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- PDB-6fqp: Crystal structure of TALE homeobox domain transcription factor TG... -

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Basic information

Entry
Database: PDB / ID: 6fqp
TitleCrystal structure of TALE homeobox domain transcription factor TGIF1 with its consensus DNA
Components
  • DNA (5'-D(P*AP*TP*TP*GP*AP*CP*AP*GP*CP*TP*GP*TP*CP*AP*AP*T)-3')
  • Homeobox protein TGIF1
KeywordsTRANSCRIPTION / homeobox / three-amino acid loop extension / TGF-beta pathway
Function / homology
Function and homology information


positive regulation of amacrine cell differentiation / regulation of gastrulation / amacrine cell differentiation / nodal signaling pathway / co-SMAD binding / negative regulation of retinoic acid receptor signaling pathway / dorsal/ventral pattern formation / determination of left/right symmetry / neural tube closure / Downregulation of SMAD2/3:SMAD4 transcriptional activity ...positive regulation of amacrine cell differentiation / regulation of gastrulation / amacrine cell differentiation / nodal signaling pathway / co-SMAD binding / negative regulation of retinoic acid receptor signaling pathway / dorsal/ventral pattern formation / determination of left/right symmetry / neural tube closure / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / cellular response to growth factor stimulus / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of fibroblast proliferation / sequence-specific double-stranded DNA binding / fibroblast proliferation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of gene expression / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / nucleoplasm
Similarity search - Function
: / Homeobox KN domain / Homeobox KN domain / '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) / Homeobox protein TGIF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsGuca, E. / Macias, M.J.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2014-53787-P Spain
COFUND Marie Sklodowska CurieIRBPostPro2.0 600404 Spain
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: TGIF1 homeodomain interacts with Smad MH1 domain and represses TGF-beta signaling.
Authors: Guca, E. / Sunol, D. / Ruiz, L. / Konkol, A. / Cordero, J. / Torner, C. / Aragon, E. / Martin-Malpartida, P. / Riera, A. / Macias, M.J.
History
DepositionFeb 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 10, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: 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_unobs_or_zero_occ_atoms / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high / _refine_hist.d_res_low / _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_label_seq_id / _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_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: DNA (5'-D(P*AP*TP*TP*GP*AP*CP*AP*GP*CP*TP*GP*TP*CP*AP*AP*T)-3')
M: DNA (5'-D(P*AP*TP*TP*GP*AP*CP*AP*GP*CP*TP*GP*TP*CP*AP*AP*T)-3')
A: Homeobox protein TGIF1
B: Homeobox protein TGIF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2935
Polymers33,2534
Non-polymers401
Water1,22568
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-32 kcal/mol
Surface area11800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.851, 67.248, 102.315
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain DNA (5'-D(P*AP*TP*TP*GP*AP*CP*AP*GP*CP*TP*GP*TP*CP*AP*AP*T)-3')


Mass: 4897.204 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Protein Homeobox protein TGIF1 / 5'-TG-3'-interacting factor 1


Mass: 11729.339 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal 'GP' sequence comes from the purification tag
Source: (gene. exp.) Homo sapiens (human) / Gene: TGIF1, TGIF / Production host: Escherichia coli (E. coli) / References: UniProt: Q15583
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.39 Å3/Da / Density % sol: 63.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium acetate trihydrate pH 4.5, 30% v/v PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972422 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972422 Å / Relative weight: 1
ReflectionResolution: 2.42→67.25 Å / Num. obs: 13814 / % possible obs: 98.9 % / Redundancy: 2 % / Rmerge(I) obs: 0.0275 / Net I/σ(I): 17.3
Reflection shellResolution: 2.42→2.51 Å / Rmerge(I) obs: 0.232 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMACrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XRM

4xrm


Resolution: 2.42→45.537 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.24
RfactorNum. reflection% reflection
Rfree0.2409 656 4.77 %
Rwork0.205 --
obs0.2069 13749 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 117.63 Å2 / Biso mean: 52.9948 Å2 / Biso min: 23.84 Å2
Refinement stepCycle: LAST / Resolution: 2.42→45.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1083 656 1 68 1808

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