9GIK: Full-lenght Nedd4-2 E3 ubiquitin ligase

Full-lenght Nedd4-2 E3 ubiquitin ligase. Determined by electron microscopy at 3.58 Å resolution. Released 4 Jun 2025.

Method: Electron microscopy
Resolution: 3.58 Å
Organism: Homo sapiens
Chains: 1
Atoms: 5,321
Mol. weight: 110.47 kDa
Released: 4 Jun 2025

Explore 9GIK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9GIK contains 37 α-helices and 34 β-strands across 1 chain. 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: 37 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	20-30	11	1
α-helix	37-39	3
β-strand	44-51	8	2
β-strand	56-62	7	2
α-helix	63-67	5
β-strand	76-82	7	1
β-strand	87-94	8	2
β-strand	104-110	7	2
β-strand	117	1	3
α-helix	124-126	3
β-strand	129-132	4	1
β-strand	134	1	2
β-strand	145-151	7	1
β-strand	152	1	3
α-helix	192-196	5
β-strand	199-203	5	4
β-strand	209-213	5	4
β-strand	218-220	3	4
α-helix	223-225	3
α-helix	233	1
α-helix	234-238	5
α-helix	239-251	13
α-helix	252	1
β-strand	253	1	5
α-helix	254	1
α-helix	255-257	3
α-helix	529-531	3
β-strand	534-538	5	6
α-helix	540-542	3
β-strand	544-548	5	6
β-strand	554-555	2	6
α-helix	577-587	11
β-strand	599-602	4	7
α-helix	604-606	3
α-helix	609-616	8
α-helix	621-625	5
β-strand	629-632	4	7
α-helix	644-655	12
α-helix	658-660	3
β-strand	663-665	3	8
β-strand	673-675	3	8
α-helix	679-682	4
α-helix	686-703	18
β-strand	711	1	8
α-helix	713-720	8
α-helix	722-724	3
α-helix	726-731	6
α-helix	734-745	12
β-strand	754	1	9
β-strand	756-761	6	10
β-strand	764-769	6	10
α-helix	774-776	3
β-strand	778	1	9
α-helix	784-792	9
α-helix	793-797	5
α-helix	801-811	11
α-helix	817-819	3
α-helix	827-833	7
β-strand	835	1	5
α-helix	840-845	6
β-strand	847-850	4	11
α-helix	858-869	12
α-helix	872-883	12
α-helix	893-895	3
β-strand	897-898	2	12
β-strand	901-902	2	12
β-strand	905-909	5	11
α-helix	916-917	2
β-strand	918-920	3	11
β-strand	925-928	4	11
α-helix	934-947	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform 5 of E3 ubiquitin-protein ligase NEDD4-like	A	protein	959	Homo sapiens	Q96PU5 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9GIK_1 Isoform 5 of E3 ubiquitin-protein ligase NEDD4-like (chains A)
GLGSMATGLGEPVYGLSEDEGESRILRVKVVSGIDLAKKDIFGASDPYVKLSLYVADENR
ELALVQTKTIKKTLNPKWNEEFYFRVNPSNHRLLFEVFDENRLTRDDFLGQVDVPLSHLP
TEDPTMERPYTFKDFLLRPRSHKSRVKGFLRLKMAYMPKNGGQDEENSDQRDDMEHGWEV
VDSNDSASQHQEELPPPPLPPGWEEKVDNLGRTYYVNHNNRTTQWHRPSLMDVSSESDNN
IRQINQEAAHRRFRSRRHISEDLEPEPSEGGDVPEPWETISEEVNIAGDSLGLALPPPPA
SPGSRTSPQELSEELSRRLQITPDSNGEQFSSLIQREPSSRLRSCSVTDAVAEQGHLPPP
SVAYVHTTPGLPSGWEERKDAKGRTYYVNHNNRTTTWTRPIMQLAEDGASGSATNSNNHL
IEPQIRRPRSLSSPTVTLSAPLEGAKDSPVRRAVKDTLSNPQSPQPSPYNSPKPQHKVTQ
SFLPPGWEMRIAPNGRPFFIDHNTKTTTWEDPRLKFPVHMRSKTSLNPNDLGPLPPGWEE
RIHLDGRTFYIDHNSKITQWEDPRLQNPAITGPAVPYSREFKQKYDYFRKKLKKPADIPN
RFEMKLHRNNIFEESYRRIMSVKRPDVLKARLWIEFESEKGLDYGGVAREWFFLLSKEMF
NPYYGLFEYSATDNYTLQINPNSGLCNEDHLSYFTFIGRVAGLAVFHGKLLDGFFIRPFY
KMMLGKQITLNDMESVDSEYYNSLKWILENDPTELDLMFCIDEENFGQTYQVDLKPNGSE
IMVTNENKREYIDLVIQWRFVNRVQKQMNAFLEGFTELLPIDLIKIFDENELELLMCGLG
DVDVNDWRQHSIYKNGYCPNHPVIQWFWKAVLLMDAEKRIRLLQFVTGTSRVPMNGFAEL
YGSNGPQLFTIEQWGSPEKLPRAHTCFNRLDLPPYETFEDLREKLLMAVENAQGFEGVD

Primary citation

Structural basis of ubiquitin ligase Nedd4-2 autoinhibition and regulation by calcium and 14-3-3 proteins. Janosev, M., Kosek, D., Tekel, A. et al. Nat Commun (2025) 16:4875-4875. DOI 10.1038/s41467-025-60207-4 · PubMed

Other PDB entries of the same protein (UniProt Q96PU5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7LP1 1.35 Å, Structure of Nedd4L WW3 domain
7LP3 1.61 Å, Structure of Nedd4L WW3 domain
6ZBT 1.8 Å, Structure of 14-3-3 gamma in complex with Nedd4-2 14-3-3 binding motif Ser342
2NSQ 1.85 Å, Crystal structure of the C2 domain of the human E3 ubiquitin-protein ligase NEDD4-like…
7LP2 1.88 Å, Structure of Nedd4L WW3 domain
6ZC9 1.9 Å, Structure of 14-3-3 gamma in complex with Nedd4-2 14-3-3 binding motif Ser448
2ONI 2.2 Å, Catalytic Domain of the Human NEDD4-like E3 Ligase
7NMZ 2.3 Å, Structure of 14-3-3 eta in complex with Nedd4-2(335-455) containing two 14-3-3 binding…
5HPK 2.43 Å, System-wide modulation of HECT E3 ligases with selective ubiquitin variant probes:…
9Z5Q 3.06 Å, HECT domain of NEDD4-2 complex with a targeted nanobody, nb.C11
3JW0 3.1 Å, E2~Ubiquitin-HECT
3JVZ 3.3 Å, E2~Ubiquitin-HECT

Browse structure collections

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