9SDY: RBR E2 variant binding to CUL5-RBX2 bound ARIH2

Name: PDB 9SDY: Structure of RBR E2 variant binding to CUL5-RBX2 bound ARIH2
Published: 2025-12-24
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Structure of RBR E2 variant binding to CUL5-RBX2 bound ARIH2. Determined by electron microscopy at 3.06 Å resolution. Released 24 Dec 2025.

Method: Electron microscopy
Resolution: 3.06 Å
Organisms: synthetic construct, Homo sapiens
Chains: 4
Atoms: 9,073
Mol. weight: 179.99 kDa
Ligands: ZN
Released: 24 Dec 2025

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

Secondary structure: helices and β-sheets

9SDY contains 55 α-helices and 35 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 C: 29 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	156-168	13
α-helix	175-187	13
α-helix	196-200	5
α-helix	203-248	46
α-helix	257-269	13
α-helix	271-273	3
α-helix	274-278	5
α-helix	281-285	5
α-helix	290-300	11
α-helix	308-328	21
α-helix	338-359	22
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	447-464	18
β-strand	467	1	8
α-helix	471-483	13
α-helix	487-513	27
α-helix	523-525	3
β-strand	526-532	7	4
α-helix	549-565	17
β-strand	569-573	5	4
β-strand	579-585	7	4
β-strand	590-596	7	4
α-helix	597-603	7
α-helix	604-606	3
β-strand	614-615	2	9
α-helix	616-623	8
α-helix	627-638	12
β-strand	648-650	3	9
α-helix	657-659	3
β-strand	665-668	4	9
β-strand	685-687	3	4
α-helix	697-699	3
α-helix	701-724	24
α-helix	734-741	8
α-helix	750-763	14

Chain G: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	5-17	13
β-strand	22	1	1
β-strand	26	1	2
β-strand	34-37	4	2
β-strand	39	1	1
β-strand	53-56	4	2
α-helix	61-63	3
α-helix	65-66	2
β-strand	67-70	4	2
β-strand	79	1	3
β-strand	85	1	3
α-helix	101-113	13
α-helix	123-129	7
α-helix	134-137	4
α-helix	139-146	8

Chain H: 17 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	62-64	3	10
α-helix	66-83	18
α-helix	88-97	10
α-helix	102-119	18
α-helix	124-125	2
α-helix	148-150	3
β-strand	151-153	3	11
β-strand	159-161	3	11
α-helix	162-175	14
β-strand	182	1	12
β-strand	191	1	12
α-helix	192-193	2
α-helix	194-196	3
α-helix	209-221	13
β-strand	225-227	3	10
β-strand	236-238	3	10
β-strand	246-248	3	13
β-strand	255-257	3	13
α-helix	270-279	10
α-helix	353-398	46
α-helix	404-406	3
α-helix	409-425	17
α-helix	428-431	4
α-helix	434-435	2
α-helix	438-462	25
α-helix	469-486	18

Chain R: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	31-43	13	4
β-strand	49	1	5
β-strand	56	1	5
α-helix	62-66	5
β-strand	75-78	4	6
β-strand	83-85	3	6
α-helix	86-93	8
β-strand	98	1	7
β-strand	105	1	7
β-strand	108-111	4	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
L3A2-1	G	protein	155	synthetic construct
RING-box protein 2	R	protein	113	Homo sapiens	Q9UBF6 (AlphaFold model)
Cullin-5	C	protein	780	Homo sapiens	Q93034 (AlphaFold model)
E3 ubiquitin-protein ligase ARIH2	H	protein	493	Homo sapiens	O95376 (AlphaFold model)

Sequence of entity 1 (G), FASTA

>9SDY_1 L3A2-1 (chains G)
MVAASSRLMKELEEIRKAGMKNFRNIQVDEANLLTWQGLIVPDNPPYDKGAFRIEINFPA
EYPFKPPKITFKTKIYHPNIDEKGQVCLPVISAENWKPATKTDQVIQSLIALVNDPQPEH
PLRADLAEEYSKDRKKFAKNAEEFTKKYGEKRPVD

Sequence of entity 2 (R), FASTA

>9SDY_2 RING-box protein 2 (chains R)
MADVEDGEETCALASHSGSSGSKSGGDKMFSLKKWNAVAMWSWDVECDTCAICRVQVMDA
CLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVVQRIGK

Sequence of entity 3 (C), FASTA

>9SDY_3 Cullin-5 (chains C)
MATSNLLKNKGSLQFEDKWDFMRPIVLKLLRQESVTKQQWFDLFSDVHAVCLWDDKGPAK
IHQALKEDILEFIKQAQARVLSHQDDTALLKAYIVEWRKFFTQCDILPKPFCQLEITLMG
KQGSNKKSNVEDSIVRKLMLDTWNESIFSNIKNRLQDSAMKLVHAERLGEAFDSQLVIGV
RESYVNLCSNPEDKLQIYRDNFEKAYLDSTERFYRTQAPSYLQQNGVQNYMKYADAKLKE
EEKRALRYLETRRECNSVEALMECCVNALVTSFKETILAECQGMIKRNETEKLHLMFSLM
DKVPNGIEPMLKDLEEHIISAGLADMVAAAETITTDSEKYVEQLLTLFNRFSKLVKEAFQ
DDPRFLTARDKAYKAVVNDATIFKLELPLKQKGVGLKTQPESKCPELLANYCDMLLRKTP
LSKKLTSEEIEAKLKEVLLVLKYVQNKDVFMRYHKAHLTRRLILDISADSEIEENMVEWL
REVGMPADYVNKLARMFQDIKVSEDLNQAFKEMHKNNKLALPADSVNIKILNAGAWSRSS
EKVFVSLPTELEDLIPEVEEFYKKNHSGRKLHWHHLMSNGIITFKNEVGQYDLEVTTFQL
AVLFAWNQRPREKISFENLKLATELPDAELRRTLWSLVAFPKLKRQVLLYEPQVNSPKDF
TEGTLFSVNQEFSLIKNAKVQKRGKINLIGRLQLTTERMREEENEGIVQLRILRTQEAII
QIMKMRKKISNAQLQTELVEILKNMFLPQKKMIKEQIEWLIEHKYIRRDESDINTFIYMA

Sequence of entity 4 (H), FASTA

>9SDY_4 E3 ubiquitin-protein ligase ARIH2 (chains H)
MSVDMNSQGSDSNEEDYDPNCEEEEEEEEDDPGDIEDYYVGVASDVEQQGADAFDPEEYQ
FTCLTYKESEGALNEHMTSLASVLKVSHSVAKLILVNFHWQVSEILDRYKSNSAQLLVEA
RVQPNPSKHVPTSHPPHHCAVCMQFVRKENLLSLACQHQFCRSCWEQHCSVLVKDGVGVG
VSCMAQDCPLRTPEDFVFPLLPNEELREKYRRYLFRDYVESHYQLQLCPGADCPMVIRVQ
EPRARRVQCNRCNEVFCFKCRQMYHAPTDCATIRKWLTKCADDSETANYISAHTKDCPKC
NICIEKNGGCNHMQCSKCKHDFCWMCLGDWKTHGSEYYECSRYKENPDIVNQSQQAQARE
ALKKYLFYFERWENHNKSLQLEAQTYQRIHEKIQERVMNNLGTWIDWQYLQNAAKLLAKC
RYTLQYTYPYAYYMESGPRKKLFEYQQAQLEAEIENLSWKVERADSYDRGDLENQMHIAE
QRRRTLLKDFHDT

Ligands and cofactors

ID	Name	Formula	Copies
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 Q9UBF6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9T7V 2.95 Å, Structure of LRRC58-EloB/C-CDO1 in complex with NEDD8-CUL5-RBX2-ARIH2-Ub
9SDX 2.97 Å, Structure of RBR binding E2 variant crosslinked with NEDD8-CUL5-RBX2 bound ARIH2 and Ub
7ONI 3.4 Å, Structure of Neddylated CUL5 C-terminal region-RBX2-ARIH2*
9EG1 3.52 Å, COP9 signalosome deneddylation complex with cullin-5
9OMA 4.14 Å, Cryo-EM structure of PCMTD1-ELOBC-CUL5-RBX2 (CRL5-PCMTD1)
2ECL Solution Structure of the RING domain of the human RING-box protein 2
9A1I Integrative structure determination of the A3G-CRL5-Vif complex (rigid)
9A1J Integrative structure determination of the A3G-CRL5-Vif complex (flexible)

Browse structure collections

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