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- PDB-5xjd: TEAD in complex with fragment -

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Basic information

Entry
Database: PDB / ID: 5xjd
TitleTEAD in complex with fragment
ComponentsTranscriptional enhancer factor TEF-3
KeywordsTRANSCRIPTION / transcription factor
Function / homology
Function and homology information


RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / trophectodermal cell fate commitment / hippo signaling / blastocyst formation / cell fate specification / positive regulation of stem cell population maintenance / cell fate commitment / embryo implantation / protein-DNA complex ...RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / trophectodermal cell fate commitment / hippo signaling / blastocyst formation / cell fate specification / positive regulation of stem cell population maintenance / cell fate commitment / embryo implantation / protein-DNA complex / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / sequence-specific DNA binding / in utero embryonic development / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / cytoplasm
Similarity search - Function
Transcriptional enhancer factor TEF-3 (TEAD4) / 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 ...Transcriptional enhancer factor TEF-3 (TEAD4) / 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
(2S)-2-phenyl-2-pyrrol-1-yl-ethanoic acid / Transcriptional enhancer factor TEF-3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsKaan, H.Y.K. / Sim, A.Y.L. / Tan, S.K.J. / Verma, C. / Song, H.
Funding support Singapore, 1items
OrganizationGrant numberCountry
BMRC1310151003 Singapore
Citation
Journal: PLoS ONE / Year: 2017
Title: Targeting YAP/TAZ-TEAD protein-protein interactions using fragment-based and computational modeling approaches.
Authors: Kaan, H.Y.K. / Sim, A.Y.L. / Tan, S.K.J. / Verma, C. / Song, H.
#1: Journal: Sci Rep / Year: 2017
Title: Crystal structure of TAZ-TEAD complex reveals a distinct interaction mode from that of YAP-TEAD complex.
Authors: Kaan, H.Y.K. / Chan, S.W. / Tan, S.K.J. / Guo, F. / Lim, C.J. / Hong, W. / Song, H.
History
DepositionMay 1, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation / citation_author
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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional enhancer factor TEF-3
B: Transcriptional enhancer factor TEF-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7523
Polymers51,5502
Non-polymers2011
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-8 kcal/mol
Surface area21410 Å2
Unit cell
Length a, b, c (Å)74.500, 74.500, 252.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 210 - 425 / Label seq-ID: 3 - 218

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles :
ID
2
1

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Components

#1: Protein Transcriptional enhancer factor TEF-3 / ETF-related factor 2 / ETFR-2 / TEA domain family member 4 / TEAD-4 / TEF-1-related factor 1 / TEF- ...ETF-related factor 2 / ETFR-2 / TEA domain family member 4 / TEAD-4 / TEF-1-related factor 1 / TEF-1-related factor FR-19 / RTEF-1


Mass: 25775.168 Da / Num. of mol.: 2 / Fragment: UNP residues 210-427
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tead4, Tcf13r1, Tef3, Tefr1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q62296
#2: Chemical ChemComp-87L / (2S)-2-phenyl-2-pyrrol-1-yl-ethanoic acid


Mass: 201.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H11NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 3.4 Å3/Da / Density % sol: 63.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 2.6M sodium formate, 0.1M Tris pH 8.4, 5 % glycerol, 2mM magnesium chloride

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 36473 / % possible obs: 99.9 % / Redundancy: 11 % / Net I/σ(I): 8.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L15

3l15


Resolution: 2.22→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.941 / SU B: 8.585 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22342 1777 4.9 %RANDOM
Rwork0.19813 ---
obs0.19937 34696 99.87 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.659 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2---0.11 Å20 Å2
3---0.22 Å2
Refinement stepCycle: 1 / Resolution: 2.22→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3450 0 15 117 3582
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193606
X-RAY DIFFRACTIONr_bond_other_d0.0020.023240
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.9434865
X-RAY DIFFRACTIONr_angle_other_deg0.9043.0017532
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1015419
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.31924.054185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.94215635
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8221518
X-RAY DIFFRACTIONr_chiral_restr0.10.2518
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023955
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02781
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4333.0321691
X-RAY DIFFRACTIONr_mcbond_other3.4283.0291689
X-RAY DIFFRACTIONr_mcangle_it5.1894.5212105
X-RAY DIFFRACTIONr_mcangle_other5.1884.5212105
X-RAY DIFFRACTIONr_scbond_it4.3123.5851914
X-RAY DIFFRACTIONr_scbond_other4.3113.5861915
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4185.1782761
X-RAY DIFFRACTIONr_long_range_B_refined8.91235.0193765
X-RAY DIFFRACTIONr_long_range_B_other8.91134.9413759
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 12642 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.215→2.273 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 131 -
Rwork0.219 2528 -
obs--100 %
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)
13.98841.46921.75520.94810.99391.9992-0.008-0.3386-0.09070.04720.0969-0.03210.0151-0.035-0.08890.07260.05910.02380.18590.00950.0391-74.999-44.59-46.305
21.4848-0.7578-0.3151.14940.50811.7302-0.02130.2394-0.07210.0001-0.054-0.02170.2240.10780.07520.09340.0260.04110.1547-0.01940.0269-68.172-22.21-14.617
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A210 - 426
2X-RAY DIFFRACTION2B209 - 427

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