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- PDB-7zjq: Human TEAD3 in complex with 1-Cyclopentyl-1H-pyrazolo[3,4-b]pyrid... -

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Basic information

Entry
Database: PDB / ID: 7zjq
TitleHuman TEAD3 in complex with 1-Cyclopentyl-1H-pyrazolo[3,4-b]pyridine-5-carboxylic acid
Components(Transcriptional enhancer factor TEF-5) x 2
KeywordsTRANSCRIPTION / IMMUNOGLOBULIN-LIKE FOLD / ACTIVATOR / DISEASE MUTATION / DNA-BINDING / NUCLEUS / PHOSPHOPROTEIN / TRANSCRIPTION REGULATION / TRANSCRIPTION-PROTEIN BINDING COMPLEX
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 / regulation of transcription by RNA polymerase II / chromatin / 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
Chem-JIK / Transcriptional enhancer factor TEF-5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.095 Å
AuthorsMusil, D. / Sousa, C.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2022
Title: Optimization of TEAD P-Site Binding Fragment Hit into In Vivo Active Lead MSC-4106 .
Authors: Heinrich, T. / Peterson, C. / Schneider, R. / Garg, S. / Schwarz, D. / Gunera, J. / Seshire, A. / Kotzner, L. / Schlesiger, S. / Musil, D. / Schilke, H. / Doerfel, B. / Diehl, P. / Bopple, P. ...Authors: Heinrich, T. / Peterson, C. / Schneider, R. / Garg, S. / Schwarz, D. / Gunera, J. / Seshire, A. / Kotzner, L. / Schlesiger, S. / Musil, D. / Schilke, H. / Doerfel, B. / Diehl, P. / Bopple, P. / Lemos, A.R. / Sousa, P.M.F. / Freire, F. / Bandeiras, T.M. / Carswell, E. / Pearson, N. / Sirohi, S. / Hooker, M. / Trivier, E. / Broome, R. / Balsiger, A. / Crowden, A. / Dillon, C. / Wienke, D.
History
DepositionApr 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)102,1768
Polymers101,2514
Non-polymers9254
Water1,51384
1
A: Transcriptional enhancer factor TEF-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5562
Polymers25,3251
Non-polymers2311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcriptional enhancer factor TEF-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5402
Polymers25,3091
Non-polymers2311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Transcriptional enhancer factor TEF-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5402
Polymers25,3091
Non-polymers2311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Transcriptional enhancer factor TEF-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5402
Polymers25,3091
Non-polymers2311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.470, 121.660, 154.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 25324.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TEAD3, TEAD5, TEF5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99594
#2: Protein Transcriptional enhancer factor TEF-5 / DTEF-1 / TEA domain family member 3 / TEAD-3


Mass: 25308.789 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TEAD3, TEAD5, TEF5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99594
#3: Chemical
ChemComp-JIK / 1-cyclopentylpyrazolo[3,4-b]pyridine-5-carboxylic acid


Mass: 231.251 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H13N3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 59.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 100 mM Sodium Acetate, 100 mM Calcium acetate,, 10% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9998 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2.095→47.771 Å / Num. obs: 72638 / % possible obs: 99.2 % / Redundancy: 6.7 % / CC1/2: 1 / Rrim(I) all: 0.095 / Net I/σ(I): 13.6
Reflection shellResolution: 2.095→2.22 Å / Num. unique obs: 11388 / CC1/2: 0.04 / % possible all: 97.6

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Processing

Software
NameVersionClassification
BUSTER2.11.8 (3-FEB-2022)refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EMW

5emw


Resolution: 2.095→47.77 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.917 / SU R Cruickshank DPI: 0.226 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.22 / SU Rfree Blow DPI: 0.185 / SU Rfree Cruickshank DPI: 0.19
RfactorNum. reflection% reflectionSelection details
Rfree0.2789 3597 5 %RANDOM
Rwork0.2566 ---
obs0.2578 71971 98.3 %-
Displacement parametersBiso max: 243.9 Å2 / Biso mean: 92.75 Å2 / Biso min: 49.53 Å2
Baniso -1Baniso -2Baniso -3
1-26.6189 Å20 Å20 Å2
2---26.4795 Å20 Å2
3----0.1394 Å2
Refine analyzeLuzzati coordinate error obs: 0.89 Å
Refinement stepCycle: final / Resolution: 2.095→47.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6770 0 68 84 6922
Biso mean--77.34 80.47 -
Num. residues----835
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2459SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1185HARMONIC5
X-RAY DIFFRACTIONt_it7084HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion881SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4600SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7084HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg9575HARMONIC20.96
X-RAY DIFFRACTIONt_omega_torsion3.05
X-RAY DIFFRACTIONt_other_torsion17.1
LS refinement shellResolution: 2.1→2.12 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.5201 71 4.93 %
Rwork0.5481 1369 -
all0.5467 1440 -
obs--72 %
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)
10.85180.35940.59611.546-1.27082.4738-0.0173-0.04-0.03570.0077-0.09330.03470.075-0.06960.1105-0.08540.0280.0532-0.0024-0.152-0.0489-10.9298-1.08910.9303
22.102-1.1424-1.18930.01690.11262.92610.01080.09210.06430.0665-0.074-0.21490.1353-0.06070.0632-0.21590.00110.03740.0901-0.0396-0.0803-1.04354.1909-23.222
32.4099-0.7137-0.41990.5745-0.71580.5927-0.0138-0.11430.013-0.23580.03220.2344-0.0252-0.0037-0.0185-0.1309-0.0159-0.05510.0632-0.152-0.0442-26.667715.1415-29.424
45.88820.8606-0.927802.81261.11270.00460.0785-0.01390.25080.0647-0.02260.22660.1087-0.0693-0.03650.1093-0.052-0.11770.14220.026914.84496.841620.0374
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A219 - 434
2X-RAY DIFFRACTION2{ B|* }B219 - 434
3X-RAY DIFFRACTION3{ C|* }C219 - 434
4X-RAY DIFFRACTION4{ D|* }D219 - 434

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