[English] 日本語
Yorodumi
- PDB-7cmm: Crystal structure of TEAD1-YBD in complex with K-975 -

+
Open data


ID or keywords:

Loading...

-
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 / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus
Similarity search - Function
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 / : ...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-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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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
Has protein modificationY

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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