[English] 日本語
Yorodumi
- PDB-8gqe: Crystal structure of the W285A mutant of UVR8 in complex with RUP2 -

+
Open data


ID or keywords:

Loading...

-
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 / response to UV-B / plastid / Cul4-RING E3 ubiquitin ligase complex / photoreceptor activity / regulation of protein-containing complex assembly / response to UV / guanyl-nucleotide exchange factor activity ...chloroplast organization / flower development / entrainment of circadian clock / response to UV-B / plastid / Cul4-RING E3 ubiquitin ligase complex / 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 / RCC1-like domain / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / 7 Propeller ...WD repeat-containing protein RUP1/2 / : / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / RCC1-like domain / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation (RCC1) signature 2. / 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 domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more