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- PDB-6od4: Human TCF4 C-terminal bHLH domain in Complex with 11-bp Oligonucl... -

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Basic information

Entry
Database: PDB / ID: 6od4
TitleHuman TCF4 C-terminal bHLH domain in Complex with 11-bp Oligonucleotide Containing E-box Sequence
Components
  • DNA (5'-D(*TP*AP*CP*AP*CP*GP*TP*GP*TP*A)-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 / 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 ...protein-DNA complex assembly / beta-catenin-TCF7L2 complex / beta-catenin-TCF complex / 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 / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / DNA-binding transcription factor activity / 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 DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / 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: 1.699 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
G: Transcription factor 4
H: Transcription factor 4
X: DNA (5'-D(*TP*AP*CP*AP*CP*GP*TP*GP*TP*A)-3')
W: DNA (5'-D(*TP*AP*CP*AP*CP*GP*TP*GP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3657
Polymers36,3036
Non-polymers621
Water72140
1
A: Transcription factor 4
B: Transcription factor 4
X: DNA (5'-D(*TP*AP*CP*AP*CP*GP*TP*GP*TP*A)-3')
W: DNA (5'-D(*TP*AP*CP*AP*CP*GP*TP*GP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5625
Polymers21,5004
Non-polymers621
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-44 kcal/mol
Surface area10390 Å2
MethodPISA
2
G: Transcription factor 4
H: Transcription factor 4


Theoretical massNumber of molelcules
Total (without water)14,8032
Polymers14,8032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-27 kcal/mol
Surface area7430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.614, 43.602, 43.557
Angle α, β, γ (deg.)97.17, 102.56, 102.53
Int Tables number1
Space group name H-MP1

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Components

#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(*TP*AP*CP*AP*CP*GP*TP*GP*TP*A)-3')


Mass: 3348.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 1.8 Å3/Da / Density % sol: 31.48 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 20% PEG4000, 10% 2-propanol, 0.1 M sodium citrate tribasic dihydrate, pH 5.6

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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: Aug 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: 1.699→41.82 Å / Num. obs: 26021 / % possible obs: 95.3 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.041 / Net I/σ(I): 16.4
Reflection shellResolution: 1.7→1.75 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.711 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 2269 / CC1/2: 0.522 / Rpim(I) all: 0.418 / % possible all: 83.1

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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: 1.699→41.817 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 34.07
RfactorNum. reflection% reflection
Rfree0.2668 1304 5.02 %
Rwork0.222 --
obs0.2242 25959 93.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.699→41.817 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1748 407 4 40 2199
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022225
X-RAY DIFFRACTIONf_angle_d0.4233080
X-RAY DIFFRACTIONf_dihedral_angle_d18.6051310
X-RAY DIFFRACTIONf_chiral_restr0.027375
X-RAY DIFFRACTIONf_plane_restr0.002325
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6989-1.76690.41611100.32591935X-RAY DIFFRACTION67
1.7669-1.84740.37221370.30682628X-RAY DIFFRACTION88
1.8474-1.94480.32831460.28522828X-RAY DIFFRACTION97
1.9448-2.06660.27371520.26162916X-RAY DIFFRACTION99
2.0666-2.22610.28751530.23832898X-RAY DIFFRACTION99
2.2261-2.45020.29281530.22722843X-RAY DIFFRACTION97
2.4502-2.80460.26661480.22522831X-RAY DIFFRACTION96
2.8046-3.53330.22791490.23422915X-RAY DIFFRACTION100
3.5333-41.82930.25751560.19232861X-RAY DIFFRACTION97
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)
12.87870.58440.35412.9365-1.09421.9189-0.14120.1356-0.4061-0.35960.0375-0.96210.479-0.00760.17330.4190.08980.08980.3001-0.02890.3489-4.0017-18.2139-29.6092
20.35760.404-1.61.2502-1.9716.59720.5413-0.5804-0.08711.2575-0.434-1.0172-1.01722.0407-0.00270.624-0.192-0.16280.59750.02050.56130.36991.9671-25.8731
36.0235-0.5991.70014.0628-4.05475.1324-0.17120.24470.74040.41460.25480.0602-0.5987-0.3035-0.02230.23870.03080.01440.2206-0.02880.3054-9.39314.8367-32.8804
43.3584-0.93051.43325.5819-4.49063.4163-0.2303-0.35510.24930.68360.2325-0.0576-0.3604-0.8275-0.21220.37620.04690.10440.2937-0.03440.264-13.658-9.0011-19.107
54.9239-3.86213.94842.9813-2.53624.59710.5338-0.0864-0.5605-1.0236-0.42481.18541.2771-0.7356-0.80150.6037-0.1709-0.02190.467-0.08290.5121-17.8013-9.3099-39.3653
65.56720.08090.30563.4594-3.1877.8872-0.07030.73860.4173-0.4185-0.221-0.49820.16530.13490.2830.16570.0210.04390.30410.01620.2084-8.0193-1.8111-40.8811
75.72410.5129-0.72417.626-5.14923.81460.13280.554-0.2452-1.07190.25980.50340.618-0.9161-0.25880.452-0.0202-0.11720.2732-0.01390.383-5.78429.9224-15.999
88.5773-0.36160.65193.4137-3.04479.6937-0.1185-0.9933-0.09440.21470.24240.3055-0.1738-0.599-0.110.1906-0.0421-0.01080.3869-0.03940.2814-1.2057.01321.1786
94.42330.2077-0.41871.8509-2.03536.14460.2734-0.55160.24980.3508-0.2791-0.8553-1.08470.3419-0.17950.4247-0.07430.00530.4560.0250.25266.159916.5144-6.8916
100.8022-0.37380.55695.659-7.93372.0114-0.05750.7296-0.6318-0.6876-1.5397-1.65950.55481.29691.38290.56440.06790.060.76580.05930.67079.00292.9221-12.7134
118.17932.1656-2.49543.6953-2.03054.1247-0.1143-0.149-1.2873-0.1675-0.0054-0.30670.49710.01080.06460.2342-0.0166-0.04280.3261-0.00680.4129-0.4011-1.196-5.7223
123.38223.422.06458.71780.92339.7538-0.05590.0401-1.0391-0.06120.3504-0.77910.1410.1248-0.26450.53080.02610.07090.255-0.01520.3452-8.9924-20.9911-18.2185
133.24011.13481.45588.02071.13879.914-0.2461-0.7252-0.29950.25950.1261-0.1663-0.1027-0.80490.11390.49990.08530.01920.30760.03930.2232-8.4295-20.8414-18.452
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 567 through 597 )
2X-RAY DIFFRACTION2chain 'A' and (resid 598 through 606 )
3X-RAY DIFFRACTION3chain 'A' and (resid 607 through 627 )
4X-RAY DIFFRACTION4chain 'B' and (resid 567 through 597 )
5X-RAY DIFFRACTION5chain 'B' and (resid 598 through 606 )
6X-RAY DIFFRACTION6chain 'B' and (resid 607 through 627 )
7X-RAY DIFFRACTION7chain 'G' and (resid 573 through 597 )
8X-RAY DIFFRACTION8chain 'G' and (resid 598 through 628 )
9X-RAY DIFFRACTION9chain 'H' and (resid 574 through 597 )
10X-RAY DIFFRACTION10chain 'H' and (resid 598 through 606 )
11X-RAY DIFFRACTION11chain 'H' and (resid 607 through 628 )
12X-RAY DIFFRACTION12chain 'X' and (resid 2 through 11 )
13X-RAY DIFFRACTION13chain 'W' and (resid 2 through 11 )

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