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- PDB-4z8e: TEAD DBD mutant -deltaL1 -

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Basic information

Entry
Database: PDB / ID: 4z8e
TitleTEAD DBD mutant -deltaL1
ComponentsTranscriptional enhancer factor TEF-1
KeywordsTRANSCRIPTION / Transcription factor / DNA binding / three helix bundle
Function / homology
Function and homology information


TEAD-YAP complex / RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / hippo signaling / EGR2 and SOX10-mediated initiation of Schwann cell myelination / embryonic organ development / positive regulation of miRNA transcription / sequence-specific double-stranded DNA binding / positive regulation of cell growth / protein-containing complex assembly ...TEAD-YAP complex / RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / hippo signaling / EGR2 and SOX10-mediated initiation of Schwann cell myelination / embryonic organ development / positive regulation of miRNA transcription / sequence-specific double-stranded DNA binding / positive regulation of cell growth / protein-containing complex assembly / transcription regulator complex / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / 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 / nucleoplasm / nucleus
Similarity search - Function
TEA/ATTS domain / Transcriptional enhancer factor, metazoa / TEA/ATTS domain superfamily / TEA/ATTS domain / TEA domain signature. / TEA domain profile. / TEA domain / YAP binding domain / YAP binding domain
Similarity search - Domain/homology
Transcriptional enhancer factor TEF-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.092 Å
AuthorsLee, D.-S. / Albarado, D.C. / Vonrhein, C. / Raman, C.S. / Veeraraghavan, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM084700 United States
American Heart Association0365134Y United States
CitationJournal: J.Mol.Biol. / Year: 2016
Title: A Potential Structural Switch for Regulating DNA-Binding by TEAD Transcription Factors.
Authors: Lee, D.S. / Vonrhein, C. / Albarado, D. / Raman, C.S. / Veeraraghavan, S.
History
DepositionApr 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional enhancer factor TEF-1
B: Transcriptional enhancer factor TEF-1
C: Transcriptional enhancer factor TEF-1


Theoretical massNumber of molelcules
Total (without water)24,5323
Polymers24,5323
Non-polymers00
Water1,22568
1
A: Transcriptional enhancer factor TEF-1


Theoretical massNumber of molelcules
Total (without water)8,1771
Polymers8,1771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcriptional enhancer factor TEF-1


Theoretical massNumber of molelcules
Total (without water)8,1771
Polymers8,1771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Transcriptional enhancer factor TEF-1


Theoretical massNumber of molelcules
Total (without water)8,1771
Polymers8,1771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: Transcriptional enhancer factor TEF-1
B: Transcriptional enhancer factor TEF-1
C: Transcriptional enhancer factor TEF-1

A: Transcriptional enhancer factor TEF-1
B: Transcriptional enhancer factor TEF-1
C: Transcriptional enhancer factor TEF-1


Theoretical massNumber of molelcules
Total (without water)49,0646
Polymers49,0646
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Buried area14490 Å2
ΔGint-70 kcal/mol
Surface area16570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.590, 96.547, 84.917
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Transcriptional enhancer factor TEF-1 / NTEF-1 / Protein GT-IIC / TEA domain family member 1 / TEAD-1 / Transcription factor 13 / TCF-13


Mass: 8177.369 Da / Num. of mol.: 3 / Fragment: UNP residues 28-104 / Mutation: A48S, deletion of P52-E63
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TEAD1, TCF13, TEF1 / Plasmid: pET21d / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta2(DE3) pLysS / References: UniProt: P28347
#2: 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

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.03 % / Description: Plate form
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 7-10 mg/mL protein, ammonium sulfate, MES/Tris-HCl, dioxane/PEG5000 MME
PH range: 6.5-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 5, 2007
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.092→48.273 Å / Num. all: 13625 / Num. obs: 13625 / % possible obs: 98.2 % / Redundancy: 7.42 % / Biso Wilson estimate: 39.82 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 26.327
Reflection shellResolution: 2.092→2.128 Å / Redundancy: 7.63 % / Rmerge(I) obs: 0.752 / Mean I/σ(I) obs: 3.15 / % possible all: 96.02

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.092→17.83 Å / Cor.coef. Fo:Fc: 0.9223 / Cor.coef. Fo:Fc free: 0.9247 / SU R Cruickshank DPI: 0.199 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.203 / SU Rfree Blow DPI: 0.161 / SU Rfree Cruickshank DPI: 0.161
RfactorNum. reflection% reflectionSelection details
Rfree0.2367 963 7.08 %RANDOM
Rwork0.2237 ---
obs0.2246 13598 98.07 %-
Displacement parametersBiso mean: 46.56 Å2
Baniso -1Baniso -2Baniso -3
1--1.4236 Å20 Å20 Å2
2---10.009 Å20 Å2
3---11.4326 Å2
Refine analyzeLuzzati coordinate error obs: 0.307 Å
Refinement stepCycle: 1 / Resolution: 2.092→17.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1352 0 0 68 1420
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011381HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.981871HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d477SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes24HARMONIC2
X-RAY DIFFRACTIONt_gen_planes206HARMONIC5
X-RAY DIFFRACTIONt_it1381HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.43
X-RAY DIFFRACTIONt_other_torsion17.13
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion187SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies3HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1638SEMIHARMONIC4
LS refinement shellResolution: 2.09→2.26 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2446 198 7.26 %
Rwork0.2282 2530 -
all0.2293 2728 -
obs--98.07 %
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)
11.15120.0335-1.67770.21560.4733.64030.2219-0.1010.0664-0.0160.0014-0.0347-0.29010.1671-0.2234-0.1202-0.00240.0364-0.0464-0.0178-0.094631.697734.011262.2549
21.6498-1.06752.70120.8442-1.74074.44290.2703-0.0112-0.1578-0.1519-0.04220.08530.4488-0.227-0.2281-0.0893-0.0352-0.036-0.0786-0.0096-0.112922.650717.205965.4182
31.46451.04641.88680.19670.80873.2517-0.08920.2992-0.0519-0.06350.131-0.0107-0.07460.7094-0.0418-0.1580.0254-0.0136-0.02870.0255-0.122537.250324.239861.8141
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

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