4P5O: Cullin-1

Structure of an RBX1-UBC12~NEDD8-CUL1-DCN1 complex: a RING-E3-E2~ubiquitin-like protein-substrate intermediate trapped in action. Determined by X-ray diffraction at 3.11 Å resolution. Released 2 Jul 2014.

Method: X-ray diffraction
Resolution: 3.11 Å
Organism: Homo sapiens
Chains: 10
Atoms: 13,577
Mol. weight: 217.84 kDa
Ligands: ZN
Released: 2 Jul 2014

Explore 4P5O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4P5O contains 81 α-helices and 80 β-strands across 10 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 A: 13 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	420-430	11
β-strand	431	1	1
α-helix	439-455	17
α-helix	459-476	18
β-strand	479	1	1
α-helix	482-496	15
α-helix	498-525	28
β-strand	534-540	7	2
α-helix	559-573	15
β-strand	577-591	15	2
β-strand	600-604	5	2
α-helix	605-609	5
β-strand	621	1	3
α-helix	622-629	8
α-helix	633-644	12
β-strand	668	1	3
α-helix	694-722	29
β-strand	724-726	3	4
α-helix	727-738	12
α-helix	746-758	13
β-strand	762-764	3	4
α-helix	765	1
β-strand	771-774	4	4

Chain B: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	26-35	10	2
β-strand	41	1	5
β-strand	48	1	5
α-helix	52-53	2
α-helix	54-57	4
β-strand	70-72	3	6
β-strand	78-80	3	6
α-helix	81-90	10
α-helix	99-101	3

Chain C: 13 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	420-430	11
β-strand	431	1	16
α-helix	439-455	17
α-helix	459-475	17
β-strand	479	1	16
α-helix	482-496	15
α-helix	498-523	26
β-strand	538-540	3	17
α-helix	559-573	15
β-strand	577-590	14	17
β-strand	601-604	4	17
α-helix	605-608	4
α-helix	622-628	7
α-helix	633-644	12
α-helix	694-722	29
β-strand	724-726	3	18
α-helix	727-738	12
α-helix	746-758	13
β-strand	762-764	3	18
α-helix	765	1
β-strand	771-774	4	18

Chain D: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	26-35	10	17
β-strand	41	1	19
β-strand	48	1	19
α-helix	52-53	2
α-helix	54-57	4
β-strand	70-72	3	20
β-strand	73	1	21
β-strand	78-80	3	20
α-helix	81-90	10
α-helix	99-101	3
β-strand	103	1	21

Chain E: 14 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	63-72	10
β-strand	80-81	2	7
α-helix	82	1
α-helix	83-92	10
α-helix	100-108	9
β-strand	113	1	8
β-strand	116	1	8
β-strand	117-118	2	7
α-helix	119-129	11
α-helix	134-138	5
α-helix	141-145	5
α-helix	155-165	11
β-strand	173	1	9
α-helix	182-185	4
α-helix	193-198	6
α-helix	207	1
β-strand	208	1	9
α-helix	209	1
α-helix	210-222	13
α-helix	238-251	14

Chain F: 13 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	65-72	8
β-strand	80-81	2	22
α-helix	82	1
α-helix	83-92	10
α-helix	100-108	9
β-strand	113	1	23
β-strand	116	1	23
β-strand	117-118	2	22
α-helix	119-128	10
α-helix	134-138	5
α-helix	141-145	5
α-helix	155-165	11
β-strand	172-173	2	24
α-helix	182-185	4
α-helix	193-198	6
α-helix	207	1
β-strand	208-209	2	24
α-helix	210-222	13
α-helix	238-251	14

Chain G: 9 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	4-12	9
α-helix	34-39	6
β-strand	47-50	4	25
β-strand	59-64	6	25
β-strand	76-81	6	25
α-helix	90-91	2
β-strand	92-95	4	25
β-strand	101	1	26
β-strand	104	1	26
β-strand	109	1	25
β-strand	110	1	26
β-strand	112	1	27
α-helix	113-115	3
α-helix	125-137	13
α-helix	147-155	9
α-helix	157-169	13
β-strand	171-172	2	28
α-helix	176	1
β-strand	177-178	2	28
α-helix	179-180	2

Chain H: 1 helix, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	29
β-strand	12-16	5	29
β-strand	22	1	30
α-helix	23-34	12
β-strand	42-45	4	29
β-strand	48-49	2	29
β-strand	55	1	30
β-strand	66-70	5	29
β-strand	75	1	27

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cullin-1	A, C	protein	368	Homo sapiens	Q13616 (AlphaFold model)
E3 ubiquitin-protein ligase RBX1	B, D	protein	106	Homo sapiens	P62877 (AlphaFold model)
DCN1-like protein 1	E, F	protein	200	Homo sapiens	Q96GG9 (AlphaFold model)
NEDD8-conjugating enzyme Ubc12	G, I	protein	189	Homo sapiens	P61081 (AlphaFold model)
NEDD8	H, K	protein	81	Homo sapiens	Q15843

Sequence of entity 1 (A, C), FASTA

>4P5O_1 Cullin-1 (chains A, C)
GSMAQSSSKSPEELARYCDSLLKKSSKNPEEAELEDTLNQVMEKFKKIEDKDVFQKFYAK
MLAKRLVHQNSASDDAEASMISKLKQACGFEYTSKLQRMFQDIGVSKDLNEQFKKHLTNS
EPLDLDFSIQVLSSGSWPFQQSCTFALPSELERSYQRFTAFYASRHSGRKLTWLYQLSKG
ELVTNCFKNRYTLQASTFQMAILLQYNTEDAYTVQQLTDSTQIKMDILAQVLQILLKSKL
LVLEDENANVDEVELKPDTLIKLYLGYKNKKLRVNINVPMKTEQKQEQETTHKNIEEDRK
LLIQAAIVRIMRMRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYLERVDGE
KDTYSYLA

Sequence of entity 2 (B, D), FASTA

>4P5O_2 E3 ubiquitin-protein ligase RBX1 (chains B, D)
GSMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQAS
ATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH

Sequence of entity 3 (E, F), FASTA

>4P5O_3 DCN1-like protein 1 (chains E, F)
GSRKKLEQLYNRYKDPQDENKIGIDGIQQFCDDLALDPASISVLIIAWKFRAATQCEFSK
QEFMDGMTELGCDSIEKLKAQIPKMEQELKEPGRFKDFYQFTFNFAKNPGQKGLDLEMAI
AYWNLVLNGRFKFLDLWNKFLLEHHKRSIPKDTWNLLLDFSTMIADDMSNYDEEGAWPVL
IDDFVEFARPQIAGTKSTTV

Sequence of entity 4 (G, I), FASTA

>4P5O_4 NEDD8-conjugating enzyme Ubc12 (chains G, I)
MIKLFSLKQQKKEEESAGGTKGSSKKASAAQLRIQKDINELNLPKTCDISFSDPDDLLNF
KLVICPDEGFYKSGKFVFSFKVGQGYPHDPPKVKCETMVYHPSIDLEGNVSLNILREDWK
PVLTINSIIYGLQYLFLEPNPEDPLNKEAAEVLQNNRRLFEQNVQRSMRGGYIGSTYFER
CLKHHHHHH

Sequence of entity 5 (H, K), FASTA

>4P5O_5 NEDD8 (chains H, K)
GSGGSMLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKT
AADYKILGGSVLHLVLALRGG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	6

Primary citation

Structure of a RING E3 Trapped in Action Reveals Ligation Mechanism for the Ubiquitin-like Protein NEDD8. Scott, D.C., Sviderskiy, V.O., Monda, J.K. et al. Cell (2014) 157:1671-1684. DOI 10.1016/j.cell.2014.04.037 · PubMed

Other PDB entries of the same protein (UniProt Q13616 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3TDU 1.5 Å, N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein…
5V89 1.55 Å, Structure of DCN4 PONY domain bound to CUL1 WHB
3TDZ 2.0 Å, N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein…
8CAF 2.66 Å, N8C_Fab3b in complex with NEDD8-CUL1(WHB)
7Z8R 2.7 Å, CAND1-CUL1-RBX1
7Z8V 2.7 Å, CAND1-SCF-SKP2 (SKP1deldel) CAND1 engaged SCF rocked
8OR3 2.9 Å, CAND1-CUL1-RBX1-SKP1-SKP2-DCNL1
9QO4 2.95 Å, Dissociation-state-3 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex
1LDJ 3.0 Å, Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex
4F52 3.0 Å, Structure of a Glomulin-RBX1-CUL1 complex
7Z8T 3.0 Å, CAND1-SCF-SKP2 CAND1 engaged SCF rocked
9XZL 3.0 Å, Cryo-EM structure of F-box helicase 1 (FBH1) bound to an SCF ubiquitin ligase complex…

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