[English] 日本語
Yorodumi
- PDB-7li5: Crystal Structure Analysis of human TEAD1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7li5
TitleCrystal Structure Analysis of human TEAD1
ComponentsTranscriptional enhancer factor TEF-1
KeywordsTRANSCRIPTION / Transcription enhancer factor / Hippo signaling pathway / tumor suppression / apoptosis
Function / homology
Function and homology information


DNA binding / nucleoplasm
Similarity search - Function
Coagulation Factor XIII; Chain A, domain 1 - #80 / YAP binding domain / : / YAP binding domain / Coagulation Factor XIII; Chain A, domain 1 / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-Y2D / TEA domain transcription factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.68 Å
AuthorsSeo, H.-S. / Dhe-Paganon, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: To Be Published
Title: Crystal Structure Analysis of human TEAD1
Authors: Seo, H.-S. / Dhe-Paganon, S.
History
DepositionJan 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1477
Polymers50,9722
Non-polymers1,1755
Water5,116284
1
A: Transcriptional enhancer factor TEF-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0263
Polymers25,4861
Non-polymers5392
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Transcriptional enhancer factor TEF-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1224
Polymers25,4861
Non-polymers6363
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.560, 89.320, 135.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Transcriptional enhancer factor TEF-1


Mass: 25486.045 Da / Num. of mol.: 2 / Fragment: UNP residues 113-328
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TEAD1 / Production host: Escherichia coli (E. coli) / References: UniProt: E9PKB7
#2: Chemical ChemComp-Y2D / 1-[(3R,4R)-3-[4-(pyridin-3-yl)-1H-1,2,3-triazol-1-yl]-4-{[4-(trifluoromethyl)phenyl]methoxy}pyrrolidin-1-yl]prop-2-en-1-one / 1-[(3~{R},4~{R})-3-(4-pyridin-3-yl-1,2,3-triazol-1-yl)-4-[[4-(trifluoromethyl)phenyl]methoxy]pyrrolidin-1-yl]prop-2-en-1-one


Mass: 443.422 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H20F3N5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.16 Å3/Da / Density % sol: 43.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 2.8 M Ammonium sulfate and 0.1 M Tris pH 9.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.68→36.56 Å / Num. obs: 50624 / % possible obs: 98.4 % / Redundancy: 4.4 % / Biso Wilson estimate: 28.49 Å2 / Rpim(I) all: 0.034 / Rrim(I) all: 0.074 / Net I/σ(I): 12.3 / Num. measured all: 223963
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
1.68-1.714.61.11145425050.7681.73999.4
4.56-36.574.135.81056926020.0160.03493.2

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
xia2data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IM5

6im5


Resolution: 1.68→35.29 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2243 2571 5.08 %
Rwork0.1969 47994 -
obs0.1983 50565 98.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.38 Å2 / Biso mean: 35.4263 Å2 / Biso min: 16.2 Å2
Refinement stepCycle: final / Resolution: 1.68→35.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3374 0 117 284 3775
Biso mean--35.61 42.55 -
Num. residues----416
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.68-1.710.36181320.36552634276699
1.71-1.750.35161390.3392714285399
1.75-1.790.30851320.3182616274899
1.79-1.830.34761400.28272673281399
1.83-1.870.28471300.24872598272898
1.87-1.920.30031440.22532663280798
1.92-1.980.24231580.21072612277099
1.98-2.040.25891410.221727122853100
2.04-2.120.21731390.215326712810100
2.12-2.20.20171210.19182684280599
2.2-2.30.2321620.18872690285299
2.3-2.420.23321550.19742656281199
2.42-2.570.27691380.20492656279498
2.57-2.770.26231430.20442646278997
2.77-3.050.22961550.20052682283798
3.05-3.490.22331510.18122636278797
3.49-4.40.15841490.16072702285197
4.4-35.290.20951420.18542749289193
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)
11.13480.3064-0.2666-0.0744-0.06890.01570.47810.0272-0.72910.21390.1461-0.71940.2080.51760.00070.3643-0.0239-0.06750.6014-0.12170.572323.6332-13.1746-33.402
20.45440.9384-0.07011.54960.1943.4640.0320.0834-0.1453-0.22210.14650.1835-0.2558-0.14750.00120.24430.0162-0.02840.2229-0.02250.23022.58664.4646-43.3602
30.75560.11550.21751.64380.85730.5218-0.03840.31290.2769-0.06850.093-0.4131-0.4480.1120.00080.3129-0.0086-0.03010.3784-0.02050.332721.7066-6.6121-28.3504
41.87880.95191.21875.2420.6741.0520.3442-0.8753-0.21170.9891-0.24031.13820.3487-0.62550.02760.4199-0.0445-0.08910.40010.0560.403810.7051-13.7595-19.9129
51.69821.1443-0.17261.49331.37933.22780.11290.13320.2855-0.2068-0.31890.1238-0.473-0.0922-0.14650.22460.0231-0.030.1933-0.05790.241610.24552.0434-32.7281
60.57660.77790.03651.06320.37991.17710.16670.0548-0.1375-0.23560.0074-0.33940.12630.18210.00030.28410.0438-0.07860.242-0.04160.26014.8307-9.5098-41.9423
70.27130.09150.14521.05370.4610.25980.0905-0.0731-0.04440.1094-0.14520.1740.1729-0.4617-0.00010.2664-0.0236-0.02040.316-0.04490.24520.8144-9.8332-29.1906
8-0.2419-0.4850.12031.63060.27220.76840.11260.08330.1368-0.4214-0.1521-0.1419-0.26030.017-0.00020.28090.0054-0.03520.3041-0.04350.29343.7091-11.2001-46.1224
91.2928-0.6326-1.04940.81721.21561.4463-0.18470.3340.5587-0.22850.36760.3489-0.3165-0.20640.00520.28740.0534-0.04910.2912-0.03350.3079-0.25349.9852-26.9275
101.48980.12810.44961.11150.02941.73960.1335-0.0972-0.03230.0651-0.0525-0.08110.1223-0.0375-0.00070.1594-0.0048-0.01910.2124-0.02070.18678.6549-4.4031-27.7927
111.17260.44490.12840.49170.73531.56730.00270.20960.31560.2658-0.2618-0.4033-0.47780.565-0.00240.2896-0.0351-0.04710.3068-0.01520.296818.62740.6297-31.8868
121.4978-0.56540.3308-0.0301-0.1732-0.12890.2577-0.1606-0.8403-0.24840.11660.4380.326-0.52630.01950.32730.0014-0.01160.54710.03970.4899-22.517-11.9473-65.9777
131.2507-1.45950.18091.7142-0.19111.20390.3634-0.6591-0.02560.5794-0.3475-0.4262-0.09540.1374-0.00060.3409-0.0309-0.02710.320.00510.2967-2.62041.0459-56.0816
140.11960.3712-0.21760.1297-0.79021.677-0.2459-0.1887-0.05140.31320.0308-0.0892-0.51450.3821-0.00930.3313-0.0254-0.08010.259-0.0080.24850.75378.5999-52.3111
151.09690.5187-0.48060.7814-0.72550.56640.1776-0.0230.13520.0898-0.08310.1099-0.1739-0.020.00030.30460.0192-0.02750.3683-0.01440.28-20.1648-4.3438-70.1598
161.66-0.434-0.17941.9271-0.27890.7509-0.04550.55630.0092-0.6312-0.2819-0.77020.12510.3671-0.01480.2862-0.00270.02990.33510.01560.2614-9.5548-10.3818-79.0931
171.1113-0.61540.37980.5750.07662.37690.0183-0.13850.28940.0146-0.0286-0.1776-0.4251-0.015-00.1895-0.01570.01530.1779-0.02480.2011-9.62192.8256-65.3186
180.72490.0585-0.68870.0051-0.43811.1993-0.0001-0.0068-0.05840.0459-0.0096-0.00730.00210.017300.2292-0.0193-0.01010.21160.02720.2245-2.8389-8.2733-62.7841
190.77180.1191-0.94052.2341-1.40211.2062-0.03430.06440.01520.2012-0.01-0.1134-0.1712-0.01020.00010.2049-0.0275-0.03510.23080.02610.216-0.2938-9.9572-58.5729
201.2750.68550.95031.36440.21152.1602-0.178-0.5141.0991-0.18550.4191-0.5098-0.83780.29950.00920.4069-0.06310.0230.29860.00730.51392.145412.0197-69.5989
212.98110.5271-0.34750.35370.67892.8255-0.17130.29640.6883-0.05610.1052-0.4308-0.6488-0.1776-0.0420.23380.0172-0.03460.20870.05650.2522-6.54944.0746-72.1493
221.31640.80980.30571.0011-0.67280.967-0.12080.00010.00870.21830.21150.20650.1376-0.0690.00060.21960.0043-0.01490.24520.00960.2135-7.6315-9.9942-67.7961
233.7174-0.90440.08961.7201-1.82042.0338-0.0749-0.68550.66150.0862-0.20140.3036-0.4968-0.4953-0.06560.25720.0894-0.00710.3723-0.05120.3027-16.9164.356-64.1525
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 205 through 216 )A205 - 216
2X-RAY DIFFRACTION2chain 'A' and (resid 217 through 242 )A217 - 242
3X-RAY DIFFRACTION3chain 'A' and (resid 243 through 261 )A243 - 261
4X-RAY DIFFRACTION4chain 'A' and (resid 262 through 281 )A262 - 281
5X-RAY DIFFRACTION5chain 'A' and (resid 282 through 303 )A282 - 303
6X-RAY DIFFRACTION6chain 'A' and (resid 304 through 318 )A304 - 318
7X-RAY DIFFRACTION7chain 'A' and (resid 319 through 341 )A319 - 341
8X-RAY DIFFRACTION8chain 'A' and (resid 342 through 359 )A342 - 359
9X-RAY DIFFRACTION9chain 'A' and (resid 360 through 374 )A360 - 374
10X-RAY DIFFRACTION10chain 'A' and (resid 375 through 409 )A375 - 409
11X-RAY DIFFRACTION11chain 'A' and (resid 410 through 424 )A410 - 424
12X-RAY DIFFRACTION12chain 'B' and (resid 205 through 216 )B205 - 216
13X-RAY DIFFRACTION13chain 'B' and (resid 217 through 228 )B217 - 228
14X-RAY DIFFRACTION14chain 'B' and (resid 229 through 242 )B229 - 242
15X-RAY DIFFRACTION15chain 'B' and (resid 243 through 261 )B243 - 261
16X-RAY DIFFRACTION16chain 'B' and (resid 262 through 281 )B262 - 281
17X-RAY DIFFRACTION17chain 'B' and (resid 282 through 304 )B282 - 304
18X-RAY DIFFRACTION18chain 'B' and (resid 305 through 330 )B305 - 330
19X-RAY DIFFRACTION19chain 'B' and (resid 331 through 359 )B331 - 359
20X-RAY DIFFRACTION20chain 'B' and (resid 360 through 374 )B360 - 374
21X-RAY DIFFRACTION21chain 'B' and (resid 375 through 393 )B375 - 393
22X-RAY DIFFRACTION22chain 'B' and (resid 394 through 409 )B394 - 409
23X-RAY DIFFRACTION23chain 'B' and (resid 410 through 424 )B410 - 424

+
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