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- PDB-5emw: Crystal structure of the palmitoylated human TEAD3 transcription ... -

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Basic information

Entry
Database: PDB / ID: 5emw
TitleCrystal structure of the palmitoylated human TEAD3 transcription factor
ComponentsTranscriptional enhancer factor TEF-5
KeywordsTRANSCRIPTION / palmitoylated protein
Function / homology
Function and homology information


asymmetric neuroblast division / RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / hippo signaling / embryonic organ development / female pregnancy / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding ...asymmetric neuroblast division / RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / hippo signaling / embryonic organ development / female pregnancy / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / 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 transcription by RNA polymerase II / nucleoplasm
Similarity search - Function
Transcriptional enhancer factor TEF-5 (TEAD3) / 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-5 (TEAD3) / 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-5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 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 / struct_conn
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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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-5
B: Transcriptional enhancer factor TEF-5
C: Transcriptional enhancer factor TEF-5
D: Transcriptional enhancer factor TEF-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,6676
Polymers100,5874
Non-polymers802
Water2,990166
1
A: Transcriptional enhancer factor TEF-5


Theoretical massNumber of molelcules
Total (without water)25,1471
Polymers25,1471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Transcriptional enhancer factor TEF-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1872
Polymers25,1471
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Transcriptional enhancer factor TEF-5


Theoretical massNumber of molelcules
Total (without water)25,1471
Polymers25,1471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Transcriptional enhancer factor TEF-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1872
Polymers25,1471
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.310, 123.530, 150.730
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-5 / DTEF-1 / TEA domain family member 3 / TEAD-3


Mass: 25146.785 Da / Num. of mol.: 4 / Fragment: YAP binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TEAD3, TEAD5, TEF5 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99594
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 3.04 Å3/Da / Density % sol: 59.5 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 100 mM Sodium Acetate, 100 mM Calcium acetate, 12% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.55→95.54 Å / Num. obs: 38149 / % possible obs: 94.9 % / Redundancy: 5 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 9.5
Reflection shellResolution: 2.55→2.66 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 2.5 / % possible all: 96.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
MOSFLMdata reduction
SCALA0.5.9data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EMV

5emv


Resolution: 2.55→95.54 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.223 1922 5.05 %
Rwork0.184 --
obs0.186 38097 93.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.65 Å2
Refinement stepCycle: LAST / Resolution: 2.55→95.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6665 0 2 166 6833
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036822
X-RAY DIFFRACTIONf_angle_d0.6749210
X-RAY DIFFRACTIONf_dihedral_angle_d13.9772496
X-RAY DIFFRACTIONf_chiral_restr0.0281017
X-RAY DIFFRACTIONf_plane_restr0.0031155
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.61380.28431590.24992586X-RAY DIFFRACTION96
2.6138-2.68450.34761370.24092603X-RAY DIFFRACTION96
2.6845-2.76350.27431290.2392629X-RAY DIFFRACTION97
2.7635-2.85270.26941370.22452573X-RAY DIFFRACTION94
2.8527-2.95460.24861440.21762589X-RAY DIFFRACTION96
2.9546-3.07290.25281280.21012612X-RAY DIFFRACTION96
3.0729-3.21280.26831340.20262599X-RAY DIFFRACTION95
3.2128-3.38220.21411330.19832581X-RAY DIFFRACTION95
3.3822-3.59410.24571550.17382557X-RAY DIFFRACTION94
3.5941-3.87160.22881370.17182554X-RAY DIFFRACTION93
3.8716-4.26120.20041550.16012570X-RAY DIFFRACTION94
4.2612-4.87780.1461260.13332575X-RAY DIFFRACTION92
4.8778-6.14540.18641100.16782564X-RAY DIFFRACTION90
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)
11.5602-1.29180.30543.3137-1.0132.5962-0.0083-0.15410.0840.1949-0.0456-0.30210.00430.0520.03270.1987-0.0563-0.04930.2328-0.06460.29031.4563-6.43523.3701
21.51040.21420.12291.65730.15363.59770.0298-0.1970.23450.0613-0.0493-0.2576-0.21060.04150.02910.1994-0.0037-0.02650.2859-0.02130.3044-2.1189-4.491223.2392
32.7844-1.59190.78424.544-1.09421.4292-0.05730.24320.17370.3793-0.010.08830.0054-0.10120.10370.2273-0.0670.00180.2998-0.00290.2403-28.8083-14.856727.076
41.59210.56-0.52341.9505-0.08023.2777-0.06550.0184-0.03870.1365-0.00310.10470.1546-0.1860.0840.1957-0.0119-0.0160.2568-0.04660.237-25.3542-16.216429.2012
52.40091.71181.54763.23951.22793.5041-0.02130.26190.05-0.17550.05180.0606-0.1975-0.1225-0.00870.15110.05750.04690.3121-0.00340.2429-13.24040.864-10.8882
61.06610.13930.25962.5484-0.84743.1144-0.04480.12970.171-0.01680.04030.1025-0.208-0.12410.05420.183-0.00030.02360.2815-0.03760.2484-9.6491.9837-10.5709
72.59-0.16860.08951.95140.72943.0174-0.0181-0.50780.6562-0.2504-0.0349-0.2867-0.33430.312-0.02220.25440.00310.07720.3447-0.07330.581617.8381-5.8918-18.0031
82.8288-0.0871-0.44471.999-0.77263.36020.0010.05790.3607-0.26950.0467-0.33940.0810.2513-0.15890.24560.01640.07090.2747-0.00940.422912.8739-6.2895-20.4079
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 437 )
3X-RAY DIFFRACTION3CHAIN 'B' AND (RESID 222 THROUGH 293 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 294 THROUGH 437 )
5X-RAY DIFFRACTION5CHAIN 'C' AND (RESID 222 THROUGH 293 )
6X-RAY DIFFRACTION6CHAIN 'C' AND (RESID 294 THROUGH 438 )
7X-RAY DIFFRACTION7CHAIN 'D' AND (RESID 223 THROUGH 304 )
8X-RAY DIFFRACTION8CHAIN 'D' AND (RESID 305 THROUGH 437 )

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