[English] 日本語
Yorodumi
- PDB-1le8: Crystal Structure of the MATa1/MATalpha2-3A Heterodimer Bound to ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1le8
TitleCrystal Structure of the MATa1/MATalpha2-3A Heterodimer Bound to DNA Complex
Components
  • 5'-D(*AP*CP*AP*TP*GP*TP*AP*AP*AP*AP*AP*TP*TP*TP*AP*CP*AP*TP*CP*A)-3'
  • 5'-D(*TP*TP*GP*AP*TP*GP*TP*AP*AP*AP*TP*TP*TP*TP*TP*AP*CP*AP*TP*G)-3'
  • MATING-TYPE PROTEIN A-1
  • Mating-type protein alpha-2
KeywordsTRANSCRIPTION/DNA / MATalpha2 / isothermal titration calorimetry / protein-DNA complex / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


regulation of mating-type specific transcription, DNA-templated / RNA polymerase II transcription repressor complex / DNA binding, bending / DNA-binding transcription repressor activity, RNA polymerase II-specific / transcription corepressor activity / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / negative regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
: / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A ...: / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Mating-type protein A1 / Mating-type protein ALPHA2 / Mating-type protein A1 / Putative mating-type protein A2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKe, A. / Mathias, J.R. / Vershon, A.K. / Wolberger, C.
CitationJournal: Structure / Year: 2002
Title: Structural and Thermodynamic Characterization of the DNA Binding Properties of a Triple Alanine Mutant of MATalpha2
Authors: Ke, A. / Mathias, J.R. / Vershon, A.K. / Wolberger, C.
History
DepositionApr 9, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: 5'-D(*AP*CP*AP*TP*GP*TP*AP*AP*AP*AP*AP*TP*TP*TP*AP*CP*AP*TP*CP*A)-3'
D: 5'-D(*TP*TP*GP*AP*TP*GP*TP*AP*AP*AP*TP*TP*TP*TP*TP*AP*CP*AP*TP*G)-3'
A: MATING-TYPE PROTEIN A-1
B: Mating-type protein alpha-2


Theoretical massNumber of molelcules
Total (without water)28,1684
Polymers28,1684
Non-polymers00
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.170, 54.170, 164.230
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

#1: DNA chain 5'-D(*AP*CP*AP*TP*GP*TP*AP*AP*AP*AP*AP*TP*TP*TP*AP*CP*AP*TP*CP*A)-3'


Mass: 6109.019 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*TP*TP*GP*AP*TP*GP*TP*AP*AP*AP*TP*TP*TP*TP*TP*AP*CP*AP*TP*G)-3'


Mass: 6153.011 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein MATING-TYPE PROTEIN A-1 / MAT a1


Mass: 6277.417 Da / Num. of mol.: 1 / Fragment: residues 74-126 / Source method: obtained synthetically
Details: The peptide was chemically synthesized with solid phase peptide synthesizer. The sequence of the peptide is naturally found in Saccharomyces cerevisiae (yeast).
References: UniProt: P01366, UniProt: P0CY10*PLUS
#4: Protein Mating-type protein alpha-2 / MAT alpha2 / Alpha-2 repressor


Mass: 9628.164 Da / Num. of mol.: 1 / Fragment: residues 128-210 / Mutation: S181A, N182A, R185A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MATalpha2 / Plasmid: pAK2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6B184, UniProt: P0CY08*PLUS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.44 Å3/Da / Density % sol: 49.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10% PEG400, 8 mM Co(NH3)6Cl3, 10 mM CaCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG40011
2Co(NH3)6Cl311
3CaCl211

-
Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: KODAK / Detector: CCD / Date: May 5, 1999
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 11201 / % possible obs: 92.5 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 4.2 % / Biso Wilson estimate: 44.9 Å2 / Rsym value: 0.03 / Net I/σ(I): 19.6
Reflection shellHighest resolution: 2.3 Å / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3 / Num. unique all: 11201 / Rsym value: 0.29 / % possible all: 53.2
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 48164 / Rmerge(I) obs: 0.03
Reflection shell
*PLUS
% possible obs: 53.2 % / Rmerge(I) obs: 0.294

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→24.28 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 1698228.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.299 548 4.9 %RANDOM
Rwork0.256 ---
all-12175 --
obs-11201 92.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.1967 Å2 / ksol: 0.29234 e/Å3
Displacement parametersBiso mean: 49.1 Å2
Baniso -1Baniso -2Baniso -3
1--3.62 Å23.08 Å20 Å2
2---3.62 Å20 Å2
3---7.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.3→24.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms993 814 0 102 1909
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d18.6
X-RAY DIFFRACTIONc_improper_angle_d1.11
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.059 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.467 63 4.9 %
Rwork0.411 1215 -
obs--63.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor obs: 0.255 / Rfactor Rfree: 0.298 / Rfactor Rwork: 0.255
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0067
X-RAY DIFFRACTIONc_angle_deg1.18
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.11
LS refinement shell
*PLUS
Rfactor Rfree: 0.467 / Rfactor Rwork: 0.411 / Rfactor obs: 0.411

+
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