5IGQ: WD40 domain of Human E3 Ubiquitin Ligase COP1

WD40 domain of Human E3 Ubiquitin Ligase COP1 (RFWD2) bound to peptide from Trib1. Determined by X-ray diffraction at 3.9 Å resolution. Released 20 Apr 2016.

Method: X-ray diffraction
Resolution: 3.9 Å
Organism: Homo sapiens
Chains: 12
Atoms: 15,349
Mol. weight: 245.67 kDa
Released: 20 Apr 2016

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

Secondary structure: helices and β-sheets

5IGQ contains 18 α-helices and 186 β-strands across 11 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.

Chains A and E: 3 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	392-399	8
β-strand	405-412	8	1
β-strand	424-429	6	2
β-strand	435-440	6	2
β-strand	444-449	6	2
α-helix	450-453	4
β-strand	465-468	4	2
β-strand	473-478	6	3
β-strand	485-490	6	3
β-strand	495-499	5	3
β-strand	505-509	5	3
β-strand	516-521	6	4
β-strand	528-533	6	4
β-strand	537-542	6	4
β-strand	550-553	4	4
β-strand	558-563	6	5
β-strand	570-575	6	5
β-strand	579-584	6	5
β-strand	587	1	5
β-strand	593-596	4	5
β-strand	602-607	6	6
β-strand	612-617	6	6
β-strand	621-626	6	6
β-strand	634-636	3	6
β-strand	644	1	7
β-strand	648-651	4	8
β-strand	654-659	6	8
β-strand	663-668	6	8
β-strand	674-679	6	8
α-helix	680-681	2
β-strand	700-705	6	1
β-strand	715-720	6	1
β-strand	724-730	7	1

Chain B: 2 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	392-399	8
β-strand	405-412	8	9
β-strand	424-429	6	10
β-strand	435-440	6	10
β-strand	444-449	6	10
α-helix	450-453	4
β-strand	465-468	4	10
β-strand	473-478	6	11
β-strand	485-490	6	11
β-strand	494-499	6	11
β-strand	505-510	6	11
β-strand	516-521	6	12
β-strand	528-533	6	12
β-strand	537-542	6	12
β-strand	550-553	4	12
β-strand	558-563	6	13
β-strand	570-575	6	13
β-strand	580-584	5	13
β-strand	587	1	13
β-strand	593-595	3	13
β-strand	596	1	14
β-strand	602-607	6	15
β-strand	612-617	6	15
β-strand	621-626	6	15
β-strand	631	1	14
β-strand	634-636	3	15
β-strand	644	1	16
β-strand	648-651	4	17
β-strand	654-659	6	17
β-strand	663-668	6	17
β-strand	674-679	6	17
β-strand	700-705	6	9
β-strand	715-720	6	9
β-strand	724-730	7	9

Chain C: 3 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	392-399	8
β-strand	405-412	8	18
β-strand	424-429	6	19
β-strand	435-440	6	19
β-strand	444-449	6	19
α-helix	450-453	4
β-strand	465-468	4	19
β-strand	473-478	6	20
β-strand	485-490	6	20
β-strand	495-499	5	20
β-strand	505-509	5	20
β-strand	516-521	6	21
β-strand	528-533	6	21
β-strand	537-542	6	21
β-strand	550-553	4	21
β-strand	558-563	6	22
β-strand	570-575	6	22
β-strand	579-584	6	22
β-strand	587	1	22
β-strand	593-596	4	22
β-strand	602-607	6	23
β-strand	612-617	6	23
β-strand	621-626	6	23
β-strand	634-636	3	23
β-strand	644	1	24
β-strand	648-651	4	25
β-strand	654-659	6	25
β-strand	663-668	6	25
β-strand	676-679	4	25
α-helix	680-681	2
β-strand	700-705	6	18
β-strand	715-720	6	18
β-strand	724-730	7	18

Chain D: 2 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	392-399	8
β-strand	405-412	8	26
β-strand	424-429	6	27
β-strand	435-440	6	27
β-strand	444-449	6	27
α-helix	450-453	4
β-strand	465-468	4	27
β-strand	473-478	6	28
β-strand	485-490	6	28
β-strand	494-499	6	28
β-strand	505-510	6	28
β-strand	516-521	6	29
β-strand	528-533	6	29
β-strand	537-542	6	29
β-strand	550-553	4	29
β-strand	558-563	6	30
β-strand	570-575	6	30
β-strand	579-584	6	30
β-strand	587	1	30
β-strand	593-596	4	30
β-strand	602-607	6	31
β-strand	612-617	6	31
β-strand	621-626	6	31
β-strand	634-636	3	31
β-strand	648-651	4	32
β-strand	654-659	6	32
β-strand	663-668	6	32
β-strand	676-679	4	32
β-strand	700-705	6	26
β-strand	715-720	6	26
β-strand	724-730	7	26

Chain F: 3 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	392-399	8
β-strand	405-412	8	41
β-strand	424-429	6	42
β-strand	435-440	6	42
β-strand	444-449	6	42
α-helix	450-453	4
β-strand	465-468	4	42
β-strand	473-478	6	43
β-strand	485-490	6	43
β-strand	494-499	6	43
β-strand	505-510	6	43
β-strand	516-521	6	44
β-strand	528-533	6	44
β-strand	537-542	6	44
β-strand	550-553	4	44
β-strand	558-563	6	45
β-strand	570-575	6	45
β-strand	580-584	5	45
β-strand	587	1	45
β-strand	593-595	3	45
β-strand	602-607	6	46
β-strand	612-617	6	46
β-strand	621-626	6	46
β-strand	634-636	3	46
β-strand	644	1	47
β-strand	648-651	4	48
β-strand	654-659	6	48
β-strand	663-668	6	48
β-strand	674-679	6	48
α-helix	680-681	2
β-strand	700-705	6	41
β-strand	715-720	6	41
β-strand	724-730	7	41

Chains U, Y and Z: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	357	1	7

Chains V and W: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	357	1	16
α-helix	358-359	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase RFWD2	A, B, C, D, E, F	protein	353	Homo sapiens	Q8NHY2 (AlphaFold model)
Tribbles homolog 1	U	protein	11	Homo sapiens	Q96RU8 (AlphaFold model)
Tribbles homolog 1	V, W, X, Y, Z	protein	8	Homo sapiens	Q96RU8 (AlphaFold model)

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

>5IGQ_1 E3 ubiquitin-protein ligase RFWD2 (chains A, B, C, D, E, F)
MHHHHHHASQLDEFQECLSKFTRYNSVRPLATLSYASDLYNGSSIVSSIEFDRDCDYFAI
AGVTKKIKVYEYDTVIQDAVDIHYPENEMTCNSKISCISWSSYHKNLLASSDYEGTVILW
DGFTGQRSKVYQEHEKRCWSVDFNLMDPKLLASGSDDAKVKLWSTNLDNSVASIEAKANV
CCVKFSPSSRYHLAFGCADHCVHYYDLRNTKQPIMVFKGHRKAVSYAKFVSGEEIVSAST
DSQLKLWNVGKPYCLRSFKGHINEKNFVGLASNGDYIACGSENNSLYLYYKGLSKTLLTF
KFDTVKSVLDKDRKEDDTNEFVSAVCWRALPDGESNVLIAANSQGTIKVLELV

Sequence of entity 2 (U), FASTA

>5IGQ_2 Tribbles homolog 1 (chains U)
SDQIVPEYQED

Sequence of entity 3 (V, W, X, Y, Z), FASTA

>5IGQ_3 Tribbles homolog 1 (chains V, W, X, Y, Z)
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 Q8NHY2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5HQG 2.0 Å, WD40 domain of Human E3 Ubiquitin Ligase COP1 (RFWD2)
9LTR 3.03 Å, Cryo-EM structure of dimeric DDB1-DDA1-DET1-Ube2e2-COP1 complex
9LU1 3.62 Å, protein structure of DDB1-DDA1-DET1-Ube2e2 bound to COP1 dimer
9W90 3.7 Å, DDB1-DDA1-DET1-Ube2e2-COP1-c-Jun-STK40 complex
9M0Y 4.25 Å, Local refinement of stacked like DDB1-DDA1-DET1-Ube2e2-COP1 complex (layer 2)
9LUL 4.99 Å, Local refinement of stacked like DDB1-DDA1-DET1-Ube2e2-COP1 complex (layer 1)

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