3DPL: Cullin-5

Name: PDB 3DPL: Structural Insights into NEDD8 Activation of Cullin-RING Ligases: Conformational Control of Conjugation.
Published: 2008-09-30
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Structural Insights into NEDD8 Activation of Cullin-RING Ligases: Conformational Control of Conjugation. Determined by X-ray diffraction at 2.6 Å resolution. Released 30 Sept 2008.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,932
Mol. weight: 57.28 kDa
Ligands: ZN
Released: 30 Sept 2008

Explore 3DPL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3DPL contains 25 α-helices and 21 β-strands across 2 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: 21 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	405-416	12
β-strand	417	1	1
α-helix	420-423	4
α-helix	427-438	12
α-helix	439-443	5
α-helix	447-463	17
β-strand	467	1	1
α-helix	470-482	13
α-helix	487-513	27
α-helix	523-525	3
β-strand	526-532	7	2
α-helix	533-536	4
α-helix	546-548	3
α-helix	549-552	4
α-helix	555-563	9
β-strand	569-573	5	2
α-helix	575-577	3
β-strand	579-585	7	2
β-strand	590-596	7	2
α-helix	597-603	7
α-helix	604-606	3
β-strand	614-615	2	3
α-helix	616-623	8
α-helix	627-638	12
β-strand	648-650	3	3
α-helix	657-659	3
β-strand	665-668	4	3
β-strand	674-675	2	4
β-strand	680-681	2	4
β-strand	683-687	5	2
α-helix	697-723	27
β-strand	728-729	2	5
α-helix	731-741	11
α-helix	750-762	13
β-strand	766-769	4	5
β-strand	772-778	7	5

Chain R: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	22-35	14	2
α-helix	40-42	3
α-helix	56-59	4
β-strand	70-73	4	6
β-strand	78-80	3	6
α-helix	81-88	8
β-strand	93	1	7
β-strand	100	1	7
α-helix	101	1
β-strand	103-105	3	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cullin-5	C	protein	382	Homo sapiens	Q93034 (AlphaFold model)
RING-box protein 1	R	protein	106	Homo sapiens	P62877 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>3DPL_1 Cullin-5 (chains C)
GSESKCPEELANYCDMLLRKTPLSKKLTSEEIEAKLKEVLKKLKYVQNKDVFMRYHKAHL
TRRLILDISADSEIEENMVEWLREVGMPADYVNKLARMFQDIKVSEDLNQAFKEMHKNNK
LALPADSVNIKILNAGAWSRSSEKVFVSLPTELEDLIPEVEEFYKKNHSGRKLHWHHLMS
NGIITFKNEVGQYDLEVTTFQLAVLFAWNQRPREKISFENLKLATELPDAELRRTLWSLV
AFPKLKRQVLLYEPQVNSPKDFTEGTLFSVNQEFSLIKNAKVQKRGKINLIGRLQLTTER
MREEENEGIVQLRILRTQEAIIQIMKMRKKISNAQLQTELVEILKNMFLPQKKMIKEQIE
WLIEHKYIRRDESDINTFIYMA

Sequence of entity 2 (R), FASTA

>3DPL_2 RING-box protein 1 (chains R)
GSMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQAS
ATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3

Primary citation

Structural insights into NEDD8 activation of cullin-RING ligases: conformational control of conjugation. Duda, D.M., Borg, L.A., Scott, D.C. et al. Cell (2008) 134:995-1006. DOI 10.1016/j.cell.2008.07.022 · PubMed

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

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
7ONI 3.4 Å, Structure of Neddylated CUL5 C-terminal region-RBX2-ARIH2*
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)

Browse structure collections

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