9SDX: NEDD8

Name: PDB 9SDX: Structure of RBR binding E2 variant crosslinked with NEDD8-CUL5-RBX2 bound ARIH2 and Ub
Published: 2025-12-24
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Structure of RBR binding E2 variant crosslinked with NEDD8-CUL5-RBX2 bound ARIH2 and Ub. Determined by electron microscopy at 2.97 Å resolution. Released 24 Dec 2025.

Method: Electron microscopy
Resolution: 2.97 Å
Organisms: Homo sapiens, synthetic construct
Chains: 6
Atoms: 10,572
Mol. weight: 197.84 kDa
Ligands: SY8, ZN
Released: 24 Dec 2025

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

Secondary structure: helices and β-sheets

9SDX contains 61 α-helices and 46 β-strands across 6 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 C: 29 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	159-168	10
α-helix	176-180	5
α-helix	204-247	44
α-helix	257-266	10
α-helix	267-271	5
α-helix	274-282	9
α-helix	290-301	12
α-helix	308-327	20
α-helix	330-333	4
α-helix	337-354	18
α-helix	355-359	5
α-helix	363-377	15
α-helix	404-416	13
β-strand	417	1	8
α-helix	420-423	4
α-helix	427-441	15
α-helix	447-460	14
β-strand	467	1	8
α-helix	470-483	14
α-helix	487-514	28
α-helix	523-525	3
β-strand	526-532	7	2
α-helix	533-536	4
α-helix	549-552	4
α-helix	554-565	12
β-strand	569-573	5	2
β-strand	579-585	7	2
β-strand	590-596	7	2
α-helix	597-603	7
α-helix	604-606	3
β-strand	614	1	9
α-helix	616-622	7
α-helix	627-638	12
β-strand	648-650	3	9
β-strand	666-668	3	9
β-strand	685-687	3	2
α-helix	701-725	25
β-strand	728-730	3	10
α-helix	732-741	10
α-helix	750-762	13
β-strand	766-768	3	10
β-strand	775-778	4	10

Chain G: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	3-16	14
β-strand	22-25	4	6
β-strand	34-39	6	6
β-strand	51-56	6	6
α-helix	61-63	3
β-strand	67-70	4	6
β-strand	79	1	7
β-strand	85	1	7
α-helix	92-94	3
α-helix	101-113	13
α-helix	123-131	9
α-helix	135-138	4
α-helix	141-143	3

Chain H: 17 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	47-49	3
β-strand	61-64	4	11
α-helix	66-84	19
α-helix	88-97	10
α-helix	102-111	10
α-helix	115-119	5
α-helix	124-125	2
α-helix	166-175	10
β-strand	182	1	12
β-strand	191	1	12
α-helix	194-196	3
α-helix	204-221	18
β-strand	225-226	2	11
β-strand	236-239	4	11
β-strand	246-247	2	13
β-strand	256-257	2	13
α-helix	271-278	8
α-helix	286-293	8
β-strand	295-296	2	5
β-strand	303-306	4	5
β-strand	312-314	3	14
β-strand	321-323	3	14
α-helix	354-380	27
α-helix	383-398	16
α-helix	404-407	4
α-helix	410-432	23
α-helix	438-462	25
α-helix	469-487	19

Chain N: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
β-strand	12-16	5	1
α-helix	23-33	11
β-strand	42-44	3	1
β-strand	49	1	1
α-helix	50-51	2
β-strand	66-70	5	1

Chain R: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	31-43	13	2
β-strand	49	1	3
β-strand	56	1	3
α-helix	60-61	2
α-helix	62-66	5
β-strand	75-78	4	4
β-strand	83-85	3	4
α-helix	86-92	7
β-strand	108-111	4	4

Chain U: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	5
β-strand	12-16	5	5
α-helix	23-33	11
α-helix	38-40	3
β-strand	41-44	4	5
β-strand	49	1	5
α-helix	57-59	3
β-strand	66-73	8	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NEDD8	N	protein	81	Homo sapiens	Q15843 (AlphaFold model)
RING-box protein 2	R	protein	113	Homo sapiens	Q9UBF6 (AlphaFold model)
Ubiquitin	U	protein	75	Homo sapiens	P0CG48 (AlphaFold model)
L3A2-1	G	protein	157	synthetic construct
Cullin-5	C	protein	780	Homo sapiens	Q93034 (AlphaFold model)
E3 ubiquitin-protein ligase ARIH2	H	protein	493	Homo sapiens	O95376

Sequence of entity 1 (N), FASTA

>9SDX_1 NEDD8 (chains N)
MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYK
ILGGSVLHLVLALRGGGGLRQ

Sequence of entity 2 (R), FASTA

>9SDX_2 RING-box protein 2 (chains R)
MADVEDGEETCALASHSGSSGSKSGGDKMFSLKKWNAVAMWSWDVECDTCAICRVQVMDA
CLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVVQRIGK

Sequence of entity 3 (U), FASTA

>9SDX_3 Ubiquitin (chains U)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRG

Sequence of entity 4 (G), FASTA

>9SDX_4 L3A2-1 (chains G)
GSMVAASSRLMKELEEIRKAGMKNFRNIQVDEANLLTWQGLIVPDNPPYDKGAFRIEINF
PAEYPFKPPKITFKTKIYHPNIDEKGQVCLPVISAENWKPATKTDQVIQSLIALVNDPQP
EHPLRADLAEEYSKDRKKFAKNAEEFTKKYGEKRPVD

Sequence of entity 5 (C), FASTA

>9SDX_5 Cullin-5 (chains C)
MATSNLLKNKGSLQFEDKWDFMRPIVLKLLRQESVTKQQWFDLFSDVHAVCLWDDKGPAK
IHQALKEDILEFIKQAQARVLSHQDDTALLKAYIVEWRKFFTQCDILPKPFCQLEITLMG
KQGSNKKSNVEDSIVRKLMLDTWNESIFSNIKNRLQDSAMKLVHAERLGEAFDSQLVIGV
RESYVNLCSNPEDKLQIYRDNFEKAYLDSTERFYRTQAPSYLQQNGVQNYMKYADAKLKE
EEKRALRYLETRRECNSVEALMECCVNALVTSFKETILAECQGMIKRNETEKLHLMFSLM
DKVPNGIEPMLKDLEEHIISAGLADMVAAAETITTDSEKYVEQLLTLFNRFSKLVKEAFQ
DDPRFLTARDKAYKAVVNDATIFKLELPLKQKGVGLKTQPESKCPELLANYCDMLLRKTP
LSKKLTSEEIEAKLKEVLLVLKYVQNKDVFMRYHKAHLTRRLILDISADSEIEENMVEWL
REVGMPADYVNKLARMFQDIKVSEDLNQAFKEMHKNNKLALPADSVNIKILNAGAWSRSS
EKVFVSLPTELEDLIPEVEEFYKKNHSGRKLHWHHLMSNGIITFKNEVGQYDLEVTTFQL
AVLFAWNQRPREKISFENLKLATELPDAELRRTLWSLVAFPKLKRQVLLYEPQVNSPKDF
TEGTLFSVNQEFSLIKNAKVQKRGKINLIGRLQLTTERMREEENEGIVQLRILRTQEAII
QIMKMRKKISNAQLQTELVEILKNMFLPQKKMIKEQIEWLIEHKYIRRDESDINTFIYMA

Sequence of entity 6 (H), FASTA

>9SDX_6 E3 ubiquitin-protein ligase ARIH2 (chains H)
MSVDMNSQGSDSNEEDYDPNCEEEEEEEEDDPGDIEDYYVGVASDVEQQGADAFDPEEYQ
FTCLTYKESEGALNEHMTSLASVLKVSHSVAKLILVNFHWQVSEILDRYKSNSAQLLVEA
RVQPNPSKHVPTSHPPHHCAVCMQFVRKENLLSLACQHQFCRSCWEQHCSVLVKDGVGVG
VSCMAQDCPLRTPEDFVFPLLPNEELREKYRRYLFRDYVESHYQLQLCPGADCPMVIRVQ
EPRARRVQCNRCNEVFCFKCRQMYHAPTDCATIRKWLTKCADDSETANYISAHTKDCPKC
NICIEKNGGCNHMQCSKCKHDFCWMCLGDWKTHGSEYYECSRYKENPDIVNQSQQAQARE
ALKKYLFYFERWENHNKSLQLEAQTYQRIHEKIQERVMNNLGTWIDWQYLQNAAKLLAKC
RYTLQYTYPYAYYMESGPRKKLFEYQQAQLEAEIENLSWKVERADSYDRGDLENQMHIAE
QRRRTLLKDFHDT

Ligands and cofactors

ID	Name	Formula	Copies
SY8	5-azanylpentan-2-one	C5 H11 N O	1
ZN	Zinc ion	Zn	7

Primary citation

E2 variants for probing E3 ubiquitin ligase activities. Du, J., Andree, G.A., Horn-Ghetko, D. et al. Proc Natl Acad Sci U S A (2026) 123:e2524899122-e2524899122. DOI 10.1073/pnas.2524899122 · PubMed

Other PDB entries of the same protein (UniProt Q15843 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1NDD 1.6 Å, Structure of NEDD8
4FBJ 1.6 Å, Structure of the Cif:Nedd8 complex - Photorhabdus luminescens Cycle Inhibiting Factor in…
8WZN 1.8 Å, ParkinK211N in complex with phospho NEDD8
2BKR 1.9 Å, NEDD8 NEDP1 complex
4F8C 1.95 Å, Structure of the Cif:Nedd8 complex - Yersinia pseudotuberculosis Cycle Inhibiting Factor…
1XT9 2.2 Å, Crystal Structure of Den1 in complex with Nedd8
8WZO 2.25 Å, Parkin in complex with phospho NEDD8
4HCP 2.52 Å, crystal structure of Burkholderia pseudomallei effector protein chbp in complex with nedd8
8CAF 2.66 Å, N8C_Fab3b in complex with NEDD8-CUL1(WHB)
2NVU 2.8 Å, Structure of APPBP1-UBA3~NEDD8-NEDD8-MgATP-Ubc12(C111A), a trapped ubiquitin-like…
3DBH 2.85 Å, Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by…
3DBL 2.9 Å, Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by…

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