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- PDB-9q1o: Crystal structure of human TEAD2-Yap binding domain covalently bo... -

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Basic information

Entry
Database: PDB / ID: 9q1o
TitleCrystal structure of human TEAD2-Yap binding domain covalently bound to an allosteric regulator
ComponentsTranscriptional enhancer factor TEF-4
KeywordsTRANSCRIPTION/INHIBITOR / TEAD / inhibitor / complex / covalent / allosteric / Transcriptional enhancer factor TEF-4 / TRANSCRIPTION / TRANSCRIPTION-INHIBITOR complex
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 / Formation of axial mesoderm / regulation of stem cell differentiation / 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 / Formation of axial mesoderm / regulation of stem cell differentiation / embryonic heart tube morphogenesis / embryonic organ development / vasculogenesis / cellular response to retinoic acid / neural tube closure / transcription coactivator binding / sequence-specific double-stranded DNA binding / disordered domain specific 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 / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol
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
: / FORMIC ACID / Transcriptional enhancer factor TEF-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsBum-Erdene, K. / Gonzalez-Gutierrez, G. / Meroueh, S.O.
Funding support United States, 2items
OrganizationGrant numberCountry
Other privateP30CA082709 United States
Other privateVera Bradley Foundation United States
CitationJournal: Acs Chem.Biol. / Year: 2025
Title: Small-Molecule Covalent Stabilization and Inhibition of the TEAD·YAP1 Transcription Factor in Cancer Cells.
Authors: Yeh, I.J. / Bum-Erdene, K. / Ghozayel, M.K. / Gonzalez-Gutierrez, G. / Meroueh, S.O.
History
DepositionAug 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)53,9815
Polymers53,2542
Non-polymers7273
Water55831
1
B: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0143
Polymers26,6271
Non-polymers3862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9682
Polymers26,6271
Non-polymers3401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.898, 61.666, 79.766
Angle α, β, γ (deg.)90.000, 117.519, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-616-

HOH

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Components

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


Mass: 26627.170 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TEAD2, TEF4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15562
#2: Chemical ChemComp-EI6 / 1-{(3aS,4R,7aR)-4-[4-(trifluoromethyl)anilino]octahydro-2H-isoindol-2-yl}propan-1-one / 1-{(3aS,4R,7aR)-4-[4-(trifluoromethyl)anilino]octahydro-2H-isoindol-2-yl}prop-2-en-1-one, bound form


Mass: 340.383 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H23F3N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.5 Å3/Da / Density % sol: 50.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Sodium Formate 1.8M - 2.4M HEPES pH 7.2 - 7.4 / PH range: 7.2 - 7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Sep 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.26→53.56 Å / Num. obs: 12980 / % possible obs: 88.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 37.71 Å2 / CC1/2: 0.994 / Rpim(I) all: 0.076 / Rrim(I) all: 0.146 / Rsym value: 0.125 / Net I/σ(I): 8.8
Reflection shellResolution: 2.26→2.57 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 650 / CC1/2: 0.713 / Rpim(I) all: 0.508 / Rrim(I) all: 0.961 / Rsym value: 0.811 / % possible all: 66.1

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6E5G

6e5g


Resolution: 2.26→53.56 Å / SU ML: 0.2561 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.7446
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.266 671 5.17 %
Rwork0.2086 12303 -
obs0.2115 12974 52.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.88 Å2
Refinement stepCycle: LAST / Resolution: 2.26→53.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3360 0 51 31 3442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00323494
X-RAY DIFFRACTIONf_angle_d0.51124723
X-RAY DIFFRACTIONf_chiral_restr0.0392507
X-RAY DIFFRACTIONf_plane_restr0.003600
X-RAY DIFFRACTIONf_dihedral_angle_d00
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.430.4456120.3588200X-RAY DIFFRACTION4.31
2.43-2.680.3757440.2839728X-RAY DIFFRACTION15.76
2.68-3.060.33461340.2752531X-RAY DIFFRACTION53.65
3.06-3.860.26142320.21424214X-RAY DIFFRACTION89.38
3.86-53.560.24862490.18654630X-RAY DIFFRACTION96.5
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)
11.75252694047-0.07710832238730.2779015603122.612194095230.2051744580013.224240945840.185338351104-0.12824153056-0.503809400385-0.00293830103123-0.154457590437-0.3621822144110.5636121710960.0856040182548-0.05611504606040.126885426747-0.0441050975879-0.03532277458130.208900423765-0.01391907260730.13260362698528.6709230586-19.682411183822.7191287777
28.19741851578-3.691312111452.298461690919.026439207693.09731717465.3724422687-0.281959481591.501178613531.52635157665-0.989525818871-0.235762278428-1.31107849718-1.108628334320.7972181328220.235413785910.310503181615-0.198916313899-0.001970685786340.6720416989770.1226828264410.52381213212942.7338794365-4.6902640222518.3011452351
32.012984857790.7913428575171.548263155313.188380931491.577884189843.54238743761-0.451984027717-0.7362485506040.158401709784-0.460330856184-0.09119983511550.439287529489-0.441294838304-0.76885923734-0.7744546000810.0525546574380.135999573789-0.1050018601580.14589430363-0.01054558561360.2797933885228.6516366432-19.293664098716.6588846752
42.711907256010.3712364981020.1554157309342.074157515260.4134796976723.477422100740.036769583402-0.5673613106930.1633765606850.0736895613305-0.0877819905237-0.195356855249-0.1007685403070.3601688947770.00797738122260.1707912474650.019286401815-0.01589112388150.100843686624-0.0007831998873390.11161706309927.3782809059-9.7819839903425.4192180159
55.9037637603-0.593963618941-3.744969887315.266586284370.3501838480936.32740967755-0.192061114727-0.360959833780.09786857951740.119547921745-0.0834985920565-0.00537815553363-0.376138377616-0.0284266086401-0.3588159631280.3170736219860.160151487859-0.06147892822370.1562932487510.07624091397950.22296328842526.7974832107-3.1293334357621.1903283758
65.882788034250.927303149022.139337191731.24020248211-0.1111806467093.069825695710.103186383775-1.582183748020.07613711278090.0794611862336-0.246148894965-0.3955702828150.281165116793-0.530416842859-0.07451294487870.2011507099160.05852958919350.200020917520.551140558305-0.04737406574410.19047330292622.2565165295-11.998016152533.6209659658
77.50751393321-2.87542016138-4.930812704973.737792154985.358980068717.80098953773-0.2188541137910.8707295440560.0193641869739-1.01792111078-0.4283615858460.379027406322-0.417147052208-1.150109616770.3324538341430.332688994975-0.00318354624579-0.04485697848490.246592618840.01346614159980.1168535200719.4945642722-14.60308997755.04796770379
81.925379967520.3357220188230.4323758978360.476213771685-1.22927830724.14432146599-0.3547313006160.223302167023-0.0932314050067-0.04758984676820.0611812237638-0.03203627314380.7364199351890.339675044295-0.2215216956130.1072244307830.0884547616965-0.05739286704570.07057309537460.02423152331450.13300529798730.6328557467-15.13222360510.3034245208
93.262560305320.6376427248530.3414338786563.539686430361.239291441564.163168868090.134734539443-0.255652418094-0.116033805532-0.089549981868-0.01698604984590.02525745889530.6622443435560.266993225773-0.03068846000010.1664519511360.0226957528031-0.03513885946340.003646185146910.01348950423820.1484360439333.7848753293-17.521633441220.194882403
108.037374901121.21702238992-1.137870877983.56017039397-1.670376192024.558546754-0.2440736056120.6148482344210.363276903229-0.2675880078240.5469282112330.473038960329-0.2825166732160.151614611026-0.3041258084740.290909495010.070695839670.08438059605080.388592167422-0.04625068891410.2514789385517.914588013616.176611063920.1302438152
112.38521212380.295449870578-2.701281762180.586775506472-1.153759166616.254347862650.0672147310306-0.4284472811880.1949212136860.1071283462590.07573318662540.0793012843926-0.1261945053010.613689753788-0.1181749674850.1676860526350.07905275999880.04211311677280.160761854187-0.01774669477280.25076098099324.004746326913.17635097820.909680259
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 218 through 277 )BA218 - 2771 - 54
22chain 'B' and (resid 278 through 293 )BA278 - 29355 - 70
33chain 'B' and (resid 294 through 325 )BA294 - 32571 - 88
44chain 'B' and (resid 326 through 351 )BA326 - 35189 - 114
55chain 'B' and (resid 352 through 362 )BA352 - 362115 - 125
66chain 'B' and (resid 363 through 380 )BA363 - 380126 - 143
77chain 'B' and (resid 381 through 395 )BA381 - 395144 - 158
88chain 'B' and (resid 396 through 414 )BA396 - 414159 - 177
99chain 'B' and (resid 415 through 446 )BA415 - 446178 - 209
1010chain 'A' and (resid 219 through 293 )AC219 - 2931 - 61
1111chain 'A' and (resid 294 through 446 )AC294 - 44662 - 197

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