[English] 日本語
Yorodumi
- PDB-1awc: MOUSE GABP ALPHA/BETA DOMAIN BOUND TO DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1awc
TitleMOUSE GABP ALPHA/BETA DOMAIN BOUND TO DNA
Components
  • DNA (5'-D(*AP*AP*(BRU)P*GP*AP*CP*CP*GP*GP*AP*AP*GP*TP*AP*(CBR)P*AP*CP*(CBR)P*GP*GP*A)-3')
  • DNA (5'-D(*TP*TP*CP*CP*GP*GP*(BRU)P*GP*(BRU)P*AP*CP*TP*TP*CP*CP*GP*GP*TP*CP*AP*T)-3')
  • PROTEIN (GA BINDING PROTEIN ALPHA)
  • PROTEIN (GA BINDING PROTEIN BETA 1)
KeywordsTRANSCRIPTION/DNA / COMPLEX (TRANSCRIPTION REGULATION-DNA) / DNA-BINDING / NUCLEAR PROTEIN / ETS DOMAIN / ANKYRIN REPEATS / TRANSCRIPTION FACTOR / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


Transcriptional activation of mitochondrial biogenesis / blastocyst formation / negative regulation of megakaryocyte differentiation / mitochondrion organization / cytoplasmic ribonucleoprotein granule / DNA-binding transcription activator activity, RNA polymerase II-specific / in utero embryonic development / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin binding ...Transcriptional activation of mitochondrial biogenesis / blastocyst formation / negative regulation of megakaryocyte differentiation / mitochondrion organization / cytoplasmic ribonucleoprotein granule / DNA-binding transcription activator activity, RNA polymerase II-specific / in utero embryonic development / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
: / Transcription factor, GA-binding, alpha subunit / GA-binding protein alpha subunit, N-terminal / GA-binding protein alpha chain / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets-domain signature 1. / Ets-domain signature 2. ...: / Transcription factor, GA-binding, alpha subunit / GA-binding protein alpha subunit, N-terminal / GA-binding protein alpha chain / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets-domain signature 1. / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Ankyrin repeats (many copies) / Ankyrin repeat-containing domain / Sterile alpha motif/pointed domain superfamily / Ankyrin repeat / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Arc Repressor Mutant, subunit A / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / GA-binding protein subunit beta-1 / GA-binding protein alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.15 Å
AuthorsBatchelor, A.H. / Wolberger, C.
CitationJournal: Science / Year: 1998
Title: The structure of GABPalpha/beta: an ETS domain- ankyrin repeat heterodimer bound to DNA.
Authors: Batchelor, A.H. / Piper, D.E. / de la Brousse, F.C. / McKnight, S.L. / Wolberger, C.
History
DepositionOct 1, 1997Deposition site: BNL / Processing site: NDB
Revision 1.0Mar 18, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
D: DNA (5'-D(*AP*AP*(BRU)P*GP*AP*CP*CP*GP*GP*AP*AP*GP*TP*AP*(CBR)P*AP*CP*(CBR)P*GP*GP*A)-3')
E: DNA (5'-D(*TP*TP*CP*CP*GP*GP*(BRU)P*GP*(BRU)P*AP*CP*TP*TP*CP*CP*GP*GP*TP*CP*AP*T)-3')
A: PROTEIN (GA BINDING PROTEIN ALPHA)
B: PROTEIN (GA BINDING PROTEIN BETA 1)


Theoretical massNumber of molelcules
Total (without water)43,1384
Polymers43,1384
Non-polymers00
Water82946
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)201.600, 34.550, 59.260
Angle α, β, γ (deg.)90.00, 99.83, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

-
Components

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


Mass: 6712.888 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*TP*TP*CP*CP*GP*GP*(BRU)P*GP*(BRU)P*AP*CP*TP*TP*CP*CP*GP*GP*TP*CP*AP*T)-3')


Mass: 6525.857 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein PROTEIN (GA BINDING PROTEIN ALPHA) / GABPALPHA / GABP-ALPHA SUBUNIT


Mass: 13065.230 Da / Num. of mol.: 1 / Fragment: ETS DOMAIN PLUS 30 C-TERMINAL RESIDUES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: GABP ALPHA / Plasmid: PALPHA8A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q00422
#4: Protein PROTEIN (GA BINDING PROTEIN BETA 1) / GABPBETA1 / GABP-BETA-1 SUBUNIT / GABPB1


Mass: 16834.010 Da / Num. of mol.: 1 / Fragment: ANKYRIN REPEAT DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: GABP BETA 1 / Plasmid: PBB-79 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q00420
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.4 Å3/Da / Density % sol: 49 %
Crystal growpH: 9
Details: 100 MM BIS-TRIS PROPANE PH 9, 12 % PEG 1000, 5 MM COBALTIC HEXAMINE CHLORIDE, 1 MM DTT, 20 MM TRIS, 1 MM EDTA, 0.001 % SODIUM AZIDE, pH 9.0
Components of the solutions
IDNameCrystal-IDSol-ID
1BIS-TRIS PROPANE11
2PEG 100011
3[CO(NH3)6]Cl311
4DTT11
5TRIS11
6EDTA11
7SODIUM AZIDE11
8PEG 100012
Crystal
*PLUS
Density % sol: 49 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14 mg/mlprotein1drop
210 mMTris1drop
30.5 mMEDTA1drop
40.5 mMdithiothreitol1drop
50.0005 %sodium azide1drop
650 mMBis-Tris propane1drop
72.5 mMcobaltic hexamine chloride1drop
84.5 %PEG10001drop
9100 mMBis-Tris propane1reservoir
105 mMcobaltic hexamine chloride1reservoir
119 %PEG10001reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A
DetectorType: FUJI / Detector: IMAGE PLATE / Date: May 15, 1996 / Details: SPHERICAL RH COATED
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 18368 / % possible obs: 88 % / Observed criterion σ(I): 1.5 / Redundancy: 8.7 % / Rsym value: 0.072 / Net I/σ(I): 21
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 5.3 / Rsym value: 0.22 / % possible all: 88
Reflection
*PLUS
Highest resolution: 2.15 Å / Lowest resolution: 30 Å / % possible obs: 88 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.072
Reflection shell
*PLUS
% possible obs: 88 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 5.3

-
Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.15→6 Å / Rfactor Rfree error: 0.7 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.282 1714 10 %RANDOM
Rwork0.211 ---
obs-17217 88 %-
Displacement parametersBiso mean: 35.3 Å2
Baniso -1Baniso -2Baniso -3
1--3.68 Å20 Å2-4.44 Å2
2---0.8 Å20 Å2
3---9.269 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.15→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2063 852 5 46 2966
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.17
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d19.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.22
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: 2.15→2.22 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.291 152 10 %
Rwork0.282 1477 -
obs--69.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2TOM_BR_RNA-DNA.PARMTOM_BR_RNA-DNA.TOP
X-RAY DIFFRACTION3PARAM19_MOD.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.15 Å / Lowest resolution: 6 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor all: 0.222 / Rfactor obs: 0.211
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 35.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.171
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg19.92
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.217
LS refinement shell
*PLUS
% reflection Rfree: 10 %

+
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