5IGO: E3 ubiquitin-protein ligase COP1

WD40 domain of Arabidopsis thaliana E3 Ubiquitin Ligase COP1 in complex with peptide from Trib1. Determined by X-ray diffraction at 1.6 Å resolution. Released 20 Apr 2016.

Method: X-ray diffraction
Resolution: 1.6 Å
Organisms: Arabidopsis thaliana, Homo sapiens
Chains: 8
Atoms: 11,580
Mol. weight: 156.46 kDa
Released: 20 Apr 2016

Explore 5IGO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5IGO contains 14 α-helices and 120 β-strands across 8 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: 3 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	356-362	7	1
β-strand	374-379	6	2
β-strand	385-390	6	2
β-strand	394-399	6	2
α-helix	400-405	6
α-helix	407	1
β-strand	415-418	4	2
β-strand	423-428	6	3
β-strand	435-440	6	3
β-strand	445-449	5	3
β-strand	454-459	6	3
β-strand	466-471	6	4
β-strand	478-483	6	4
β-strand	487-492	6	4
β-strand	500-503	4	4
β-strand	508-513	6	5
β-strand	520-525	6	5
β-strand	530-534	5	5
β-strand	543-545	3	5
β-strand	552-557	6	6
β-strand	562-567	6	6
β-strand	571-576	6	6
β-strand	581-586	6	6
β-strand	594	1	7
β-strand	598-600	3	8
β-strand	604-607	4	8
β-strand	613-618	6	8
β-strand	626-629	4	8
α-helix	633-636	4
β-strand	647-652	6	1
β-strand	658-663	6	1
β-strand	668-673	6	1

Chain B: 3 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	355-362	8	9
β-strand	374-379	6	10
β-strand	385-390	6	10
β-strand	394-399	6	10
α-helix	400-404	5
β-strand	415-418	4	10
β-strand	423-428	6	11
β-strand	435-440	6	11
β-strand	445-449	5	11
β-strand	454-459	6	11
β-strand	466-471	6	12
β-strand	478-483	6	12
β-strand	487-492	6	12
β-strand	500-503	4	12
β-strand	508-514	7	13
β-strand	517-525	9	13
β-strand	530-534	5	13
β-strand	543-545	3	13
β-strand	552-557	6	14
β-strand	562-567	6	14
β-strand	571-576	6	14
β-strand	581-586	6	14
β-strand	594	1	15
β-strand	598-600	3	16
β-strand	604-607	4	16
β-strand	613-618	6	16
β-strand	626-629	4	16
α-helix	633-636	4
β-strand	647-652	6	9
α-helix	653	1
β-strand	658-663	6	9
β-strand	668-674	7	9

Chain C: 3 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	355-362	8	17
β-strand	374-379	6	18
β-strand	385-390	6	18
β-strand	394-399	6	18
α-helix	400-405	6
β-strand	415-418	4	18
β-strand	423-428	6	19
β-strand	435-440	6	19
β-strand	445-449	5	19
β-strand	454-459	6	19
β-strand	466-471	6	20
β-strand	478-483	6	20
β-strand	487-492	6	20
β-strand	500-503	4	20
β-strand	508-513	6	21
β-strand	520-525	6	21
β-strand	530-534	5	21
β-strand	543-545	3	21
β-strand	552-557	6	22
β-strand	562-567	6	22
β-strand	571-576	6	22
β-strand	581-586	6	22
β-strand	594	1	23
β-strand	598-600	3	24
β-strand	604-607	4	24
β-strand	613-618	6	24
β-strand	626-629	4	24
α-helix	633-636	4
α-helix	640-644	5
β-strand	647-652	6	17
β-strand	658-663	6	17
β-strand	668-674	7	17

Chain D: 2 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	355-362	8	25
β-strand	374-379	6	26
β-strand	385-390	6	26
β-strand	394-399	6	26
α-helix	400-405	6
β-strand	415-418	4	26
β-strand	423-428	6	27
β-strand	435-440	6	27
β-strand	445-449	5	27
β-strand	454-459	6	27
β-strand	466-471	6	28
β-strand	478-483	6	28
β-strand	487-492	6	28
β-strand	500-503	4	28
β-strand	508-513	6	29
β-strand	520-525	6	29
β-strand	530-534	5	29
β-strand	543-545	3	29
β-strand	552-557	6	30
β-strand	562-567	6	30
β-strand	571-576	6	30
β-strand	581-586	6	30
β-strand	594	1	31
β-strand	598-600	3	32
β-strand	604-607	4	32
β-strand	613-618	6	32
β-strand	626-629	4	32
α-helix	633-635	3
β-strand	647-652	6	25
β-strand	658-663	6	25
β-strand	668-674	7	25

Chain U: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	357	1	7

Chains V and X: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	357	1	15
α-helix	358-359	2

Chain W: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	357	1	23
α-helix	358-360	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase COP1	A, B, C, D	protein	336	Arabidopsis thaliana	P43254 (AlphaFold model)
Tribbles homolog 1	U, V, W, X	protein	8	Homo sapiens	Q96RU8 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>5IGO_1 E3 ubiquitin-protein ligase COP1 (chains A, B, C, D)
MHHHHHHHHTFTRYSRLRVIAEIRHGDIFHSANIVSSIEFDRDDELFATAGVSRCIKVFD
FSSVVNEPADMQCPIVEMSTRSKLSCLSWNKHEKNHIASSDYEGIVTVWDVTTRQSLMEY
EEHEKRAWSVDFSRTEPSMLVSGSDDCKVKVWCTRQEASVINIDMKANICCVKYNPGSSN
YIAVGSADHHIHYYDLRNISQPLHVFSGHKKAVSYVKFLSNNELASASTDSTLRLWDVKD
NLPVRTFRGHTNEKNFVGLTVNSEYLACGSETNEVYVYHKEITRPVTSHRFGSPDMDDAE
EEAGSYFISAVCWKSDSPTMLTANSQGTIKVLVLAA

Sequence of entity 2 (U, V, W, X), FASTA

>5IGO_2 Tribbles homolog 1 (chains U, V, W, X)
SDQIVPEY

Primary citation

Structural Basis for Substrate Selectivity of the E3 Ligase COP1. Uljon, S., Xu, X., Durzynska, I. et al. Structure (2016) 24:687-696. DOI 10.1016/j.str.2016.03.002 · PubMed

Other PDB entries of the same protein (UniProt P43254 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6QTS 1.11 Å, Crystal structure of a mutant Arabidopsis WD40 domain in complex with a photoreceptor
6QTO 1.27 Å, Crystal structure of an Arabidopsis WD40 domain in complex with a transcription factor
6QTQ 1.3 Å, Crystal structure of an Arabidopsis WD40 domain in complex with photoreceptor
6QTU 1.3 Å, Crystal structure of Arabidopsis WD40 domain in complex with a BBX transcription factor
6QTV 1.31 Å, Crystal structure of an Arabidopsis WD40 domain in complex with an atypical bHLH…
6QTR 1.37 Å, Crystal structure of a mutant Arabidopsis WD40 domain in complex with a transcription…
6QTW 1.39 Å, Crystal structure of an Arabidopsis WD40 domain in complex with a blue light photoreceptor
5KWN 1.42 Å, The WD domain ofArabidopsis thaliana E3 Ubiquitin Ligase COP1 in complex with peptide…
6QTT 1.51 Å, Crystal structure of an Arabidopsis WD40 domain in complex with a transcription factor…
6QTX 1.95 Å, Crystal structure of an Arabidopsis WD40 domain in complex with a flowering…
7VGG 3.1 Å, Cryo-EM structure of Ultraviolet-B activated UVR8 in complex with COP1

Browse structure collections

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