[English] 日本語
Yorodumi
- PDB-6xzm: Arabidopsis UV-B photoreceptor UVR8 mutant D96N D107N W285A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xzm
TitleArabidopsis UV-B photoreceptor UVR8 mutant D96N D107N W285A
ComponentsUltraviolet-B receptor UVR8
KeywordsPLANT PROTEIN / UVB / photoreceptor
Function / homology
Function and homology information


entrainment of circadian clock / response to UV-B / plastid / photoreceptor activity / response to UV / guanyl-nucleotide exchange factor activity / chromatin binding / chromatin / protein homodimerization activity / identical protein binding ...entrainment of circadian clock / response to UV-B / plastid / photoreceptor activity / response to UV / guanyl-nucleotide exchange factor activity / chromatin binding / chromatin / protein homodimerization activity / identical protein binding / nucleus / cytosol
Similarity search - Function
: / 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
Similarity search - Domain/homology
NITRATE ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Ultraviolet-B receptor UVR8
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.10009315021 Å
AuthorsLau, K. / Hothorn, M.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_175774 Switzerland
European Research Council (ERC)310539 Switzerland
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: A constitutively monomeric UVR8 photoreceptor confers enhanced UV-B photomorphogenesis.
Authors: Podolec, R. / Lau, K. / Wagnon, T.B. / Hothorn, M. / Ulm, R.
History
DepositionFeb 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ultraviolet-B receptor UVR8
B: Ultraviolet-B receptor UVR8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,90410
Polymers80,1872
Non-polymers7178
Water1,35175
1
A: Ultraviolet-B receptor UVR8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3244
Polymers40,0941
Non-polymers2303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ultraviolet-B receptor UVR8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5806
Polymers40,0941
Non-polymers4865
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.266, 98.266, 138.836
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

-
Components

#1: Protein Ultraviolet-B receptor UVR8 / Protein UV-B RESISTANCE 8 / RCC1 domain-containing protein UVR8


Mass: 40093.723 Da / Num. of mol.: 2 / Mutation: D96N D107N W285A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: UVR8, At5g63860, MGI19.7 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9FN03
#2: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49.03 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 22% PEG3350, 0.2M NaNO3, 5mg/mL. 20% PEG400 cryoprotectant

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→49.13 Å / Num. obs: 45831 / % possible obs: 99.95 % / Redundancy: 20.1 % / Biso Wilson estimate: 42.1418773177 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.84
Reflection shellResolution: 2.1→2.175 Å / Num. unique obs: 4521 / CC1/2: 0.483

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D9S

4d9s


Resolution: 2.10009315021→49.13 Å / SU ML: 0.289283250111 / Cross valid method: FREE R-VALUE / σ(F): 1.33648739498 / Phase error: 30.6166883102
RfactorNum. reflection% reflection
Rfree0.248131330672 2200 4.80192076831 %
Rwork0.197002582858 --
obs0.199549219029 45815 99.9650891318 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 53.3098685346 Å2
Refinement stepCycle: LAST / Resolution: 2.10009315021→49.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5492 0 47 75 5614
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01110078115955667
X-RAY DIFFRACTIONf_angle_d1.140695702137677
X-RAY DIFFRACTIONf_chiral_restr0.0636319687915814
X-RAY DIFFRACTIONf_plane_restr0.007121874003251008
X-RAY DIFFRACTIONf_dihedral_angle_d14.73911302943216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.14580.3895131481651290.3463467622832684X-RAY DIFFRACTION99.9644633973
2.1458-2.19570.3488687923211460.3189839123522666X-RAY DIFFRACTION99.9644507643
2.1957-2.25060.3410332527651330.2893775161892710X-RAY DIFFRACTION100
2.2506-2.31140.3571061706721590.2753156864992646X-RAY DIFFRACTION99.9643620813
2.3114-2.37940.2564203980591020.2624146956152754X-RAY DIFFRACTION99.9649982499
2.3794-2.45620.3336666856611440.2440762548392701X-RAY DIFFRACTION99.8595998596
2.4562-2.5440.3001557970491440.2261418918912673X-RAY DIFFRACTION100
2.544-2.64590.3002657542211260.2246067833642733X-RAY DIFFRACTION99.965034965
2.6459-2.76630.288783890811190.2242346668192686X-RAY DIFFRACTION100
2.7663-2.91210.3023135924231340.2274252542392723X-RAY DIFFRACTION100
2.9121-3.09450.302367295441460.2282112463322752X-RAY DIFFRACTION100
3.0945-3.33340.231278573241330.2235876754252716X-RAY DIFFRACTION99.9649122807
3.3334-3.66880.2599327315941480.1914778997912723X-RAY DIFFRACTION100
3.6688-4.19940.2055168898251460.1526849446652742X-RAY DIFFRACTION100
4.1994-5.28980.1718439627311210.1405108367252826X-RAY DIFFRACTION100
5.2898-49.130.22107295861700.1719714517172880X-RAY DIFFRACTION99.8363338789

+
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