[English] 日本語
Yorodumi
- PDB-1h6f: Human TBX3, a transcription factor responsible for ulnar-mammary ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1h6f
TitleHuman TBX3, a transcription factor responsible for ulnar-mammary syndrome, bound to a palindromic DNA site
Components
  • 5'-D(*TP*AP*AP*TP*TP*TP*CP*AP*CP*AP*CP*CP*TP* AP*GP*GP*TP*GP*TP*GP*AP*AP*AP*T)-3'
  • T-BOX TRANSCRIPTION FACTOR TBX3
KeywordsTRANSCRIPTION FACTOR / TBX3 / T-BOX TRANSCRIPTION FACTOR / ULNAR-MAMMARY SYNDROME / HOLT-ORAM-SYNDROME / IG-FOLD / DNA-BINDING / REPRESSOR / NUCLEAR PROTEIN / DEVELOPMENTAL PROTEIN
Function / homology
Function and homology information


cardiac chamber development / mammary placode formation / ureteric peristalsis / sinoatrial node cell development / atrioventricular bundle cell differentiation / specification of animal organ position / : / female genitalia development / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 ...cardiac chamber development / mammary placode formation / ureteric peristalsis / sinoatrial node cell development / atrioventricular bundle cell differentiation / specification of animal organ position / : / female genitalia development / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / limbic system development / luteinizing hormone secretion / follicle-stimulating hormone secretion / mesoderm morphogenesis / forelimb morphogenesis / anterior/posterior axis specification, embryo / cardiac muscle cell fate commitment / chromatin => GO:0000785 / smooth muscle cell differentiation / male genitalia development / mammary gland development / negative regulation of myoblast differentiation / embryonic forelimb morphogenesis / embryonic hindlimb morphogenesis / branching involved in mammary gland duct morphogenesis / cell fate specification / negative regulation of epithelial cell differentiation / embryonic digit morphogenesis / stem cell population maintenance / ventricular septum morphogenesis / roof of mouth development / positive regulation of stem cell proliferation / heart looping / blood vessel development / outflow tract morphogenesis / positive regulation of cell cycle / central nervous system development / skeletal system development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / animal organ morphogenesis / DNA-binding transcription repressor activity, RNA polymerase II-specific / cellular senescence / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / in utero embryonic development / sequence-specific DNA 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 / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
T-box transcription factor 2/3, transcription activation domain / T-box transcription factor 2/3, TAD domain / 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 transcription factor 2/3, transcription activation domain / T-box transcription factor 2/3, TAD domain / 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 TBX3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsColl, M. / Muller, C.W.
Citation
Journal: Structure / Year: 2002
Title: Structure of the DNA-Bound T-Box Domain of Human Tbx3, a Transcription Factor Responsible for Ulnar- Mammary Syndrome
Authors: Coll, M. / Seidman, J.G. / Muller, C.W.
#1: Journal: Nature / Year: 1997
Title: Crystallographic Structure of the T Domain-DNA Complex of the Brachyury Transcription Factor
Authors: Muller, C.W. / Hermann, B.
History
DepositionJun 13, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 28, 2018Group: Advisory / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / struct
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant / _struct.title
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: T-BOX TRANSCRIPTION FACTOR TBX3
B: T-BOX TRANSCRIPTION FACTOR TBX3
C: 5'-D(*TP*AP*AP*TP*TP*TP*CP*AP*CP*AP*CP*CP*TP* AP*GP*GP*TP*GP*TP*GP*AP*AP*AP*T)-3'
D: 5'-D(*TP*AP*AP*TP*TP*TP*CP*AP*CP*AP*CP*CP*TP* AP*GP*GP*TP*GP*TP*GP*AP*AP*AP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1575
Polymers60,1324
Non-polymers241
Water11,007611
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)39.040, 104.910, 125.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99996, 0.00365, 0.00778), (0.00359, 0.99996, -0.00813), (-0.00781, -0.0081, -0.99994)
Vector: 14.478, 0.52063, 63.14726)

-
Components

#1: Protein T-BOX TRANSCRIPTION FACTOR TBX3 / TBX3 TRANSCRIPTION FACTOR / T-BOX PROTEIN 3


Mass: 22698.367 Da / Num. of mol.: 2 / Fragment: T-DOMAIN RESIDUES 101-291
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PT7-7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O15119
#2: DNA chain 5'-D(*TP*AP*AP*TP*TP*TP*CP*AP*CP*AP*CP*CP*TP* AP*GP*GP*TP*GP*TP*GP*AP*AP*AP*T)-3'


Mass: 7367.791 Da / Num. of mol.: 2 / Fragment: PALINDROMIC BINDING SITE / Source method: obtained synthetically / Source: (synth.) SYNTHETIC (others)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 611 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTRANSCRIPTIONAL REPRESSOR INVOLVED IN DEVELOPMENTAL PROCESSES.
Sequence detailsFIRST TWO RESIDUES, MET AND LYS, WERE ADDED AT THE N-TERMINUS FOR CLONING AND EXPRESSION THE ...FIRST TWO RESIDUES, MET AND LYS, WERE ADDED AT THE N-TERMINUS FOR CLONING AND EXPRESSION THE PROTEIN IS THE SPLICE ISOFORM I

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 42.35 %
Crystal growpH: 6 / Details: pH 6.00
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.76 mMDNA duplex1drop
20.59 mMprotein1drop
340 mMmagnesium acetate1reservoir
450 mMsodium cacodylate1reservoirpH6.0
530 %MPD1reservoir

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.956
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.956 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 55690 / % possible obs: 96.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 12
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 4 / % possible all: 91.1
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 204582 / Rmerge(I) obs: 0.073
Reflection shell
*PLUS
% possible obs: 91.1 % / Rmerge(I) obs: 0.298

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XBR

1xbr


Resolution: 1.7→20 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2388 -9.7 %RANDOM
Rwork0.2007 ---
obs0.2007 55690 96.6 %-
Displacement parametersBiso mean: 25.0945 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3065 978 1 611 4655
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.8581.5
X-RAY DIFFRACTIONc_mcangle_it2.0262
X-RAY DIFFRACTIONc_scbond_it1.9362
X-RAY DIFFRACTIONc_scangle_it2.722.5
LS refinement shellResolution: 1.7→1.76 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.2974 491
Rwork-4626
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor obs: 0.2007 / Rfactor Rfree: 0.2388 / Rfactor Rwork: 0.2007
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.2974

+
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