6QTU: Arabidopsis WD40 domain

Crystal structure of Arabidopsis WD40 domain in complex with a BBX transcription factor. Determined by X-ray diffraction at 1.3 Å resolution. Released 10 Jul 2019.

Method: X-ray diffraction
Resolution: 1.3 Å
Organism: Arabidopsis thaliana
Chains: 2
Atoms: 2,891
Mol. weight: 38.66 kDa
Ligands: MLI
Released: 10 Jul 2019

Explore 6QTU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6QTU contains 2 α-helices and 30 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 A: 1 helix, 29 β-strands

Element	Residues	Length	Sheet
β-strand	355-362	8	1
β-strand	374-379	6	2
β-strand	385-390	6	2
β-strand	394-399	6	2
α-helix	400-405	6
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	455-459	5	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
β-strand	647-652	6	1
β-strand	658-663	6	1
β-strand	668-674	7	1

Chain B: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	243	1	7
α-helix	244-245	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase COP1	A	protein	330	Arabidopsis thaliana	P43254 (AlphaFold model)
B-box zinc finger protein 24	B	protein	10	Arabidopsis thaliana	Q96288 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6QTU_1 E3 ubiquitin-protein ligase COP1 (chains A)
GAMTFTRYSRLRVIAEIRHGDIFHSANIVSSIEFDRDDELFATAGVSRCIKVFDFSSVVN
EPADMQCPIVEMSTRSKLSCLSWNKHEKNHIASSDYEGIVTVWDVTTRQSLMEYEEHEKR
AWSVDFSRTEPSMLVSGSDDCKVKVWCTRQEASVINIDMKANICCVKYNPGSSNYIAVGS
ADHHIHYYDLRNISQPLHVFSGHKKAVSYVKFLSNNELASASTDSTLRLWDVKDNLPVRT
FRGHTNEKNFVGLTVNSEYLACGSETNEVYVYHKEITRPVTSHRFGSPDMDDAEEEAGSY
FISAVCWKSDSPTMLTANSQGTIKVLVLAA

Sequence of entity 2 (B), FASTA

>6QTU_2 B-box zinc finger protein 24 (chains B)
XEHFIVPDLY

Ligands and cofactors

ID	Name	Formula	Copies
MLI	Malonate ion	C3 H2 O4	2

Water and common crystallization additives (GOL) are not listed.

Primary citation

Plant photoreceptors and their signaling components compete for COP1 binding via VP peptide motifs. Lau, K., Podolec, R., Chappuis, R. et al. EMBO J (2019) 38:e102140-e102140. DOI 10.15252/embj.2019102140 · 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
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…
5IGO 1.6 Å, WD40 domain of Arabidopsis thaliana E3 Ubiquitin Ligase COP1 in complex with peptide…
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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