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

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Basic information

Entry
Database: PDB / ID: 6fqq
TitleCrystal structure of TALE homeobox domain transcription factor TGIF1 double alanine mutant bound to 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: 3.25000253887 Å
AuthorsGuca, E. / Macias, M.J.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2014-53787P 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 1.3Nov 6, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name
Revision 1.4Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)52,9109
Polymers52,8758
Non-polymers351
Water57632
1
A: Homeobox protein TGIF1
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')
B: Homeobox protein TGIF1
D: Homeobox protein TGIF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7946
Polymers34,7595
Non-polymers351
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-33 kcal/mol
Surface area11540 Å2
MethodPISA
2
G: DNA (5'-D(P*AP*TP*TP*GP*AP*CP*AP*GP*CP*TP*GP*TP*CP*AP*AP*T)-3')
H: DNA (5'-D(P*AP*TP*TP*GP*AP*CP*AP*GP*CP*TP*GP*TP*CP*AP*AP*T)-3')
E: Homeobox protein TGIF1


Theoretical massNumber of molelcules
Total (without water)18,1163
Polymers18,1163
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-24 kcal/mol
Surface area11670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.058, 93.016, 100.711
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
32
42

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNLYSLYS(chain 'A' and (resid 170 through 176 or (resid 177...AA170 - 22912 - 71
21ASNASNLYSLYS(chain 'B' and (resid 170 through 172 or (resid 173...BD170 - 22912 - 71
31ASNASNLYSLYS(chain 'D' and (resid 170 through 172 or (resid 173...DG170 - 22912 - 71
41ASNASNLYSLYS(chain 'E' and (resid 170 through 172 or (resid 173...EH170 - 22912 - 71
12DADADTDTchain 'G'GE1 - 161 - 16
22DADADTDTchain 'H'HF1 - 161 - 16
32DADADTDTchain 'L'LB1 - 161 - 16
42DADADTDTchain 'M'MC1 - 161 - 16

NCS ensembles :
ID
1
2

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Components

#1: Protein
Homeobox protein TGIF1 / 5'-TG-3'-interacting factor 1


Mass: 8321.522 Da / Num. of mol.: 4 / Mutation: R167A R168A
Source method: isolated from a genetically manipulated source
Details: N-terminal 'GP' sequence comes from the purification tag the protein construct corresponds to a double mutant: R167A/R168A
Source: (gene. exp.) Homo sapiens (human) / Gene: TGIF1, TGIF / Production host: Escherichia coli (E. coli) / References: UniProt: Q15583
#2: 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.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.83 Å3/Da / Density % sol: 56.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2M L-Proline, 0.1M HEPES pH 7.5, 24% v/v PEG 1,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07227 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07227 Å / Relative weight: 1
ReflectionResolution: 3.25→45.11 Å / Num. obs: 9236 / % possible obs: 99.01 % / Redundancy: 6.7 % / Biso Wilson estimate: 75.2518542619 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 4.4
Reflection shellResolution: 3.25→3.36 Å / Rmerge(I) obs: 0.288

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FQP

6fqp


Resolution: 3.25000253887→45.1103050601 Å / SU ML: 0.380460958511 / Cross valid method: FREE R-VALUE / σ(F): 0.311475378067 / Phase error: 29.2330837403
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.27291093312 435 4.70983109571 %
Rwork0.215170778982 8801 -
obs0.217663827964 9236 99.0137221269 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.5957979986 Å2
Refinement stepCycle: LAST / Resolution: 3.25000253887→45.1103050601 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1979 1312 1 32 3324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01157669012043494
X-RAY DIFFRACTIONf_angle_d1.297856215995009
X-RAY DIFFRACTIONf_chiral_restr0.0718785812007562
X-RAY DIFFRACTIONf_plane_restr0.00807836936075410
X-RAY DIFFRACTIONf_dihedral_angle_d20.95966281181855
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.25-3.72010.2857752899041340.2263232487122842X-RAY DIFFRACTION98.0560131796
3.7201-4.68610.2890666914631410.2332835230612922X-RAY DIFFRACTION99.4480519481
4.6861-45.11460.2582194880021600.1998273794373037X-RAY DIFFRACTION99.5020230314

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