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- PDB-5hgu: Crystal structure of human transcription factor TEAD2 in complex ... -

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Basic information

Entry
Database: PDB / ID: 5hgu
TitleCrystal structure of human transcription factor TEAD2 in complex with palmitate
ComponentsTranscriptional enhancer factor TEF-4
KeywordsTRANSCRIPTION / Transcription Factor / palmitoylation / Hippo Pathway
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 / embryonic organ development / vasculogenesis / 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
PALMITIC ACID / Transcriptional enhancer factor TEF-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.046 Å
AuthorsLuo, X. / Xiao, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM107415 United States
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: Autopalmitoylation of TEAD proteins regulates transcriptional output of the Hippo pathway.
Authors: Chan, P. / Han, X. / Zheng, B. / DeRan, M. / Yu, J. / Jarugumilli, G.K. / Deng, H. / Pan, D. / Luo, X. / Wu, X.
History
DepositionJan 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2Mar 30, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Advisory / Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_validate_close_contact / struct_conn
Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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: Transcriptional enhancer factor TEF-4
B: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7724
Polymers54,2592
Non-polymers5132
Water2,792155
1
A: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3862
Polymers27,1301
Non-polymers2561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3862
Polymers27,1301
Non-polymers2561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)122.486, 61.146, 80.307
Angle α, β, γ (deg.)90.00, 117.17, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 27129.654 Da / Num. of mol.: 2 / Fragment: residues 217-447
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TEAD2, TEF4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15562
#2: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.47 Å3/Da / Density % sol: 50.11 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.2 / Details: 0.1 M HEPES pH 7.2, 2.4 M sodium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.04→40 Å / Num. obs: 28795 / % possible obs: 95.9 % / Redundancy: 4 % / Net I/σ(I): 26.3

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L15

3l15


Resolution: 2.046→36.101 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 24.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2215 1440 5 %
Rwork0.1848 --
obs0.1866 28795 85.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.046→36.101 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3291 0 36 155 3482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153400
X-RAY DIFFRACTIONf_angle_d1.4814576
X-RAY DIFFRACTIONf_dihedral_angle_d18.1861276
X-RAY DIFFRACTIONf_chiral_restr0.066492
X-RAY DIFFRACTIONf_plane_restr0.006584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0461-2.11930.2838880.22281682X-RAY DIFFRACTION53
2.1193-2.20410.24281140.20162155X-RAY DIFFRACTION68
2.2041-2.30440.21541270.20192421X-RAY DIFFRACTION77
2.3044-2.42590.23411420.20652688X-RAY DIFFRACTION85
2.4259-2.57780.27431500.20652864X-RAY DIFFRACTION90
2.5778-2.77680.26371580.21652985X-RAY DIFFRACTION94
2.7768-3.05610.2541620.20893077X-RAY DIFFRACTION97
3.0561-3.4980.22151650.18463136X-RAY DIFFRACTION99
3.498-4.40580.19021670.15313178X-RAY DIFFRACTION99
4.4058-36.10630.19531670.16933169X-RAY DIFFRACTION97
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)
13.9563-0.9005-2.32243.3243-0.55874.3158-0.01070.33510.1454-0.26120.15870.5129-0.2595-0.5998-0.06970.23370.0294-0.00150.21930.03010.2185-18.418619.526991.1514
22.49270.4234-1.76131.0293-0.31664.50470.0888-0.2830.13840.02260.04230.1621-0.14240.2255-0.07260.18990.0599-0.00360.08470.01430.1931-12.715318.074992.5489
33.3550.22752.1241.5715-0.53654.57930.3729-0.5265-0.7388-0.0042-0.1967-0.39180.6805-0.0021-0.14330.09420.0213-0.05820.2143-0.02790.2195-6.0184-12.954399.7306
44.58210.75322.08832.01670.95474.2626-0.25020.2969-0.0666-0.24750.1426-0.17560.05110.36040.11150.18860.03760.01030.13670.0390.1278-4.2855-10.983290.1273
52.01780.2471.61.35620.8235.28190.0266-0.30070.3086-0.036-0.1844-0.105-0.08040.12520.1310.0830.034-0.02340.1669-0.01120.188-8.7651-4.555997.2623
64.52181.8398-3.89734.6084-0.99284.4377-0.0155-0.20920.2099-0.69590.17940.14660.29890.1579-0.04650.28110.1614-0.03930.1980.0020.2286-9.30931.988293.3827
75.85680.0164.67831.35730.51024.13830.0266-0.907-0.30850.1586-0.0326-0.02320.2777-0.611-0.13380.16130.03140.04250.32870.00890.1984-14.146-7.1671104.9776
85.59380.0838-1.34843.7514.69896.3724-0.10270.45970.0657-0.5896-0.40040.3363-0.2317-0.67380.30710.28190.0541-0.02880.24430.00160.1181-16.6141-9.273476.7917
92.34610.86661.1782.03721.55786.9888-0.0722-0.10050.0962-0.2738-0.067-0.1905-0.1062-0.06690.17430.06390.0963-0.00510.06940.05140.2059-3.8957-7.551388.2184
107.00893.69471.90177.11931.92344.043-0.05230.1066-1.2683-0.12360.4386-0.49120.6580.5217-0.2450.36970.11390.06790.05370.01860.2379-2.6274-19.599588.4424
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 222 through 293 )
2X-RAY DIFFRACTION2chain 'A' and (resid 294 through 446 )
3X-RAY DIFFRACTION3chain 'B' and (resid 219 through 238 )
4X-RAY DIFFRACTION4chain 'B' and (resid 239 through 325 )
5X-RAY DIFFRACTION5chain 'B' and (resid 326 through 351 )
6X-RAY DIFFRACTION6chain 'B' and (resid 352 through 362 )
7X-RAY DIFFRACTION7chain 'B' and (resid 363 through 380 )
8X-RAY DIFFRACTION8chain 'B' and (resid 381 through 395 )
9X-RAY DIFFRACTION9chain 'B' and (resid 396 through 430 )
10X-RAY DIFFRACTION10chain 'B' and (resid 431 through 446 )

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