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- PDB-6im5: YAP-binding domain of human TEAD1 -

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Basic information

Entry
Database: PDB / ID: 6im5
TitleYAP-binding domain of human TEAD1
ComponentsTranscriptional enhancer factor TEF-1
KeywordsTRANSCRIPTION / TEAD1 / YAP-binding domain / Hippo pathway / Transcription factor
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
Coagulation Factor XIII; Chain A, domain 1 - #80 / 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 ...Coagulation Factor XIII; Chain A, domain 1 - #80 / 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 / Coagulation Factor XIII; Chain A, domain 1 / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Transcriptional enhancer factor TEF-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.701 Å
AuthorsMo, Y. / Lee, H.S. / Kim, S.J. / Ku, B.
Funding support Korea, Republic Of, 4items
OrganizationGrant numberCountry
National Research Foundation (Korea)2015M3A9B5030308 Korea, Republic Of
Ministry of Science, ICT and Future PlanningCreative Research Korea, Republic Of
Ministry of Science, ICT and Future PlanningDisease Target Structure Research Korea, Republic Of
Ministry of Science, ICT and Future PlanningKK1803 Korea, Republic Of
CitationJournal: Bull.Korean Chem.Soc. / Year: 2019
Title: Crystal Structure of the YAP-binding Domain of Human TEAD1
Authors: Mo, Y. / Lee, H.S. / Lee, C.H. / Lim, H.J. / Park, S.J. / Shin, H.-C. / Kim, C.-H. / Kim, S.J. / Ku, B.
History
DepositionOct 22, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs
Revision 1.2Nov 22, 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

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Assembly

Deposited unit
A: Transcriptional enhancer factor TEF-1
B: Transcriptional enhancer factor TEF-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6434
Polymers53,4532
Non-polymers1902
Water7,134396
1
A: Transcriptional enhancer factor TEF-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8212
Polymers26,7261
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-7 kcal/mol
Surface area11550 Å2
MethodPISA
2
B: Transcriptional enhancer factor TEF-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8212
Polymers26,7261
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-7 kcal/mol
Surface area11400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.537, 89.356, 135.569
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 26726.395 Da / Num. of mol.: 2 / Fragment: YAP-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TEAD1, TCF13, TEF1 / Production host: Escherichia coli (E. coli) / References: UniProt: P28347
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 2.07 Å3/Da / Density % sol: 40.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 4% (v/v) 2-propanol, 100 mM sodium phosphate dibasic/citric acid (pH 4.5), and 200 mM lithium sulfate

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 49632 / % possible obs: 99.5 % / Redundancy: 6 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 35.4
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.29 / Num. unique obs: 2451

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KYS

3kys


Resolution: 1.701→28.412 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.51 / Phase error: 20.21
RfactorNum. reflection% reflection
Rfree0.2302 1999 4.03 %
Rwork0.1953 --
obs0.1967 49583 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.701→28.412 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3489 0 10 396 3895
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063576
X-RAY DIFFRACTIONf_angle_d0.8994813
X-RAY DIFFRACTIONf_dihedral_angle_d14.742143
X-RAY DIFFRACTIONf_chiral_restr0.058520
X-RAY DIFFRACTIONf_plane_restr0.005616
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7011-1.74370.28291400.23443338X-RAY DIFFRACTION99
1.7437-1.79080.27381400.2233315X-RAY DIFFRACTION99
1.7908-1.84350.22331390.20753332X-RAY DIFFRACTION99
1.8435-1.9030.24911410.19483353X-RAY DIFFRACTION99
1.903-1.9710.21251410.18583341X-RAY DIFFRACTION100
1.971-2.04990.24871430.19143386X-RAY DIFFRACTION100
2.0499-2.14310.2321420.19133390X-RAY DIFFRACTION100
2.1431-2.25610.23651410.18573357X-RAY DIFFRACTION100
2.2561-2.39730.21221420.1893383X-RAY DIFFRACTION100
2.3973-2.58230.24191430.2073404X-RAY DIFFRACTION100
2.5823-2.8420.25851440.2033435X-RAY DIFFRACTION100
2.842-3.25270.25821450.19333433X-RAY DIFFRACTION100
3.2527-4.09610.20411460.17883489X-RAY DIFFRACTION100
4.0961-28.4160.20691520.20253628X-RAY DIFFRACTION99

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