7ONI: Neddylated CUL5 C-terminal region-RBX2-ARIH2*

Name: PDB 7ONI: Structure of Neddylated CUL5 C-terminal region-RBX2-ARIH2*
Published: 2021-09-15
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Structure of Neddylated CUL5 C-terminal region-RBX2-ARIH2*. Determined by electron microscopy at 3.4 Å resolution. Released 15 Sept 2021.

Method: Electron microscopy
Resolution: 3.4 Å
Organism: Homo sapiens
Chains: 4
Atoms: 8,840
Mol. weight: 171.08 kDa
Ligands: ZN
Released: 15 Sept 2021

Explore 7ONI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7ONI contains 51 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: 28 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	153-168	16
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	274-284	11
α-helix	290-302	13
α-helix	308-328	21
α-helix	337-359	23
α-helix	363-377	15
α-helix	404-416	13
β-strand	417	1	1
α-helix	420-424	5
α-helix	427-441	15
α-helix	447-464	18
β-strand	467	1	1
α-helix	470-483	14
α-helix	487-514	28
α-helix	523-525	3
β-strand	526-527	2	2
β-strand	530-532	3	3
α-helix	549-552	4
α-helix	555-565	11
β-strand	569-573	5	3
β-strand	579-585	7	2
β-strand	590-596	7	2
α-helix	597-604	8
β-strand	614-615	2	4
α-helix	616-622	7
α-helix	627-638	12
β-strand	648-650	3	4
α-helix	657-659	3
β-strand	665-668	4	4
β-strand	685	1	2
α-helix	701-725	25
β-strand	728-729	2	5
α-helix	732-741	10
α-helix	747-749	3
α-helix	750-761	12
β-strand	766-768	3	5
β-strand	776-778	3	5

Chain H: 17 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	42-45	4
α-helix	61	1
β-strand	62-64	3	6
α-helix	66-84	19
α-helix	88-97	10
α-helix	102-111	10
α-helix	113-119	7
β-strand	151-152	2	7
β-strand	160-161	2	7
α-helix	162-174	13
β-strand	182	1	8
β-strand	191	1	8
α-helix	194-197	4
α-helix	198-200	3
α-helix	204-221	18
β-strand	225-227	3	6
β-strand	236-238	3	6
β-strand	246-249	4	9
β-strand	254-257	4	9
α-helix	272-281	10
α-helix	354-380	27
α-helix	382-398	17
α-helix	409-425	17
α-helix	428-432	5
α-helix	438-461	24
α-helix	469-488	20

Chain N: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	11
β-strand	12-16	5	11
β-strand	22	1	12
α-helix	23-33	11
α-helix	38-40	3
β-strand	41-45	5	11
β-strand	48-49	2	11
α-helix	50-51	2
β-strand	55	1	12
α-helix	56-59	4
β-strand	66-71	6	11

Chain R: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	31-36	6	2
β-strand	39-43	5	3
α-helix	62-67	6
β-strand	75-78	4	10
β-strand	84-85	2	10
α-helix	86-95	10
β-strand	108-111	4	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cullin-5	C	protein	780	Homo sapiens	Q93034 (AlphaFold model)
E3 ubiquitin-protein ligase ARIH2	H	protein	495	Homo sapiens	O95376 (AlphaFold model)
RING-box protein 2	R	protein	111	Homo sapiens	Q9UBF6 (AlphaFold model)
NEDD8	N	protein	83	Homo sapiens	Q15843 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>7ONI_1 Cullin-5 (chains C)
MATSNLLKNKGSLQFEDKWDFMRPIVLKLLRQESVTKQQWFDLFSDVHAVCLWDDKGPAK
IHQALKEDILEFIKQAQARVLSHQDDTALLKAYIVEWRKFFTQCDILPKPFCQLEITLMG
KQGSNKKSNVEDSIVRKLMLDTWNESIFSNIKNRLQDSAMKLVHAERLGEAFDSQLVIGV
RESYVNLCSNPEDKLQIYRDNFEKAYLDSTERFYRTQAPSYLQQNGVQNYMKYADAKLKE
EEKRALRYLETRRECNSVEALMECCVNALVTSFKETILAECQGMIKRNETEKLHLMFSLM
DKVPNGIEPMLKDLEEHIISAGLADMVAAAETITTDSEKYVEQLLTLFNRFSKLVKEAFQ
DDPRFLTARDKAYKAVVNDATIFKLELPLKQKGVGLKTQPESKCPELLANYCDMLLRKTP
LSKKLTSEEIEAKLKEVLLVLKYVQNKDVFMRYHKAHLTRRLILDISADSEIEENMVEWL
REVGMPADYVNKLARMFQDIKVSEDLNQAFKEMHKNNKLALPADSVNIKILNAGAWSRSS
EKVFVSLPTELEDLIPEVEEFYKKNHSGRKLHWHHLMSNGIITFKNEVGQYDLEVTTFQL
AVLFAWNQRPREKISFENLKLATELPDAELRRTLWSLVAFPKLKRQVLLYEPQVNSPKDF
TEGTLFSVNQEFSLIKNAKVQKRGKINLIGRLQLTTERMREEENEGIVQLRILRTQEAII
QIMKMRKKISNAQLQTELVEILKNMFLPQKKMIKEQIEWLIEHKYIRRDESDINTFIYMA

Sequence of entity 2 (H), FASTA

>7ONI_2 E3 ubiquitin-protein ligase ARIH2 (chains H)
GSMSVDMNSQGSDSNEEDYDPNCEEEEEEEEDDPGDIEDYYVGVASDVEQQGADAFDPEE
YQFTCLTYKESEGALNEHMTSLASVLKVSHSVAKLILVNFHWQVSEILDRYKSNSAQLLV
EARVQPNPSKHVPTSHPPHHCAVCMQFVRKENLLSLACQHQFCRSCWEQHCSVLVKDGVG
VGVSCMAQDCPLRTPEDFVFPLLPNEELREKYRRYLFRDYVESHYQLQLCPGADCPMVIR
VQEPRARRVQCNRCNEVFCFKCRQMYHAPTDCATIRKWLTKCADDSETANYISAHTKDCP
KCNICIEKNGGCNHMQCSKCKHDFCWMCLGDWKTHGSEYYECSRYKENPDIVNQSQQAQA
REALKKYLFYFERWENHNKSLQAAAQTYQRIHEKIQERVMNNLGTWIDWQYLQNAAKLLA
KCRYTLQYTYPYAYYMESGPRKKLFEYQQAQLEAEIANLSWKVERADSYDRGDLENQMHI
AEQRRRTLLKDFHDT

Sequence of entity 3 (R), FASTA

>7ONI_3 RING-box protein 2 (chains R)
GSEDGEETCALASHSGSSGSKSGGDKMFSLKKWNAVAMWSWDVECDTCAICRVQVMDACL
RCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVVQRIGK

Sequence of entity 4 (N), FASTA

>7ONI_4 NEDD8 (chains N)
GSMLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAAD
YKILGGSVLHLVLALRGGGGLRQ

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	7

Primary citation

CUL5-ARIH2 E3-E3 ubiquitin ligase structure reveals cullin-specific NEDD8 activation. Kostrhon, S., Prabu, J.R., Baek, K. et al. Nat Chem Biol (2021) 17:1075-1083. DOI 10.1038/s41589-021-00858-8 · PubMed

Other PDB entries of the same protein (UniProt Q93034 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3DPL 2.6 Å, Structural Insights into NEDD8 Activation of Cullin-RING Ligases: Conformational Control…
8EI2 2.8 Å, Crystal structure of the N-terminal domain of CUL5 in complex with H314, a Helicon…
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
3DQV 3.0 Å, Structural Insights into NEDD8 Activation of Cullin-RING Ligases: Conformational Control…
4JGH 3.0 Å, Structure of the SOCS2-Elongin BC complex bound to an N-terminal fragment of Cullin5
9SDY 3.06 Å, Structure of RBR E2 variant binding to CUL5-RBX2 bound ARIH2
8FVI 3.24 Å, Human APOBEC3H bound to HIV-1 Vif in complex with CBF-beta, ELOB, ELOC, and CUL5
4N9F 3.3 Å, Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex
9EG1 3.52 Å, COP9 signalosome deneddylation complex with cullin-5
8FVJ 3.54 Å, Dimeric form of HIV-1 Vif in complex with human CBF-beta, ELOB, ELOC, and CUL5
9OMA 4.14 Å, Cryo-EM structure of PCMTD1-ELOBC-CUL5-RBX2 (CRL5-PCMTD1)

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