[English] 日本語
Yorodumi
- PDB-5t1j: Crystal Structure of the Tbox DNA binding domain of the transcrip... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5t1j
TitleCrystal Structure of the Tbox DNA binding domain of the transcription factor T-bet
Components
  • DNA
  • T-box transcription factor TBX21
KeywordsTRANSCRIPTION/DNA / T-bet / Tbox / Tbx21 / DNA looping / transcriptional regulation / master regulator / transcription factor / DNA binding / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


negative regulation of T-helper 17 cell lineage commitment / lymphocyte migration / negative regulation of T-helper 17 cell differentiation / negative regulation of T-helper 2 cell cytokine production / positive regulation of isotype switching to IgG isotypes / cell fate specification / negative regulation of interleukin-2 production / regulation of T cell differentiation / : / heart looping ...negative regulation of T-helper 17 cell lineage commitment / lymphocyte migration / negative regulation of T-helper 17 cell differentiation / negative regulation of T-helper 2 cell cytokine production / positive regulation of isotype switching to IgG isotypes / cell fate specification / negative regulation of interleukin-2 production / regulation of T cell differentiation / : / heart looping / T cell differentiation / regulation of immune response / response to virus / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / proteasome-mediated ubiquitin-dependent protein catabolic process / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / neuronal cell body / positive regulation of gene expression / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
Transcription factor, T-box / T-box transcription factor / Transcription factor, T-box, conserved site / T-box superfamily / T-box domain signature 2. / T-box domain signature 1. / T-box domain profile. / Domain first found in the mice T locus (Brachyury) protein / T-box / p53-like transcription factor, DNA-binding ...Transcription factor, T-box / T-box transcription factor / Transcription factor, T-box, conserved site / T-box superfamily / T-box domain signature 2. / T-box domain signature 1. / T-box domain profile. / Domain first found in the mice T locus (Brachyury) protein / T-box / p53-like transcription factor, DNA-binding / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / T-box transcription factor TBX21
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.947 Å
AuthorsLiu, C.F. / Brandt, G.S. / Hoang, Q. / Hwang, E.S. / Naumova, N. / Lazarevic, V. / Dekker, J. / Glimcher, L.H. / Ringe, D. / Petsko, G.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Crystal structure of the DNA binding domain of the transcription factor T-bet suggests simultaneous recognition of distant genome sites.
Authors: Liu, C.F. / Brandt, G.S. / Hoang, Q.Q. / Naumova, N. / Lazarevic, V. / Hwang, E.S. / Dekker, J. / Glimcher, L.H. / Ringe, D. / Petsko, G.A.
History
DepositionAug 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: T-box transcription factor TBX21
B: T-box transcription factor TBX21
C: DNA
D: DNA
E: DNA
F: DNA


Theoretical massNumber of molelcules
Total (without water)76,3726
Polymers76,3726
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10930 Å2
ΔGint-70 kcal/mol
Surface area33860 Å2
2
A: T-box transcription factor TBX21
E: DNA
F: DNA


Theoretical massNumber of molelcules
Total (without water)38,1863
Polymers38,1863
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-32 kcal/mol
Surface area18170 Å2
MethodPISA
3
B: T-box transcription factor TBX21
C: DNA
D: DNA


Theoretical massNumber of molelcules
Total (without water)38,1863
Polymers38,1863
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-33 kcal/mol
Surface area18280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.450, 70.450, 438.389
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein T-box transcription factor TBX21 / T-box protein 21 / T-cell-specific T-box transcription factor T-bet / Transcription factor TBLYM


Mass: 23450.535 Da / Num. of mol.: 2 / Fragment: Tbox DNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tbx21, Tbet, Tblym / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q9JKD8
#2: DNA chain
DNA /


Mass: 7367.791 Da / Num. of mol.: 4 / Fragment: 24bp DNA / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.27 Å3/Da / Density % sol: 71.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.1 / Details: sodium citrate, sodium formate, ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.94→50 Å / Num. obs: 22707 / % possible obs: 87.3 % / Redundancy: 8.7 % / Biso Wilson estimate: 81.42 Å2 / Rmerge(I) obs: 0.124 / Net I/av σ(I): 11.242 / Net I/σ(I): 15.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.94-2.993.10.848131.4
2.99-3.053.70.673144.6
3.05-3.14.10.543156.3
3.1-3.174.60.301164.3
3.17-3.245.20.203179.4
3.24-3.315.90.227191
3.31-3.397.10.287198.1
3.39-3.498.30.376199.7
3.49-3.599.20.2711100
3.59-3.79.80.29199.8
3.7-3.8410.30.2511100
3.84-3.9910.50.2821100
3.99-4.1710.50.183199.9
4.17-4.3910.50.151199.8
4.39-4.6710.50.128199.5
4.67-5.0310.50.121199.5
5.03-5.5310.30.114199.5
5.53-6.3310.40.099199.4
6.33-7.9710.20.084197.7
7.97-508.80.08185.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Blu-Icedata collection
PDB_EXTRACT3.15data extraction
PHASERphasing
HKL-2000data scaling
HKL-2000data reduction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.947→43.702 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 37.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2944 1155 5.09 %Random selection
Rwork0.266 ---
obs0.2674 22676 87.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.947→43.702 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3106 1956 0 0 5062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125380
X-RAY DIFFRACTIONf_angle_d1.7417694
X-RAY DIFFRACTIONf_dihedral_angle_d24.9132106
X-RAY DIFFRACTIONf_chiral_restr0.075838
X-RAY DIFFRACTIONf_plane_restr0.012660
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9474-3.08150.2728600.34611268X-RAY DIFFRACTION41
3.0815-3.2440.37461060.30612078X-RAY DIFFRACTION68
3.244-3.44710.29511480.29852931X-RAY DIFFRACTION95
3.4471-3.71320.33891650.28823082X-RAY DIFFRACTION100
3.7132-4.08660.34251720.28213041X-RAY DIFFRACTION100
4.0866-4.67730.27191600.24293066X-RAY DIFFRACTION100
4.6773-5.89070.27261740.26683049X-RAY DIFFRACTION100
5.8907-43.70640.28441700.24773006X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6168-0.8385-0.3072.82130.96891.0815-0.0767-0.10610.39640.06980.034-0.3907-0.08140.0369-0.16211.39821.21350.17440.4207-0.20380.591159.3504-22.11681.4907
22.134-1.0328-0.47292.82930.18211.2223-0.07550.00650.1784-0.0353-0.0229-0.7279-0.03350.1306-0.12591.3951.2550.09420.4039-0.25450.678145.80431.3894-3.6173
30.81710.55820.10591.3282.46217.1009-0.13410.3462-0.2478-0.53990.27290.23880.4965-1.20440.18242.22020.4281-0.08091.4249-0.3720.508521.8778-9.4416-14.6006
41.52080.9395-1.3460.82420.44738.20440.0338-0.7664-0.10720.13490.1670.47290.6101-1.43330.04132.01620.85870.26071.8063-0.01280.609938.3899-36.379212.5292
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'
3X-RAY DIFFRACTION3chain 'C' or chain 'D'
4X-RAY DIFFRACTION4chain 'E' or chain 'F'

+
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