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- PDB-6od5: Human TCF4 C-terminal bHLH domain in Complex with 12-bp Oligonucl... -

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Basic information

Entry
Database: PDB / ID: 6od5
TitleHuman TCF4 C-terminal bHLH domain in Complex with 12-bp Oligonucleotide Containing E-box Sequence with 5-carboxylcytosines
Components
  • DNA (5'-D(*AP*(1CC)P*GP*CP*AP*CP*GP*TP*GP*(1CC)P*G)-3')
  • Transcription factor 4
KeywordsTRANSCRIPTION/DNA / protein-DNA complex / transcription factor / bHTH / E-Box / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


protein-DNA complex assembly / beta-catenin-TCF7L2 complex / beta-catenin-TCF complex / TGFBR3 expression / Myogenesis / E-box binding / TFIIB-class transcription factor binding / positive regulation of neuron differentiation / beta-catenin binding / sequence-specific double-stranded DNA binding ...protein-DNA complex assembly / beta-catenin-TCF7L2 complex / beta-catenin-TCF complex / TGFBR3 expression / Myogenesis / E-box binding / TFIIB-class transcription factor binding / positive regulation of neuron differentiation / beta-catenin binding / sequence-specific double-stranded DNA binding / nervous system development / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / protein heterodimerization activity / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / identical protein binding / nucleus
Similarity search - Function
: / Helix-loop-helix DNA-binding domain / MYOD Basic-Helix-Loop-Helix Domain, subunit B / Helix-loop-helix DNA-binding domain / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcription factor 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsHorton, J.R. / Cheng, X. / Yang, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049245-23 United States
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structural basis for preferential binding of human TCF4 to DNA containing 5-carboxylcytosine.
Authors: Yang, J. / Horton, J.R. / Li, J. / Huang, Y. / Zhang, X. / Blumenthal, R.M. / Cheng, X.
History
DepositionMar 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription factor 4
B: Transcription factor 4
X: DNA (5'-D(*AP*(1CC)P*GP*CP*AP*CP*GP*TP*GP*(1CC)P*G)-3')
Y: DNA (5'-D(*AP*(1CC)P*GP*CP*AP*CP*GP*TP*GP*(1CC)P*G)-3')
C: Transcription factor 4
D: Transcription factor 4
E: DNA (5'-D(*AP*(1CC)P*GP*CP*AP*CP*GP*TP*GP*(1CC)P*G)-3')
F: DNA (5'-D(*AP*(1CC)P*GP*CP*AP*CP*GP*TP*GP*(1CC)P*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,05015
Polymers44,6138
Non-polymers4387
Water2,450136
1
A: Transcription factor 4
B: Transcription factor 4
X: DNA (5'-D(*AP*(1CC)P*GP*CP*AP*CP*GP*TP*GP*(1CC)P*G)-3')
Y: DNA (5'-D(*AP*(1CC)P*GP*CP*AP*CP*GP*TP*GP*(1CC)P*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5588
Polymers22,3064
Non-polymers2524
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6220 Å2
ΔGint-53 kcal/mol
Surface area10760 Å2
MethodPISA
2
C: Transcription factor 4
D: Transcription factor 4
E: DNA (5'-D(*AP*(1CC)P*GP*CP*AP*CP*GP*TP*GP*(1CC)P*G)-3')
F: DNA (5'-D(*AP*(1CC)P*GP*CP*AP*CP*GP*TP*GP*(1CC)P*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4937
Polymers22,3064
Non-polymers1863
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6430 Å2
ΔGint-39 kcal/mol
Surface area10550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.677, 44.757, 54.640
Angle α, β, γ (deg.)78.63, 78.88, 79.27
Int Tables number1
Space group name H-MP1

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Components

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Protein / DNA chain , 2 types, 8 molecules ABCDXYEF

#1: Protein
Transcription factor 4 / TCF-4 / Class B basic helix-loop-helix protein 19 / bHLHb19 / Immunoglobulin transcription factor 2 ...TCF-4 / Class B basic helix-loop-helix protein 19 / bHLHb19 / Immunoglobulin transcription factor 2 / ITF-2 / SL3-3 enhancer factor 2 / SEF-2


Mass: 7401.737 Da / Num. of mol.: 4 / Fragment: C-terminal bHLH domain (UNP residues 405-464)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TCF4, BHLHB19, ITF2, SEF2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-Codon Plus(DE3)-RIL / References: UniProt: P15884
#2: DNA chain
DNA (5'-D(*AP*(1CC)P*GP*CP*AP*CP*GP*TP*GP*(1CC)P*G)-3')


Mass: 3751.412 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 143 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.34 Å3/Da / Density % sol: 47.52 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG4000, 0.1 M Tris, pH 8.5, 0.2 M lithium sulfate monohydrate or 0.2 M sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 16, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→36.661 Å / Num. obs: 24281 / % possible obs: 96.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.263 / Rpim(I) all: 0.138 / Net I/σ(I): 5.4
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.554 / Num. unique obs: 2094 / CC1/2: 0.361 / Rpim(I) all: 0.412 / % possible all: 82.8

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2QL2

2ql2


Resolution: 2.05→36.661 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 28.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2803 1215 5.01 %
Rwork0.2342 --
obs0.2364 24247 96.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→36.661 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1931 965 27 136 3059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033045
X-RAY DIFFRACTIONf_angle_d0.5524284
X-RAY DIFFRACTIONf_dihedral_angle_d20.0791665
X-RAY DIFFRACTIONf_chiral_restr0.025487
X-RAY DIFFRACTIONf_plane_restr0.002392
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0501-2.13210.32081210.29772155X-RAY DIFFRACTION80
2.1321-2.22920.32231240.28622407X-RAY DIFFRACTION91
2.2292-2.34670.32581350.26942600X-RAY DIFFRACTION97
2.3467-2.49370.30381410.25632659X-RAY DIFFRACTION99
2.4937-2.68610.24531380.2612604X-RAY DIFFRACTION99
2.6861-2.95640.28381380.26132663X-RAY DIFFRACTION99
2.9564-3.38390.30171420.23982633X-RAY DIFFRACTION99
3.3839-4.26230.27341410.19672675X-RAY DIFFRACTION100
4.2623-36.66710.2411350.20232636X-RAY DIFFRACTION99
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)
18.5376-5.5811-2.92235.39952.41913.9956-0.4637-0.6920.55370.37540.5768-0.4316-0.10840.4052-0.14130.2183-0.0197-0.09040.2086-0.00530.2084-1.9274-8.927431.9508
24.0409-5.88010.96348.6422-1.23210.93820.94621.09740.6903-0.0962-0.5762-0.8092-0.03421.5756-0.18580.30920.014-0.01930.7906-0.08940.334110.4318-13.647117.1023
36.4951-4.0310.42199.0048-1.46344.42150.35630.3838-0.4466-0.2646-0.5067-0.0010.60830.54990.0940.21150.0574-0.00270.2431-0.04080.1387.5448-28.254222.0001
43.4586-3.25142.99567.1397-6.55966.7279-0.00270.1215-0.1407-0.0287-0.09970.13660.1334-0.08090.07040.22160.036-0.00490.2086-0.08670.1549-7.2477-18.359722.2166
53.9564-3.3049-1.95627.47391.8322.5287-0.2764-0.36360.23250.4810.0952-0.59730.24460.39940.21870.22660.0841-0.00560.34680.01940.17266.3431-25.856131.8051
65.04430.325-1.2060.87740.80722.17670.1017-0.00920.65810.00630.127-0.0447-0.07020.4228-0.25660.18760.01650.03550.2532-0.01260.3018-10.4525-4.414125.0128
73.28812.0615-0.2375.1498-2.99034.2621-0.2150.31830.2383-0.54920.28820.11230.3036-0.19640.06850.2035-0.0354-0.00960.21350.01160.1976-11.5433-5.220424.3669
87.4309-7.9704-7.88878.01157.20147.2694-0.099-0.24930.2220.2597-0.0036-0.2475-0.04920.21870.12470.25170.0343-0.0510.2225-0.00890.206621.1566.06965.258
96.3637-3.0305-0.3738.97191.11331.50330.16830.5226-0.2484-0.457-0.19460.10830.37610.46340.02920.33590.1201-0.00710.2609-0.02820.107428.3077-5.6301-7.8515
103.2187-2.62121.49045.9632-1.30424.68750.14350.0242-0.2498-0.1286-0.05160.32610.3123-0.3824-0.11050.1573-0.0220.00440.2264-0.07760.180812.30350.812-4.6712
118.6158-4.689-2.0058.09171.99156.2998-0.0660.05520.16040.22720.0683-0.460.25180.3450.03950.19850.0214-0.02410.1256-0.00140.105429.0427-10.22012.6391
125.93551.258-1.75723.08290.68545.2625-0.1381-0.47650.2438-0.15320.16650.10290.06830.20470.00160.1590.05740.02190.1942-0.05950.161210.776513.6657-1.0628
135.88590.504-2.41784.5718-0.03166.60790.00190.0694-0.0275-0.26430.14880.47160.0033-0.078-0.26740.20460.0111-0.03810.04560.0620.26659.894812.6739-1.0995
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 567 through 599 )
2X-RAY DIFFRACTION2chain 'A' and (resid 600 through 606 )
3X-RAY DIFFRACTION3chain 'A' and (resid 607 through 628 )
4X-RAY DIFFRACTION4chain 'B' and (resid 568 through 606 )
5X-RAY DIFFRACTION5chain 'B' and (resid 607 through 627 )
6X-RAY DIFFRACTION6chain 'X' and (resid 1 through 12 )
7X-RAY DIFFRACTION7chain 'Y' and (resid 1 through 12 )
8X-RAY DIFFRACTION8chain 'C' and (resid 569 through 598 )
9X-RAY DIFFRACTION9chain 'C' and (resid 599 through 627 )
10X-RAY DIFFRACTION10chain 'D' and (resid 567 through 606 )
11X-RAY DIFFRACTION11chain 'D' and (resid 607 through 628 )
12X-RAY DIFFRACTION12chain 'E' and (resid 2 through 12 )
13X-RAY DIFFRACTION13chain 'F' and (resid 1 through 12 )

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