038/NSMB.2566 · 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
2XBB 2.68 Å, Nedd4 HECT: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…

Browse structure collections

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