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- PDB-7cmm: Crystal structure of TEAD1-YBD in complex with K-975 -

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Basic information

Entry
Database: PDB / ID: 7cmm
TitleCrystal structure of TEAD1-YBD in complex with K-975
ComponentsTranscriptional enhancer factor TEF-1
KeywordsTRANSCRIPTION / Transcriptional enhancer factor TEF-1 / TEAD / TEAD1 / YAP binding domain / YBD / inhibitor / covalent binder
Function / homology
Function and homology information


TEAD-YAP complex / RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / hippo signaling / EGR2 and SOX10-mediated initiation of Schwann cell myelination / embryonic organ development / positive regulation of miRNA transcription / sequence-specific double-stranded DNA binding / positive regulation of cell growth / protein-containing complex assembly ...TEAD-YAP complex / RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / hippo signaling / EGR2 and SOX10-mediated initiation of Schwann cell myelination / embryonic organ development / positive regulation of miRNA transcription / sequence-specific double-stranded DNA binding / positive regulation of cell growth / protein-containing complex assembly / transcription regulator complex / 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 DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus
Similarity search - Function
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
Similarity search - Domain/homology
Chem-KK9 / Transcriptional enhancer factor TEF-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsTsuji, Y. / Suzuki, M. / Yasunaga, M. / Hamguchi, K. / Saito, J.
CitationJournal: Am J Cancer Res / Year: 2020
Title: The novel potent TEAD inhibitor, K-975, inhibits YAP1/TAZ-TEAD protein-protein interactions and exerts an anti-tumor effect on malignant pleural mesothelioma.
Authors: Kaneda, A. / Seike, T. / Danjo, T. / Nakajima, T. / Otsubo, N. / Yamaguchi, D. / Tsuji, Y. / Hamaguchi, K. / Yasunaga, M. / Nishiya, Y. / Suzuki, M. / Saito, J.I. / Yatsunami, R. / Nakamura, ...Authors: Kaneda, A. / Seike, T. / Danjo, T. / Nakajima, T. / Otsubo, N. / Yamaguchi, D. / Tsuji, Y. / Hamaguchi, K. / Yasunaga, M. / Nishiya, Y. / Suzuki, M. / Saito, J.I. / Yatsunami, R. / Nakamura, S. / Sekido, Y. / Mori, K.
History
DepositionJul 28, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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-1
B: Transcriptional enhancer factor TEF-1
C: Transcriptional enhancer factor TEF-1
D: Transcriptional enhancer factor TEF-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,4408
Polymers106,2814
Non-polymers1,1594
Water724
1
A: Transcriptional enhancer factor TEF-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8602
Polymers26,5701
Non-polymers2901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcriptional enhancer factor TEF-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8602
Polymers26,5701
Non-polymers2901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Transcriptional enhancer factor TEF-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8602
Polymers26,5701
Non-polymers2901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Transcriptional enhancer factor TEF-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8602
Polymers26,5701
Non-polymers2901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)147.990, 151.810, 67.530
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 210 through 226 or (resid 227...
21(chain B and (resid 210 through 227 or resid 236...
31(chain C and (resid 210 through 226 or (resid 227...
41(chain D and (resid 210 through 226 or (resid 227...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERGLUGLU(chain A and (resid 210 through 226 or (resid 227...AA210 - 22614 - 30
12GLNGLNGLNGLN(chain A and (resid 210 through 226 or (resid 227...AA22731
13SERSERASPASP(chain A and (resid 210 through 226 or (resid 227...AA210 - 42614 - 230
14SERSERASPASP(chain A and (resid 210 through 226 or (resid 227...AA210 - 42614 - 230
15SERSERASPASP(chain A and (resid 210 through 226 or (resid 227...AA210 - 42614 - 230
16SERSERASPASP(chain A and (resid 210 through 226 or (resid 227...AA210 - 42614 - 230
27SERSERGLNGLN(chain B and (resid 210 through 227 or resid 236...BB210 - 22714 - 31
28LYSLYSLEULEU(chain B and (resid 210 through 227 or resid 236...BB236 - 25340 - 57
29LEULEULEULEU(chain B and (resid 210 through 227 or resid 236...BB25458
210SERSERLYSLYS(chain B and (resid 210 through 227 or resid 236...BB210 - 42514 - 229
211SERSERLYSLYS(chain B and (resid 210 through 227 or resid 236...BB210 - 42514 - 229
212SERSERLYSLYS(chain B and (resid 210 through 227 or resid 236...BB210 - 42514 - 229
213SERSERLYSLYS(chain B and (resid 210 through 227 or resid 236...BB210 - 42514 - 229
314SERSERGLUGLU(chain C and (resid 210 through 226 or (resid 227...CC210 - 22614 - 30
315GLNGLNGLNGLN(chain C and (resid 210 through 226 or (resid 227...CC22731
316SERSERASPASP(chain C and (resid 210 through 226 or (resid 227...CC210 - 42614 - 230
317SERSERASPASP(chain C and (resid 210 through 226 or (resid 227...CC210 - 42614 - 230
318SERSERASPASP(chain C and (resid 210 through 226 or (resid 227...CC210 - 42614 - 230
319SERSERASPASP(chain C and (resid 210 through 226 or (resid 227...CC210 - 42614 - 230
420SERSERGLUGLU(chain D and (resid 210 through 226 or (resid 227...DD210 - 22614 - 30
421GLNGLNLYSLYS(chain D and (resid 210 through 226 or (resid 227...DD227 - 23631 - 40
422SERSERLYSLYS(chain D and (resid 210 through 226 or (resid 227...DD210 - 42514 - 229
423SERSERLYSLYS(chain D and (resid 210 through 226 or (resid 227...DD210 - 42514 - 229
424SERSERLYSLYS(chain D and (resid 210 through 226 or (resid 227...DD210 - 42514 - 229
425SERSERLYSLYS(chain D and (resid 210 through 226 or (resid 227...DD210 - 42514 - 229

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Components

#1: Protein
Transcriptional enhancer factor TEF-1 / NTEF-1 / Protein GT-IIC / TEA domain family member 1 / TEAD-1 / Transcription factor 13 / TCF-13


Mass: 26570.162 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TEAD1, TCF13, TEF1 / Production host: Escherichia coli (E. coli) / References: UniProt: P28347
#2: Chemical
ChemComp-KK9 / N-[3-(4-chloranylphenoxy)-4-methyl-phenyl]propanamide


Mass: 289.757 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H16ClNO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.57 Å3/Da / Density % sol: 65.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: ammonium sulfate, PEG 3350, Bis-Tris / PH range: 5.5-6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→49.33 Å / Num. obs: 19877 / % possible obs: 99.7 % / Redundancy: 18.6 % / CC1/2: 0.989 / Rmerge(I) obs: 0.546 / Rpim(I) all: 0.129 / Rrim(I) all: 0.562 / Net I/σ(I): 8 / Num. measured all: 369455 / Scaling rejects: 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.5-3.8319.53.299079146470.6140.7583.3771.399.7
8.57-49.3316.80.072498414840.9970.0170.07234.799.5

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KYS

3kys


Resolution: 3.5→10 Å / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.284 959 5.12 %
Rwork0.2337 17771 -
obs0.2363 18730 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 213.94 Å2 / Biso mean: 92.6784 Å2 / Biso min: 49.13 Å2
Refinement stepCycle: final / Resolution: 3.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6408 0 80 4 6492
Biso mean--90.11 53.7 -
Num. residues----803
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2300X-RAY DIFFRACTION7.013TORSIONAL
12B2300X-RAY DIFFRACTION7.013TORSIONAL
13C2300X-RAY DIFFRACTION7.013TORSIONAL
14D2300X-RAY DIFFRACTION7.013TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5-3.680.39961500.37192357250795
3.68-3.890.33981430.33292525266899
3.89-4.170.34591360.27532505264199
4.17-4.560.25331100.206325832693100
4.56-5.140.24841290.175825632692100
5.14-6.20.25251560.205925682724100
6.2-100.24761350.205526702805100
Refinement TLS params.Method: refined / Origin x: 46.3445 Å / Origin y: -4.806 Å / Origin z: 11.0434 Å
111213212223313233
T0.9807 Å20.0197 Å20.0881 Å2-0.632 Å2-0.0667 Å2--0.2647 Å2
L0.7389 °2-0.8429 °20.5332 °2-3.6731 °2-1.2175 °2--0.1312 °2
S0.1043 Å °-0.0567 Å °-0.0217 Å °0.1871 Å °-0.1013 Å °0.048 Å °-0.1007 Å °-0.0494 Å °-0.0144 Å °
Refinement TLS groupSelection details: all

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