[English] 日本語
Yorodumi
- PDB-4qtk: Complex of WOPR domain of Wor1 in Candida albicans with the 17bp dsDNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4qtk
TitleComplex of WOPR domain of Wor1 in Candida albicans with the 17bp dsDNA
Components
  • DNA (5'-D(*AP*AP*GP*TP*TP*AP*AP*AP*CP*TP*TP*TP*TP*TP*TP*GP*A)-3')
  • DNA (5'-D(*TP*CP*AP*AP*AP*AP*AP*AP*GP*TP*TP*TP*AP*AP*CP*TP*T)-3')
  • White-opaque regulator 1
KeywordsTRANSCRIPTION/DNA / Wor1 / WOPR domain / white-opaque switching / protein-DNA recognition / transcriptional regulation / DNA binding domain / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


positive regulation of phenotypic switching / parasexual reproduction with cellular fusion / regulation of single-species biofilm formation on inanimate substrate / regulation of phenotypic switching / biological process involved in symbiotic interaction / filamentous growth of a population of unicellular organisms / mating / single-species biofilm formation on inanimate substrate / phenotypic switching / adhesion of symbiont to host ...positive regulation of phenotypic switching / parasexual reproduction with cellular fusion / regulation of single-species biofilm formation on inanimate substrate / regulation of phenotypic switching / biological process involved in symbiotic interaction / filamentous growth of a population of unicellular organisms / mating / single-species biofilm formation on inanimate substrate / phenotypic switching / adhesion of symbiont to host / sequence-specific DNA binding / cell adhesion / DNA-binding transcription factor activity / regulation of DNA-templated transcription / chromatin / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
Gti1/Pac2 family / Gti1/Pac2 family
Similarity search - Domain/homology
DNA / DNA (> 10) / White-opaque regulator 1
Similarity search - Component
Biological speciesCandida albicans SC5314 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.99 Å
AuthorsZhang, S. / Zhang, T. / Ding, J.
CitationJournal: Cell Res. / Year: 2014
Title: Crystal structure of the WOPR-DNA complex and implications for Wor1 function in white-opaque switching of Candida albicans.
Authors: Zhang, S. / Zhang, T. / Yan, M. / Ding, J. / Chen, J.
History
DepositionJul 8, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 24, 2022Group: Database references / Category: citation / database_2 / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: White-opaque regulator 1
B: White-opaque regulator 1
C: DNA (5'-D(*TP*CP*AP*AP*AP*AP*AP*AP*GP*TP*TP*TP*AP*AP*CP*TP*T)-3')
D: DNA (5'-D(*AP*AP*GP*TP*TP*AP*AP*AP*CP*TP*TP*TP*TP*TP*TP*GP*A)-3')
E: DNA (5'-D(*TP*CP*AP*AP*AP*AP*AP*AP*GP*TP*TP*TP*AP*AP*CP*TP*T)-3')
F: DNA (5'-D(*AP*AP*GP*TP*TP*AP*AP*AP*CP*TP*TP*TP*TP*TP*TP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)82,4556
Polymers82,4556
Non-polymers00
Water905
1
A: White-opaque regulator 1
C: DNA (5'-D(*TP*CP*AP*AP*AP*AP*AP*AP*GP*TP*TP*TP*AP*AP*CP*TP*T)-3')
D: DNA (5'-D(*AP*AP*GP*TP*TP*AP*AP*AP*CP*TP*TP*TP*TP*TP*TP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)41,2283
Polymers41,2283
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-17 kcal/mol
Surface area12880 Å2
MethodPISA
2
B: White-opaque regulator 1
E: DNA (5'-D(*TP*CP*AP*AP*AP*AP*AP*AP*GP*TP*TP*TP*AP*AP*CP*TP*T)-3')
F: DNA (5'-D(*AP*AP*GP*TP*TP*AP*AP*AP*CP*TP*TP*TP*TP*TP*TP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)41,2283
Polymers41,2283
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-18 kcal/mol
Surface area13170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.713, 49.910, 84.307
Angle α, β, γ (deg.)90.000, 97.960, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein White-opaque regulator 1


Mass: 30818.729 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 6-272
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans SC5314 (yeast) / Gene: WOR1, EAP2, TOS9, CaO19.12348, CaO19.4884 / Plasmid: pETDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: Q5AP80
#2: DNA chain DNA (5'-D(*TP*CP*AP*AP*AP*AP*AP*AP*GP*TP*TP*TP*AP*AP*CP*TP*T)-3')


Mass: 5193.423 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*AP*AP*GP*TP*TP*AP*AP*AP*CP*TP*TP*TP*TP*TP*TP*GP*A)-3')


Mass: 5215.419 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.71 % / Mosaicity: 1.254 °
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 0.10M Bis-Tris, 0.2M ammonnuim sulfate, 20% PEG 3350, pH 5.7, temperature 289K, VAPOR DIFFUSION, HANGING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.99→50 Å / Num. obs: 12474 / % possible obs: 97.7 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.107 / Χ2: 1.943 / Net I/σ(I): 15.7
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3-3.117.40.45612531.14298.5
3.11-3.237.30.24112191.4297.4
3.23-3.387.20.17612451.67797.6
3.38-3.567.30.14112311.96798.6
3.56-3.787.30.13212582.09898.4
3.78-4.077.30.11912372.29198.3
4.07-4.487.20.10212682.38998.7
4.48-5.137.10.0912461.81498.3
5.13-6.467.20.08312542.15996.4
6.46-5070.09312632.49894.6

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.14data extraction
REFMAC5.7.0029refinement
RefinementMethod to determine structure: SAD / Resolution: 2.99→38.86 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.911 / SU B: 22.974 / SU ML: 0.415 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.469 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2711 609 4.9 %RANDOM
Rwork0.2209 ---
obs0.2232 12453 96.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 207.4 Å2 / Biso mean: 84.634 Å2 / Biso min: 40.46 Å2
Baniso -1Baniso -2Baniso -3
1-7.96 Å2-0 Å25.43 Å2
2---2.42 Å20 Å2
3----6.07 Å2
Refinement stepCycle: LAST / Resolution: 2.99→38.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2351 1382 0 5 3738
LS refinement shellResolution: 2.994→3.072 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 38 -
Rwork0.33 786 -
all-824 -
obs--87.47 %

+
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