[English] 日本語
Yorodumi
- PDB-7tyq: TEAD2 bound to Compound 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7tyq
TitleTEAD2 bound to Compound 1
ComponentsTranscriptional enhancer factor TEF-4
KeywordsTRANSCRIPTION / Small molecule PPI 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 / 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 / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / intracellular membrane-bounded organelle / regulation of DNA-templated transcription / chromatin / 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
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-KUI / Transcriptional enhancer factor TEF-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsNoland, C.L. / Fong, R.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: Novel mechanism of YAP-TEAD inhibition results in targeted chromatin remodeling and reveals an expanded Hippo dependent landscape in cancers
Authors: Hagenbeek, T.J. / Zbieg, J.R. / Noland, C.L. / Yao, X. / Schmidt, S. / Clausen, S. / Steffek, M. / Lee, W. / Beroza, P. / Martin, S. / Lin, E. / Fong, R. / Di Lello, P. / Kubala, M.H. / ...Authors: Hagenbeek, T.J. / Zbieg, J.R. / Noland, C.L. / Yao, X. / Schmidt, S. / Clausen, S. / Steffek, M. / Lee, W. / Beroza, P. / Martin, S. / Lin, E. / Fong, R. / Di Lello, P. / Kubala, M.H. / Lacap, J.A. / Yang, M.N.Y. / Maddalo, D. / Lau, J.T. / An, L. / Levy, E. / Lorenzo, M.N. / Lee, H.J. / Pham, T.H. / Modrusan, Z. / Zang, R. / Chen, Y.C. / Li, J. / Hafner, M. / Chang, M.T. / Crawford, J.J. / Dey, A.
History
DepositionFeb 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)53,3044
Polymers52,6022
Non-polymers7032
Water1,20767
1
A: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6522
Polymers26,3011
Non-polymers3511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6522
Polymers26,3011
Non-polymers3511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.854, 61.183, 79.951
Angle α, β, γ (deg.)90.000, 111.608, 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

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


Mass: 26300.773 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 (E. coli) / References: UniProt: Q15562
#2: Chemical ChemComp-KUI / ethyl (8S)-7-oxo-5-[4-(trifluoromethyl)phenyl]-4,7-dihydropyrazolo[1,5-a]pyrimidine-3-carboxylate


Mass: 351.280 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H12F3N3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Na/K Tartrate, 0.1 M Bis Tris pH 6.5, 35% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.878→74.33 Å / Num. obs: 28082 / % possible obs: 94.4 % / Redundancy: 6.8 % / Biso Wilson estimate: 34.9 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.2
Reflection shellResolution: 1.878→2.059 Å / Num. unique obs: 1405 / CC1/2: 0.711

-
Processing

Software
NameVersionClassification
PHENIX1.18rc5_3822refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EMV

5emv


Resolution: 1.88→74.33 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.7281
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2467 1415 5.04 %
Rwork0.206 26664 -
obs0.208 28079 66.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.99 Å2
Refinement stepCycle: LAST / Resolution: 1.88→74.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3208 0 50 67 3325
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00383393
X-RAY DIFFRACTIONf_angle_d0.66674618
X-RAY DIFFRACTIONf_chiral_restr0.0453504
X-RAY DIFFRACTIONf_plane_restr0.0032630
X-RAY DIFFRACTIONf_dihedral_angle_d22.08511257
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.940.381160.306274X-RAY DIFFRACTION6.88
1.94-2.020.3967410.2783624X-RAY DIFFRACTION15.86
2.02-2.110.2808630.27071190X-RAY DIFFRACTION29.78
2.11-2.230.3022980.26011975X-RAY DIFFRACTION49.63
2.23-2.370.28861410.26722817X-RAY DIFFRACTION69.95
2.37-2.550.31992000.26913575X-RAY DIFFRACTION90.35
2.55-2.80.29372220.27084019X-RAY DIFFRACTION99.95
2.8-3.210.26912140.23434020X-RAY DIFFRACTION99.93
3.21-4.040.24992030.17924059X-RAY DIFFRACTION99.98
4.04-74.330.19352170.16854111X-RAY DIFFRACTION99.84
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)
12.26589134638-0.5393087613871.758165079162.284954899920.748552310315.02134202909-0.137859361628-0.0909835481605-0.158081662059-0.1998778984120.207914542977-0.445624762290.2492241458720.413821959331-3.98442053074E-60.256787086801-0.03791136940280.01071260330070.275574878961-0.03737804992020.283336363491-26.4295261638-11.899956246621.1433104716
23.081006485940.2268314308720.3409438060651.701188531610.8180540993385.02862455171-0.0561661617833-0.1984434796260.00548228117749-0.2046136881710.189201561994-0.1914009737020.0458075380001-0.1773616523310.00440129145110.2142950214770.027470320569-0.0101924271190.11474557205-0.007399386384270.215599968545-28.9952002637-8.8115610093219.7685449739
31.623838993940.302861029252-1.818123004012.50359296036-1.245646167992.339045719940.1585229313910.2207776138320.0308533540724-0.2440269497350.07850163724130.293131905359-0.32572017494-0.0388171166176-0.0001603932906260.3469884977830.0374394588877-0.02151976866060.420100803974-0.02955672296460.368154255928-36.365405345821.222512951520.9719600454
40.471028371748-1.02104381668-0.5252163824772.548387610560.08802872464563.606486939540.0912402927311-0.2437929771150.09044952146-0.154936514407-0.05808001218240.0830219908458-0.0188517465876-0.0104392709657-0.0002631496790450.2462749683470.01979798970060.03330357365840.2733004049060.01513341920180.331740429074-37.337149932718.945252094923.5278074151
52.642287726930.0683725482959-1.741006270590.8160110850050.01461512226721.206828837040.232033709409-0.5304352010640.25612456693-0.7849670779490.09588527593010.3066908269291.070120870620.698854910240.2711985375190.608810452650.229403724952-0.08702049208140.06451148672480.1188700529470.216094821741-34.8477335989.2995102397422.2000877481
61.174282672160.77761033797-0.03607199049110.819175415492-0.3843425084290.6415430347820.0958869179214-0.6377856473350.152465509575-0.124095450120.149720888461-0.1679993536720.04406017745091.498959481010.002955535808390.3879270991610.159785197338-0.01952663414850.6490609615740.03493762233340.371512452652-26.015620827316.732836483524.319856259
71.110425474870.1668427694540.5315108314990.402607035060.4685720729520.6380010261610.2606015487710.1287755397910.305638432963-0.279941083410.2397730277160.000554566737012-0.3895785454130.1656218861930.001463896768940.4227009681810.0552090253090.06691858995150.214423307241-0.01643716696430.287001490699-32.515668451918.565214117912.1423082693
81.88820238584-1.315151241550.8259762322442.196076052390.9391804678843.172044045450.1592948468260.00908787210070.59811827581-0.1113229580310.4177925419070.376069571155-0.239043264463-0.5060473329120.02168917587090.2446892399920.07758244196650.0395115349620.1756549739290.03868984057320.348124659117-38.463935012822.663494044320.3028659287
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 220 through 293 )AA220 - 2931 - 70
22chain 'A' and (resid 294 through 446 )AA294 - 44671 - 218
33chain 'B' and (resid 222 through 284 )BC222 - 2841 - 46
44chain 'B' and (resid 285 through 339 )BC285 - 33947 - 87
55chain 'B' and (resid 340 through 362 )BC340 - 36288 - 112
66chain 'B' and (resid 363 through 395 )BC363 - 395113 - 147
77chain 'B' and (resid 396 through 414 )BC396 - 414148 - 166
88chain 'B' and (resid 415 through 446 )BC415 - 446167 - 200

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more