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- PDB-8gqe: Crystal structure of the W285A mutant of UVR8 in complex with RUP2 -

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Basic information

Entry
Database: PDB / ID: 8gqe
TitleCrystal structure of the W285A mutant of UVR8 in complex with RUP2
Components
  • Ultraviolet-B receptor UVR8
  • WD repeat-containing protein RUP2
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


chloroplast organization / flower development / entrainment of circadian clock / Cul4-RING E3 ubiquitin ligase complex / response to UV-B / plastid / photoreceptor activity / regulation of protein-containing complex assembly / response to UV / guanyl-nucleotide exchange factor activity ...chloroplast organization / flower development / entrainment of circadian clock / Cul4-RING E3 ubiquitin ligase complex / response to UV-B / plastid / photoreceptor activity / regulation of protein-containing complex assembly / response to UV / guanyl-nucleotide exchange factor activity / chromatin binding / chromatin / protein homodimerization activity / identical protein binding / nucleus / cytosol
Similarity search - Function
WD repeat-containing protein RUP1/2 / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / : / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / 7 Propeller / Methylamine Dehydrogenase; Chain H ...WD repeat-containing protein RUP1/2 / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / : / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / 7 Propeller / Methylamine Dehydrogenase; Chain H / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
WD repeat-containing protein RUP2 / Ultraviolet-B receptor UVR8
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWang, Y.D. / Wang, L.X. / Guan, Z.Y. / chang, H.F. / Yin, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Plant Commun. / Year: 2023
Title: RUP2 facilitates UVR8 redimerization via two interfaces.
Authors: Wang, L. / Wang, Y. / Chang, H. / Ren, H. / Wu, X. / Wen, J. / Guan, Z. / Ma, L. / Qiu, L. / Yan, J. / Zhang, D. / Huang, X. / Yin, P.
History
DepositionAug 30, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2022Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 25, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WD repeat-containing protein RUP2
B: Ultraviolet-B receptor UVR8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,7013
Polymers87,5062
Non-polymers1951
Water8,107450
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint6 kcal/mol
Surface area25990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.393, 173.393, 76.737
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

#1: Protein WD repeat-containing protein RUP2 / Protein EARLY FLOWERING BY OVEREXPRESSION 2 / Protein REPRESSOR OF UV-B PHOTOMORPHOGENESIS 2


Mass: 40236.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: RUP2 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9FFA7
#2: Protein Ultraviolet-B receptor UVR8 / Protein UV-B RESISTANCE 8 / RCC1 domain-containing protein UVR8


Mass: 47269.160 Da / Num. of mol.: 1 / Mutation: W285A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: UVR8 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9FN03
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 450 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 62.68 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 6000, Ammonium chloride, Hexamminecobalt (III) chloride, sucrose

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2→45 Å / Num. obs: 76777 / % possible obs: 100 % / Redundancy: 13.8 % / CC1/2: 0.957 / CC star: 0.989 / Rpim(I) all: 0.044 / Rrim(I) all: 0.166 / Net I/σ(I): 23.9
Reflection shellResolution: 2→2.07 Å / Num. unique obs: 7644 / CC1/2: 0.89 / CC star: 0.97 / Rpim(I) all: 0.241 / Rrim(I) all: 0.884

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DNV

4dnv


Resolution: 2→34.01 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 19.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2003 3905 5.1 %
Rwork0.1733 72595 -
obs0.1747 76500 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.29 Å2 / Biso mean: 40.4232 Å2 / Biso min: 18.62 Å2
Refinement stepCycle: final / Resolution: 2→34.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5566 0 145 450 6161
Biso mean--39.39 45.57 -
Num. residues----717
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.030.24651460.21112555270198
2.03-2.050.26161470.202925772724100
2.05-2.080.21161090.198626242733100
2.08-2.110.21641140.184626152729100
2.11-2.140.22051400.181525652705100
2.14-2.170.18971290.173625972726100
2.17-2.20.20581240.178526002724100
2.2-2.240.21961490.179425822731100
2.24-2.280.20351630.176725822745100
2.28-2.320.18631270.17126002727100
2.32-2.360.21371350.184225872722100
2.36-2.410.21511620.179125862748100
2.41-2.460.21851590.176525782737100
2.46-2.520.20171370.175925902727100
2.52-2.580.19371370.180725912728100
2.58-2.650.21321170.185226192736100
2.65-2.730.22641390.185526072746100
2.73-2.820.21181450.179525772722100
2.82-2.920.20631210.18426422763100
2.92-3.040.21031290.178425872716100
3.04-3.180.22041450.175825992744100
3.18-3.340.1931690.164125842753100
3.34-3.550.20991530.170425992752100
3.55-3.830.18861530.160125892742100
3.83-4.210.15851550.158326152770100
4.21-4.820.18431200.14422620274099
4.82-6.070.1881510.17162603275499
6.07-34.010.21331300.19792525265593
Refinement TLS params.Method: refined / Origin x: 41.4805 Å / Origin y: 69.8859 Å / Origin z: 62.1317 Å
111213212223313233
T0.2104 Å2-0.0045 Å2-0.0016 Å2-0.2259 Å20.0031 Å2--0.1994 Å2
L0.358 °20.2133 °20.0558 °2-1.9551 °2-0.185 °2--0.3991 °2
S0.0006 Å °-0.0085 Å °0.0687 Å °0.0547 Å °0.0284 Å °0.3963 Å °-0.1132 Å °-0.062 Å °-0.024 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA20 - 367
2X-RAY DIFFRACTION1allB13 - 381
3X-RAY DIFFRACTION1allB397 - 413
4X-RAY DIFFRACTION1allB501
5X-RAY DIFFRACTION1allS1 - 453

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