[English] 日本語
Yorodumi
- PDB-5bqd: Crystal Structure of TBX5 (1-239) Dimer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5bqd
TitleCrystal Structure of TBX5 (1-239) Dimer
ComponentsT-box transcription factor TBX5
KeywordsTRANSCRIPTION / cardiac / transcription factor / chd / NKX / TBX / DNA binding
Function / homology
Function and homology information


cardiac left ventricle formation / positive regulation of cell communication by electrical coupling involved in cardiac conduction / positive regulation of cardiac conduction / atrioventricular bundle cell differentiation / positive regulation of secondary heart field cardioblast proliferation / cell-cell signaling involved in cardiac conduction / bundle of His cell to Purkinje myocyte communication by electrical coupling / atrioventricular node cell fate commitment / cell migration involved in coronary vasculogenesis / bundle of His development ...cardiac left ventricle formation / positive regulation of cell communication by electrical coupling involved in cardiac conduction / positive regulation of cardiac conduction / atrioventricular bundle cell differentiation / positive regulation of secondary heart field cardioblast proliferation / cell-cell signaling involved in cardiac conduction / bundle of His cell to Purkinje myocyte communication by electrical coupling / atrioventricular node cell fate commitment / cell migration involved in coronary vasculogenesis / bundle of His development / sinoatrial node development / atrioventricular node cell development / positive regulation of cardioblast differentiation / forelimb morphogenesis / atrial septum morphogenesis / endocardial cushion development / Physiological factors / pericardium development / negative regulation of cardiac muscle cell proliferation / YAP1- and WWTR1 (TAZ)-stimulated gene expression / regulation of atrial cardiac muscle cell membrane depolarization / negative regulation of epithelial to mesenchymal transition / pattern specification process / embryonic forelimb morphogenesis / embryonic limb morphogenesis / Cardiogenesis / cell fate specification / atrioventricular valve morphogenesis / cardiac muscle cell proliferation / ventricular septum development / positive regulation of gap junction assembly / positive regulation of cardiac muscle cell proliferation / negative regulation of cell migration / protein-DNA complex / morphogenesis of an epithelium / lung development / cell-cell signaling / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Transcription factor, T-box / T-box transcription factor, DNA-binding domain / 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 ...Transcription factor, T-box / T-box transcription factor, DNA-binding domain / 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
T-box transcription factor TBX5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.583 Å
AuthorsPradhan, L. / Gopal, S. / Patel, A. / Kasahara, H. / Nam, H.J.
Funding support United States, 1items
OrganizationGrant numberCountry
American Heart Association13BGIA13960001 United States
CitationJournal: Biochemistry / Year: 2016
Title: Intermolecular Interactions of Cardiac Transcription Factors NKX2.5 and TBX5.
Authors: Pradhan, L. / Gopal, S. / Li, S. / Ashur, S. / Suryanarayanan, S. / Kasahara, H. / Nam, H.J.
History
DepositionMay 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 6, 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 ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: T-box transcription factor TBX5
B: T-box transcription factor TBX5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6725
Polymers53,5992
Non-polymers733
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-26 kcal/mol
Surface area19380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.455, 81.455, 341.022
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein T-box transcription factor TBX5 / T-box protein 5


Mass: 26799.686 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TBX5 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): RIPL / References: UniProt: Q99593
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 100mM Sodium Cacodylate pH 6.4 10mM MgSO4 1.8M Ammonium Sulphate

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.977 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.583→49.23 Å / Num. obs: 21874 / % possible obs: 92.06 % / Redundancy: 5 % / Rsym value: 0.106 / Net I/σ(I): 8.88

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000704kdata reduction
HKL-2000704kdata scaling
PHENIX1.9-1692phasing
RefinementResolution: 2.583→49.033 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2889 1989 9.09 %Random selection
Rwork0.2463 ---
obs0.2503 21874 98.75 %-
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.583→49.033 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3025 0 3 11 3039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113113
X-RAY DIFFRACTIONf_angle_d1.2594210
X-RAY DIFFRACTIONf_dihedral_angle_d14.3861152
X-RAY DIFFRACTIONf_chiral_restr0.048451
X-RAY DIFFRACTIONf_plane_restr0.006534
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5833-2.64790.37411320.33351333X-RAY DIFFRACTION95
2.6479-2.71950.40551420.32211413X-RAY DIFFRACTION99
2.7195-2.79950.39621370.2881373X-RAY DIFFRACTION100
2.7995-2.88990.29791380.26291384X-RAY DIFFRACTION100
2.8899-2.99320.32361410.26861403X-RAY DIFFRACTION100
2.9932-3.1130.33311400.26351395X-RAY DIFFRACTION100
3.113-3.25460.34341430.26811422X-RAY DIFFRACTION99
3.2546-3.42620.31791390.26581388X-RAY DIFFRACTION99
3.4262-3.64080.31851390.27591396X-RAY DIFFRACTION98
3.6408-3.92180.3251410.26221384X-RAY DIFFRACTION96
3.9218-4.31620.25331430.2171427X-RAY DIFFRACTION99
4.3162-4.94030.22841430.18971445X-RAY DIFFRACTION99
4.9403-6.22230.27821510.23271501X-RAY DIFFRACTION100
6.2223-49.04220.25871600.25421621X-RAY DIFFRACTION99

+
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