[English] 日本語
Yorodumi
- PDB-7t2j: Crystal Structure of TEAD2 in a covalent complex with TED-642 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7t2j
TitleCrystal Structure of TEAD2 in a covalent complex with TED-642
ComponentsTranscriptional enhancer factor TEF-4
KeywordsTRANSCRIPTION / TEAD / inhibitor / complex / covalent / allosteric / Transcriptional enhancer factor TEF-4
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 / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / intracellular membrane-bounded organelle / chromatin / regulation of DNA-templated transcription / 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-E8Y / Transcriptional enhancer factor TEF-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBum-Erdene, K. / Gonzalez-Gutierrez, G. / Meroueh, S.O.
Funding support United States, 4items
OrganizationGrant numberCountry
American Cancer SocietyRSG-12-092-01-CDD United States
Other privateVera Bradley Foundation United States
Other governmentIndiana University Simon Cancer Center Near Miss Initiative grant United States
Other private100 Voices of Hope United States
CitationJournal: J.Med.Chem. / Year: 2023
Title: Small-Molecule Cyanamide Pan-TEAD·YAP1 Covalent Antagonists.
Authors: Bum-Erdene, K. / Yeh, I.J. / Gonzalez-Gutierrez, G. / Ghozayel, M.K. / Pollok, K. / Meroueh, S.O.
History
DepositionDec 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 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
B: Transcriptional enhancer factor TEF-4
A: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8614
Polymers53,2542
Non-polymers6072
Water23413
1
B: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9302
Polymers26,6271
Non-polymers3031
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9302
Polymers26,6271
Non-polymers3031
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.077, 61.590, 79.556
Angle α, β, γ (deg.)90.000, 117.611, 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: 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-E8Y / 4-[3-(trifluoromethyl)anilino]-1,3-dihydro-2H-isoindole-2-carbonitrile


Mass: 303.282 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H12F3N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.47 Å3/Da / Density % sol: 50.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Sodium Formate 1.8 - 2.4 M Hepes pH 7.2 - 7.4 / PH range: 7.2 - 7.4

-
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: 2.69→53.64 Å / Num. obs: 8897 / % possible obs: 91.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 37.91 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.093 / Rrim(I) all: 0.18 / Rsym value: 0.154 / Net I/σ(I): 4.7
Reflection shellResolution: 2.69→3.02 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 446 / CC1/2: 0.684 / Rpim(I) all: 0.406 / Rrim(I) all: 0.777 / Rsym value: 0.66 / % possible all: 59.2

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6e5g

6e5g


Resolution: 2.7→53.64 Å / SU ML: 0.4236 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.6761
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2793 470 5.29 %
Rwork0.2217 8422 -
obs0.2246 8892 61.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.87 Å2
Refinement stepCycle: LAST / Resolution: 2.7→53.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3292 0 44 13 3349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00363418
X-RAY DIFFRACTIONf_angle_d0.84964620
X-RAY DIFFRACTIONf_chiral_restr0.0408494
X-RAY DIFFRACTIONf_plane_restr0.0051587
X-RAY DIFFRACTIONf_dihedral_angle_d00
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-3.090.4008360.3022640X-RAY DIFFRACTION14.08
3.09-3.890.30511760.2293194X-RAY DIFFRACTION70.55
3.89-53.640.2572580.21344588X-RAY DIFFRACTION98.7
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)
10.0310731488938-0.008479114808820.02108314018450.04138120466320.05054518909580.0918291427876-0.03717200946750.04638940219790.03723401620190.154707051857-0.104649951713-0.2006559202510.16555295524-0.1464961627584.22165179819E-9-0.1350662533050.01525857336270.02414911900850.07247821523510.05301278595770.063954408121231.0513662937-17.314718223920.7773174825
20.1585276526210.0680150047123-0.03468488414650.025911126036-0.01811975789160.0689375161203-0.303964258878-0.179452290495-0.371498355999-0.2962144913220.288238693408-0.4602811104330.192300301308-0.3851288223932.23668798504E-90.03179818247730.0718695824055-0.06842457651410.06794445981710.027057274035-0.054155001236827.4553852852-13.046313618219.6867318795
30.0360597759587-0.0030211028954-0.04007496751440.0213566217772-0.03461716698080.05366939364730.0192747570718-0.04826320858560.1090589256230.06990563713050.08329700668190.180313604645-0.2927702006040.1604897347214.43089356897E-80.1078390193410.05693402152110.0269393187380.5943842058250.01429972462910.32091159698917.841962486715.286551050919.7813285781
40.00310383375576-0.025912951472-0.00600901012513-0.0431593667644-0.01233804329320.071855656110.0348707825998-0.3940108984790.1939940055480.0132091650932-0.02840814226820.190847227763-0.07414359230870.444097429897-3.06808637138E-9-0.5634935152521.029978559130.43418591191-1.0153666792-0.43206000002-0.042863780538523.780852035613.146178016820.9216523765
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 325 )BA218 - 3251 - 83
22chain 'B' and (resid 326 through 446 )BA326 - 44684 - 204
33chain 'A' and (resid 222 through 293 )AC222 - 2931 - 58
44chain 'A' and (resid 294 through 446 )AC294 - 44659 - 194

+
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