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- PDB-6od3: Human TCF4 C-terminal bHLH domain in Complex with 13-bp Oligonucl... -

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Basic information

Entry
Database: PDB / ID: 6od3
TitleHuman TCF4 C-terminal bHLH domain in Complex with 13-bp Oligonucleotide Containing E-box Sequence
Components
  • DNA (5'-D(*CP*AP*TP*AP*CP*AP*CP*GP*TP*GP*TP*AP*T)-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 / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / chromatin / 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: 1.494 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(*CP*AP*TP*AP*CP*AP*CP*GP*TP*GP*TP*AP*T)-3')
W: DNA (5'-D(*CP*AP*TP*AP*CP*AP*CP*GP*TP*GP*TP*AP*T)-3')
E: Transcription factor 4
F: Transcription factor 4
Y: DNA (5'-D(*CP*AP*TP*AP*CP*AP*CP*GP*TP*GP*TP*AP*T)-3')
Z: DNA (5'-D(*CP*AP*TP*AP*CP*AP*CP*GP*TP*GP*TP*AP*T)-3')
G: Transcription factor 4
H: Transcription factor 4
I: Transcription factor 4
J: Transcription factor 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,96426
Polymers75,01612
Non-polymers94814
Water6,323351
1
A: Transcription factor 4
B: Transcription factor 4
X: DNA (5'-D(*CP*AP*TP*AP*CP*AP*CP*GP*TP*GP*TP*AP*T)-3')
W: DNA (5'-D(*CP*AP*TP*AP*CP*AP*CP*GP*TP*GP*TP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,17512
Polymers22,7054
Non-polymers4708
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6810 Å2
ΔGint-56 kcal/mol
Surface area11110 Å2
MethodPISA
2
E: Transcription factor 4
F: Transcription factor 4
Y: DNA (5'-D(*CP*AP*TP*AP*CP*AP*CP*GP*TP*GP*TP*AP*T)-3')
Z: DNA (5'-D(*CP*AP*TP*AP*CP*AP*CP*GP*TP*GP*TP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8647
Polymers22,7054
Non-polymers1603
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5990 Å2
ΔGint-57 kcal/mol
Surface area12230 Å2
MethodPISA
3
G: Transcription factor 4
H: Transcription factor 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8663
Polymers14,8032
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-26 kcal/mol
Surface area8620 Å2
MethodPISA
4
I: Transcription factor 4
J: Transcription factor 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0604
Polymers14,8032
Non-polymers2562
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-28 kcal/mol
Surface area7430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.180, 58.946, 62.720
Angle α, β, γ (deg.)104.63, 90.34, 94.86
Int Tables number1
Space group name H-MP1

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Components

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Protein / DNA chain , 2 types, 12 molecules ABEFGHIJXWYZ

#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.: 8 / 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(*CP*AP*TP*AP*CP*AP*CP*GP*TP*GP*TP*AP*T)-3')


Mass: 3950.598 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 365 molecules

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


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.24 Å3/Da / Density % sol: 45.11 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% PEG3350, 0.1 M Tris, pH 8.5, 0.2 M sodium chloride

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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: 1.49→37.904 Å / Num. obs: 169064 / % possible obs: 80.3 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.033 / Net I/σ(I): 21.6
Reflection shellResolution: 1.49→1.54 Å / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 12726 / CC1/2: 0.627 / Rpim(I) all: 0.471 / % possible all: 60.5

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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: 1.494→37.904 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 28.86
RfactorNum. reflection% reflection
Rfree0.2366 1901 2.28 %
Rwork0.2214 --
obs0.2218 168745 79.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.494→37.904 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3697 1032 59 351 5139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024947
X-RAY DIFFRACTIONf_angle_d0.3976843
X-RAY DIFFRACTIONf_dihedral_angle_d18.9551971
X-RAY DIFFRACTIONf_chiral_restr0.034811
X-RAY DIFFRACTIONf_plane_restr0.002701
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4937-1.51260.35891060.34723931X-RAY DIFFRACTION51
1.5126-1.53250.36151180.34014619X-RAY DIFFRACTION61
1.5325-1.55350.27491070.33144969X-RAY DIFFRACTION65
1.5535-1.57570.35351400.31865153X-RAY DIFFRACTION67
1.5757-1.59920.2798830.29865157X-RAY DIFFRACTION67
1.5992-1.62420.33961210.29944762X-RAY DIFFRACTION62
1.6242-1.65080.31691350.28185672X-RAY DIFFRACTION75
1.6508-1.67930.27371540.26726569X-RAY DIFFRACTION86
1.6793-1.70980.27411570.2656526X-RAY DIFFRACTION86
1.7098-1.74270.27161340.25466875X-RAY DIFFRACTION88
1.7427-1.77830.28481660.2596601X-RAY DIFFRACTION87
1.7783-1.81690.2451580.25286699X-RAY DIFFRACTION87
1.8169-1.85920.25221650.25176542X-RAY DIFFRACTION86
1.8592-1.90570.23281470.25256622X-RAY DIFFRACTION86
1.9057-1.95720.27531540.26046521X-RAY DIFFRACTION85
1.9572-2.01480.27191600.25866360X-RAY DIFFRACTION84
2.0148-2.07980.30141350.25376248X-RAY DIFFRACTION82
2.0798-2.15420.30481400.24816043X-RAY DIFFRACTION79
2.1542-2.24040.25051180.23155231X-RAY DIFFRACTION68
2.2404-2.34230.23361420.21696243X-RAY DIFFRACTION82
2.3423-2.46580.23511710.21317101X-RAY DIFFRACTION92
2.4658-2.62030.26351670.21997056X-RAY DIFFRACTION92
2.6203-2.82250.24041610.22816987X-RAY DIFFRACTION92
2.8225-3.10640.23461690.22386923X-RAY DIFFRACTION90
3.1064-3.55570.19991490.19726640X-RAY DIFFRACTION87
3.5557-4.47860.19671280.18345795X-RAY DIFFRACTION76
4.4786-37.91670.20451640.19197051X-RAY DIFFRACTION92
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)
18.1999-7.0505-2.89078.90413.5913.5695-0.08110.0520.28940.13260.1103-0.4702-0.06980.0163-0.04680.1622-0.05030.00360.17940.00210.1901-1.49283.467732.2317
24.9817-3.28251.61386.1819-1.97475.02830.11310.2813-0.1245-0.8766-0.2443-0.59570.83580.26880.17330.29250.01110.10320.1995-0.06040.30566.9118-15.46926.0187
34.1193-4.76175.37746.2301-5.83588.4440.14610.0118-0.1351-0.22860.07340.16140.3247-0.1942-0.04330.151-0.07910.02710.1763-0.01730.1492-7.2403-5.619120.3363
45.6418-2.42380.31446.1928-1.76925.1385-0.374-0.3281-0.06010.48480.3717-0.58380.42540.03360.0330.23570.0305-0.04470.1448-0.04350.19552.7125-13.106337.6195
53.8409-0.6099-2.05962.4416-1.08133.6780.0983-0.33810.4359-0.00790.2247-0.0288-0.12410.2809-0.31320.147-0.01820.03870.2327-0.02610.1839-10.06316.921225.258
63.79740.0297-1.33692.9975-0.79744.8886-0.17850.34770.1463-0.23360.2789-0.03890.0714-0.1541-0.08280.1674-0.05380.0020.17990.01460.1158-10.39425.533523.0771
78.5624-6.2519-4.05556.70243.61284.40650.13980.2280.4432-0.1063-0.1472-0.287-0.07210.0417-0.02330.1622-0.07070.01550.160.05050.1611-23.203513.22871.5134
84.2305-0.26580.02872.4637-0.10843.06030.23570.5826-0.5645-0.3923-0.394-0.11150.82250.44540.11970.37070.06890.07030.2776-0.07320.2227-14.7017-6.0606-5.1196
98.4851-6.35396.62697.7899-6.16655.46070.39060.4132-0.536-0.46-0.13470.38040.7815-0.1466-0.1480.2541-0.02030.02680.2337-0.06150.2073-29.65451.7323-7.8355
108.3792-5.74696.57853.9266-4.50565.1617-0.1323-0.8918-1.06080.59561.41641.63460.7876-0.9145-1.18720.5479-0.06110.12660.44360.1440.4325-27.9994-3.083110.7809
116.076-4.77191.44986.5957-0.65126.3306-0.218-0.258-0.06920.33740.2692-0.18870.63470.5762-0.06060.33190.0190.04180.17060.00870.1706-14.1115-3.89955.9252
124.05590.1856-2.30741.949-0.67465.19580.34270.24750.2860.0227-0.02540.2627-0.332-0.4095-0.32050.1810.00860.07070.24880.00060.224-33.057315.1726-4.3112
132.2446-0.1167-0.31972.97-0.11645.13390.00660.20520.1642-0.21820.0201-0.0220.0589-0.3072-0.02060.14740.01530.00670.27530.06430.1609-32.759214.2524-8.2045
142.2181-2.18812.03317.3515-1.2611.97081.2562-1.49871.7089-0.47530.5348-0.14630.10550.7695-1.95170.69740.04710.02370.631-0.22540.7033-26.315931.348332.6618
152.9780.17894.72935.51-1.57178.2815-0.0422-0.4993-0.10150.78970.07460.49890.2012-0.62960.02160.37440.00410.09420.3103-0.0410.295-30.225623.670419.6854
163.9989-2.62981.228.1739-3.98865.58980.12080.09240.3354-0.4562-0.08340.5324-0.3309-0.0969-0.0480.3172-0.0417-0.02620.129-0.01930.3062-28.474931.52928.0474
176.3216-1.0586-0.03949.57870.96314.82180.1528-0.1548-0.4417-0.151-0.33810.57140.885-0.20940.21240.40970.0050.00110.30720.02630.2255-18.4562.085616.0072
186.1764-4.41773.08893.3051-2.88674.81150.50740.68740.8377-0.5416-0.773-1.1643-0.43040.34510.23150.3919-0.07450.08020.20560.02220.4549-17.238429.30411.0057
197.8171-0.40053.18714.0807-3.25485.216-0.3503-0.07480.50310.74140.19050.1299-0.72770.05650.19080.4927-0.01110.020.1981-0.0930.3528-25.010738.60316.8374
205.4617-0.64245.57471.5044-0.98775.6559-0.198-1.8918-0.56171.43330.6179-0.1626-0.8314-1.7058-0.39050.98120.1944-0.08940.7837-0.01880.4937-52.424632.0989-1.5886
214.08871.35460.09974.4467-2.03965.6223-0.18190.1133-0.11990.27340.3160.3788-0.1284-0.157-0.11910.21910.0842-0.03540.319-0.08430.2433-55.523534.6788-19.6555
223.68021.22780.18871.1056-1.49473.7592-0.1868-0.0961-0.03450.55390.1221-1.2666-0.26480.21550.04220.33640.0787-0.18360.3492-0.13890.4972-44.306336.6357-15.8335
237.63710.3353.41745.7852-2.78568.6409-0.6721-0.53060.70731.07590.7765-0.1068-0.7542-0.3907-0.10210.43380.1089-0.04210.2416-0.06790.276-56.228344.6208-14.6352
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 628 )
3X-RAY DIFFRACTION3chain 'B' and (resid 567 through 599 )
4X-RAY DIFFRACTION4chain 'B' and (resid 600 through 627 )
5X-RAY DIFFRACTION5chain 'X' and (resid 1 through 13 )
6X-RAY DIFFRACTION6chain 'W' and (resid 2 through 13 )
7X-RAY DIFFRACTION7chain 'E' and (resid 567 through 599 )
8X-RAY DIFFRACTION8chain 'E' and (resid 600 through 628 )
9X-RAY DIFFRACTION9chain 'F' and (resid 568 through 599 )
10X-RAY DIFFRACTION10chain 'F' and (resid 600 through 606 )
11X-RAY DIFFRACTION11chain 'F' and (resid 607 through 627 )
12X-RAY DIFFRACTION12chain 'Y' and (resid 1 through 13 )
13X-RAY DIFFRACTION13chain 'Z' and (resid 1 through 13 )
14X-RAY DIFFRACTION14chain 'G' and (resid 574 through 583 )
15X-RAY DIFFRACTION15chain 'G' and (resid 584 through 603 )
16X-RAY DIFFRACTION16chain 'G' and (resid 604 through 628 )
17X-RAY DIFFRACTION17chain 'H' and (resid 568 through 580 )
18X-RAY DIFFRACTION18chain 'H' and (resid 581 through 597 )
19X-RAY DIFFRACTION19chain 'H' and (resid 598 through 628 )
20X-RAY DIFFRACTION20chain 'I' and (resid 570 through 594 )
21X-RAY DIFFRACTION21chain 'I' and (resid 595 through 628 )
22X-RAY DIFFRACTION22chain 'J' and (resid 577 through 606 )
23X-RAY DIFFRACTION23chain 'J' and (resid 607 through 628 )

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