[English] 日本語
Yorodumi
- PDB-1akh: MAT A1/ALPHA2/DNA TERNARY COMPLEX -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1akh
TitleMAT A1/ALPHA2/DNA TERNARY COMPLEX
Components
  • DNA (5'-D(*TP*AP*CP*AP*TP*GP*TP*AP*AP*AP*AP*AP*TP*TP*TP*AP*C P*AP*TP*CP*A)-3')
  • DNA (5'-D(*TP*AP*TP*GP*AP*TP*GP*TP*AP*AP*AP*TP*TP*TP*TP*TP*A P*CP*AP*TP*G)-3')
  • PROTEIN (MATING-TYPE PROTEIN A-1)
  • PROTEIN (MATING-TYPE PROTEIN ALPHA-2)
KeywordsDNA BINDING PROTEIN/DNA / COMPLEX (TWO DNA-BINDING PROTEINS-DNA) / COMPLEX / DNA-BINDING PROTEIN / DNA / TRANSCRIPTION REGULATION / DNA BINDING PROTEIN-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 / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II ...: / 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 / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / 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 / Silenced mating-type protein ALPHA2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLi, T. / Jin, Y. / Vershon, A.K. / Wolberger, C.
Citation
Journal: Nucleic Acids Res. / Year: 1998
Title: Crystal structure of the MATa1/MATalpha2 homeodomain heterodimer in complex with DNA containing an A-tract.
Authors: Li, T. / Jin, Y. / Vershon, A.K. / Wolberger, C.
#1: Journal: Proteins / Year: 1995
Title: Crystallization and Preliminary X-Ray Diffraction Studies of an A1/Alpha 2/DNA Ternary Complex
Authors: Li, T. / Stark, M. / Johnson, A.D. / Wolberger, C.
#2: Journal: Science / Year: 1995
Title: Crystal Structure of the MATa1/MAT Alpha 2 Homeodomain Heterodimer Bound to DNA
Authors: Li, T. / Stark, M.R. / Johnson, A.D. / Wolberger, C.
#3: Journal: Science / Year: 1995
Title: Erratum. Crystal Structure of the MATa1/MAT Alpha 2 Homeodomain Heterodimer Bound to DNA
Authors: Li, T. / Stark, M.R. / Johnson, A.D. / Wolberger, C.
History
DepositionMay 19, 1997Deposition site: BNL / Processing site: NDB
Revision 1.0May 20, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: DNA (5'-D(*TP*AP*CP*AP*TP*GP*TP*AP*AP*AP*AP*AP*TP*TP*TP*AP*C P*AP*TP*CP*A)-3')
D: DNA (5'-D(*TP*AP*TP*GP*AP*TP*GP*TP*AP*AP*AP*TP*TP*TP*TP*TP*A P*CP*AP*TP*G)-3')
A: PROTEIN (MATING-TYPE PROTEIN A-1)
B: PROTEIN (MATING-TYPE PROTEIN ALPHA-2)


Theoretical massNumber of molelcules
Total (without water)29,8184
Polymers29,8184
Non-polymers00
Water91951
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.250, 132.250, 45.250
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

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


Mass: 6413.210 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*TP*AP*TP*GP*AP*TP*GP*TP*AP*AP*AP*TP*TP*TP*TP*TP*A P*CP*AP*TP*G)-3')


Mass: 6466.217 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein PROTEIN (MATING-TYPE PROTEIN A-1)


Mass: 7165.479 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MAT A1 RESIDUES 66 - 126 / Plasmid: PMS-K66 / Gene (production host): MAT A1 RESIDUES 66 - 126 / Production host: Escherichia coli (E. coli) / References: UniProt: P01366, UniProt: P0CY10*PLUS
#4: Protein PROTEIN (MATING-TYPE PROTEIN ALPHA-2)


Mass: 9773.306 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MAT ALPHA2 RESIDUES 128 - 210 / Plasmid: PAV105 / Gene (production host): MAT ALPHA2 RESIDUES 128 - 210 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6B2C0, UniProt: P0CY08*PLUS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

CrystalDensity Matthews: 3.78 Å3/Da / Density % sol: 67.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100MM HEPES PH 7.0, 20MM CACL2, 5MM [CO(NH3)6]CL3., VAPOR DIFFUSION, HANGING DROP, temperature 295.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2HEPES BUFFER11
3CACL211
4COBALT HEXAMINE11
5WATER12
6HEPES BUFFER12
7CACL212
Crystal
*PLUS
Density % sol: 67.6 %
Crystal grow
*PLUS
pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMHEPES1drop
210 mM1dropCaCl2
32.5-5 mMcobaltic hexamine1drop
4150-200 mMHEPES1reservoir
520 mM1reservoirCaCl2
61
71

-
Data collection

DiffractionMean temperature: 94 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: May 1, 1995
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 15656 / % possible obs: 83.6 % / Observed criterion σ(I): 1 / Redundancy: 2 % / Rmerge(I) obs: 0.054 / Rsym value: 7.4
Reflection shellResolution: 2.4→2.48 Å / % possible all: 67
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 20 Å / % possible obs: 83.6 % / Observed criterion σ(I): 1 / Num. measured all: 31013 / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
Mean I/σ(I) obs: 2.5

-
Processing

Software
NameVersionClassification
X-PLOR3model building
X-PLOR3refinement
R-AXISdata reduction
R-AXISdata scaling
X-PLOR3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YRN

1yrn


Resolution: 2.5→6 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.302 -10 %RANDOM
Rwork0.201 ---
obs-12913 --
Displacement parametersBiso mean: 34.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 6 Å
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 855 0 51 1907
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.87
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.5→2.58 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.389 1 10 %
Rwork0.324 935 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2RNA-DNA.PARMTOPH19.PEP
X-RAY DIFFRACTION3PARAM11.INTRNA-DNA.TOP
Software
*PLUS
Name: X-PLOR / Version: 3 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 6 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.324

+
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