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- PDB-5emv: Crystal structure of the palmitoylated human TEAD2 transcription ... -

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Basic information

Entry
Database: PDB / ID: 5emv
TitleCrystal structure of the palmitoylated human TEAD2 transcription factor
ComponentsTranscriptional enhancer factor TEF-4
KeywordsTRANSCRIPTION / palmitoylated protein
Function / homology
Function and homology information


TEAD-YAP complex / lateral mesoderm development / RUNX3 regulates YAP1-mediated transcription / notochord development / YAP1- and WWTR1 (TAZ)-stimulated gene expression / paraxial mesoderm development / hippo signaling / regulation of stem cell differentiation / Formation of axial mesoderm / embryonic heart tube morphogenesis ...TEAD-YAP complex / lateral mesoderm development / RUNX3 regulates YAP1-mediated transcription / notochord development / YAP1- and WWTR1 (TAZ)-stimulated gene expression / paraxial mesoderm development / hippo signaling / regulation of stem cell differentiation / Formation of axial mesoderm / embryonic heart tube morphogenesis / vasculogenesis / embryonic organ development / cellular response to retinoic acid / neural tube closure / transcription coactivator binding / disordered domain specific binding / sequence-specific double-stranded DNA binding / protein-containing complex assembly / transcription regulator complex / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / intracellular membrane-bounded organelle / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol
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
Transcriptional enhancer factor TEF-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsNoland, C.L. / Gierke, S. / Schnier, P.D. / Murray, J. / Sandoval, W.N. / Sagolla, M. / Dey, A. / Hannoush, R.N. / Fairbrother, W.J. / Cunningham, C.N.
CitationJournal: Structure / Year: 2016
Title: Palmitoylation of TEAD Transcription Factors Is Required for Their Stability and Function in Hippo Pathway Signaling.
Authors: Noland, C.L. / Gierke, S. / Schnier, P.D. / Murray, J. / Sandoval, W.N. / Sagolla, M. / Dey, A. / Hannoush, R.N. / Fairbrother, W.J. / Cunningham, C.N.
History
DepositionNov 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional enhancer factor TEF-4
B: Transcriptional enhancer factor TEF-4


Theoretical massNumber of molelcules
Total (without water)53,8832
Polymers53,8832
Non-polymers00
Water3,009167
1
A: Transcriptional enhancer factor TEF-4


Theoretical massNumber of molelcules
Total (without water)26,9421
Polymers26,9421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Transcriptional enhancer factor TEF-4


Theoretical massNumber of molelcules
Total (without water)26,9421
Polymers26,9421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.830, 61.250, 112.672
Angle α, β, γ (deg.)90.000, 101.890, 90.000
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Transcriptional enhancer factor TEF-4 / TEA domain family member 2 / TEAD-2


Mass: 26941.543 Da / Num. of mol.: 2 / Fragment: YAP binding domain, unp residues 219-435
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TEAD2, TEF4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15562
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.56 Å3/Da / Density % sol: 51.9 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: 1.7-2.1 M Sodium Formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2→58.32 Å / Num. obs: 36163 / % possible obs: 100 % / Redundancy: 3.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.043 / Net I/σ(I): 9.9 / Num. measured all: 137128 / Scaling rejects: 35
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2-2.053.80.67421018526960.8120.405100
8.94-58.323.40.02426.214744320.9960.01698.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA0.5.4data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L15

3l15


Resolution: 2→53.543 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2313 1761 4.88 %
Rwork0.202 34326 -
obs0.2034 36087 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.39 Å2 / Biso mean: 47.2304 Å2 / Biso min: 16.26 Å2
Refinement stepCycle: final / Resolution: 2→53.543 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3261 0 0 167 3428
Biso mean---48.44 -
Num. residues----398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033354
X-RAY DIFFRACTIONf_angle_d0.6684530
X-RAY DIFFRACTIONf_chiral_restr0.027491
X-RAY DIFFRACTIONf_plane_restr0.003576
X-RAY DIFFRACTIONf_dihedral_angle_d13.8571231
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.05410.31831370.30642645100
2.0541-2.11460.35211220.28612620100
2.1146-2.18280.29241280.26752633100
2.1828-2.26080.37251450.3286258799
2.2608-2.3513137261899
2.3513-2.45840.24271380.232634100
2.4584-2.5880.24341270.21772621100
2.588-2.75010.27721430.22942647100
2.7501-2.96240.26041380.21352632100
2.9624-3.26050.24141190.20452675100
3.2605-3.73220.19621500.1762621100
3.7322-4.70180.16621470.14792661100
4.70180.22931300.18132732100
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)
18.60610.30868.0212.64871.85789.1356-0.3142-1.00621.085-0.093-0.20720.3702-0.2203-0.81620.66570.2904-0.0110.02420.49550.01440.4028-3.0459-12.6079-22.3055
24.47670.41072.16264.58841.11466.4244-0.18530.63340.0749-0.7340.06560.16040.01270.2660.15990.2976-0.02070.02070.33170.07230.39684.9343-16.3113-32.6135
34.2631-0.92850.13521.2941-0.62861.3187-0.1553-0.3124-0.06150.0390.07150.1053-0.0808-0.18650.08040.28080.0006-0.02330.26530.0470.39131.5421-16.3295-23.916
44.5371-3.1312-5.3432.9732.9877.2481-0.28660.41650.14720.34550.30350.12720.1656-0.55980.02340.4654-0.00810.06580.2980.09510.60512.2859-26.9578-23.8431
58.24940.08944.64620.8573-0.29992.6234-0.3012-1.935-0.1214-0.05130.28030.1857-0.2728-0.42810.08520.3279-0.01270.050.60550.05650.3938-6.382-17.6627-16.8675
65.77085.37640.33165.13360.85926.40880.5528-1.1689-0.8830.3572-0.4733-1.03320.24110.18570.01280.29650.0030.01220.39120.05170.452919.697-18.0718-16.6432
72.78041.05041.79661.6250.64231.7088-0.3271-0.10070.1198-0.30220.2041-0.0170.04330.03390.04150.31190.01980.02060.25280.03080.343313.2668-16.1521-26.9267
87.83281.56291.8083.29531.23453.9262-0.2763-0.0160.2828-0.15560.11340.0901-0.2515-0.26420.20650.31650.0378-0.03110.20020.08120.33443.584-12.4092-28.9933
93.5440.634-1.48351.22621.50389.43050.1033-0.3613-0.08640.2475-0.0612-0.0880.8656-0.53260.10860.3278-0.00830.00820.3267-0.00020.23910.9393-48.0742-13.1839
105.255-0.3425-0.17694.33780.04055.3439-0.10111.2283-0.9094-0.44270.04280.16460.1153-1.01440.23480.3201-0.04610.01970.6128-0.11890.38730.0175-50.9715-33.903
114.8001-0.952-0.76842.85741.8369.46090.1267-0.81790.46420.28950.1987-0.7131-0.31961.7536-0.37920.3887-0.0427-0.03110.7192-0.07290.487815.7556-41.9471-7.7862
124.5371-0.6593-0.34892.76921.564.37790.14230.1039-0.4638-0.024-0.0323-0.28440.1582-0.0572-0.23650.2358-0.0153-0.00560.19870.02610.369110.4818-49.2948-19.5412
137.6601-1.9141-4.1643.2960.46253.0716-0.1904-0.26710.32290.4150.24060.14260.4098-0.31510.08220.2682-0.03390.02520.3796-0.03740.422-3.8421-41.9988-17.7355
147.6903-1.8246-3.86981.00751.61342.83320.10930.22731.3257-0.12620.1914-0.5102-0.3047-0.11-0.37630.3626-0.00070.08670.29380.1120.5227.4996-34.521-19.5604
155.8773-2.0592-1.50132.45622.32945.16790.1620.09880.07380.2182-0.0834-0.01890.0214-1.13590.10260.2476-0.0003-0.0450.40950.01080.3069-5.408-41.2718-20.3159
163.5235-5.2554-2.0498.80850.99895.7940.67321.2167-0.0693-0.2951-0.6627-0.5690.2222-0.49040.05060.2830.01780.03730.47450.04670.491316.701-44.8436-34.7566
175.8712-1.8385-4.91121.05722.31235.9342-0.10980.08230.09120.11240.0215-0.1140.08090.0620.03870.2629-0.00950.0090.25590.06490.497616.5561-44.3077-22.0655
185.4458-0.9149-1.28423.46761.77185.1641-0.0291-0.4027-0.0662-0.01810.0365-0.12070.16360.02410.00430.2335-0.0163-0.02720.17160.06050.25569.1448-46.5407-14.1682
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 222 through 238 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 239 through 293 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 294 through 351 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 352 through 362 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 363 through 381 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 382 through 395 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 396 through 414 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 415 through 446 )A0
9X-RAY DIFFRACTION9chain 'B' and (resid 218 through 238 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 239 through 255 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 256 through 293 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 294 through 325 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 326 through 339 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 340 through 362 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 363 through 381 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 382 through 395 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 396 through 414 )B0
18X-RAY DIFFRACTION18chain 'B' and (resid 415 through 446 )B0

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