PDB-3l15: Human Tead2 transcriptional factor

ID or keywords:

Entry

Database: PDB / ID: 3l15

Title

Human Tead2 transcriptional factor

Components

Transcriptional enhancer factor TEF-4

Keywords

TRANSCRIPTION / Activator / DNA-binding / Nucleus / Transcription regulation

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 ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2 Å

Authors

Tomchick, D.R. / Luo, X. / Tian, W.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural and functional analysis of the YAP-binding domain of human TEAD2.
Authors: Tian, W. / Yu, J. / Tomchick, D.R. / Pan, D. / Luo, X.

History

Deposition	Dec 10, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 7, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3l15.cif.gz	249.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3l15.ent.gz	216.9 KB	Display	PDB format
PDBx/mmJSON format	3l15.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3l15_validation.pdf.gz	446.3 KB	Display	wwPDB validaton report
Full document	3l15_full_validation.pdf.gz	451.3 KB	Display
Data in XML	3l15_validation.xml.gz	18.4 KB	Display
Data in CIF	3l15_validation.cif.gz	25.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/l1/3l15 ftp://data.pdbj.org/pub/pdb/validation_reports/l1/3l15	HTTPS FTP

-
Related structure data

Similar structure data	5dq8-1 4tjw-2 6cdy-1 6tkm-2 4p58-d 6y73-2 6s66-1 7cmm-2 4tk5-3 4km6-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Transcriptional enhancer factor TEF-4

B: Transcriptional enhancer factor TEF-4

hetero molecules

53.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Transcriptional enhancer factor TEF-4

defined by author&software
26.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Transcriptional enhancer factor TEF-4

hetero molecules

defined by author&software
26.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	121.144, 61.567, 80.472
Angle α, β, γ (deg.)	90.00, 117.27, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	B-154- HOH
2	1	B-158- HOH

#1: Protein	Transcriptional enhancer factor TEF-4 / TEA domain family member 2 / TEAD-2 Mass: 26488.354 Da / Num. of mol.: 2 / Fragment: C-terminal residues 217-447 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TEAD2, TEF4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15562
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.52 Å³/Da / Density % sol: 51.14 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4 Details: 0.1 M Tris, 2.5 M Sodium Formate, 100 mM NaCl, 2 mM MgCl2, 1 mM TCEP, 5% (w/v) Glycerol;, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-BM / Wavelength: 0.9798 Å

Detector

Type: SBC-3 / Detector: CCD / Date: Nov 19, 2009 / Details: monochromator

Radiation

Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SAD / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9798 Å / Relative weight: 1

Reflection

Resolution: 2→50 Å / Num. all: 34385 / Num. obs: 34385 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / R_merge(I) obs: 0.1 / Net I/σ(I): 10.5

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	% possible all
2-2.03	3.8	0.711	70.9
2.03-2.07	3.9	0.748	78.8
2.07-2.11	4	0.716	93.4
2.11-2.15	4.4	0.677	97.8
2.15-2.2	4.9	0.556	98.2
2.2-2.25	5	0.537	98.1
2.25-2.31	5.1	0.5	98.3
2.31-2.37	5.2	0.425	98.5
2.37-2.44	5.2	0.429	98.4
2.44-2.52	5.2	0.343	98.6
2.52-2.61	5.2	0.281	98.7
2.61-2.71	5.2	0.23	98.8
2.71-2.84	5.2	0.194	99
2.84-2.99	5.2	0.147	98.9
2.99-3.17	5.2	0.114	99.2
3.17-3.42	5.1	0.081	99.2
3.42-3.76	5.1	0.066	99.3
3.76-4.31	5.1	0.058	99.5
4.31-5.43	5	0.052	99.6
5.43-50	4.8	0.064	97.8

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHENIX		refinement
PDB_EXTRACT	3.005	data extraction
ADSC	Quantum	data collection
HKL-3000		data reduction
HKL-3000		data scaling
SHELXS		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2→33.738 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 1.75 / Isotropic thermal model: ISOTROPIC AND TLS / σ(F): 0.19 / Phase error: 27.73 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2445	1878	5.79 %
R_work	0.1885	-	-
obs	0.1918	32458	90.62 %
all	-	32458	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 54.647 Å² / k_sol: 0.441 e/Å³

Displacement parameters

B_iso mean: 52.545 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	11.024 Å²	-0 Å²	11.577 Å²
2-	-	-0.416 Å²	0 Å²
3-	-	-	-10.608 Å²

Refinement step

Cycle: LAST / Resolution: 2→33.738 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3277	0	18	160	3455

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	6605
X-RAY DIFFRACTION	f_angle_d	1.056	11866
X-RAY DIFFRACTION	f_dihedral_angle_d	13.93	1650
X-RAY DIFFRACTION	f_chiral_restr	0.102	490
X-RAY DIFFRACTION	f_plane_restr	0.005	986

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2-2.0532	0.3576	88	0.2953	1571	X-RAY DIFFRACTION	60
2.0532-2.1136	0.3516	114	0.2825	2023	X-RAY DIFFRACTION	78
2.1136-2.1818	0.3077	142	0.2505	2234	X-RAY DIFFRACTION	88
2.1818-2.2597	0.3139	148	0.2196	2346	X-RAY DIFFRACTION	90
2.2597-2.3502	0.2989	148	0.2018	2355	X-RAY DIFFRACTION	92
2.3502-2.4571	0.2416	148	0.2014	2387	X-RAY DIFFRACTION	92
2.4571-2.5866	0.2816	148	0.1941	2403	X-RAY DIFFRACTION	93
2.5866-2.7486	0.268	148	0.187	2439	X-RAY DIFFRACTION	95
2.7486-2.9607	0.2488	154	0.1869	2489	X-RAY DIFFRACTION	96
2.9607-3.2585	0.2388	158	0.1768	2557	X-RAY DIFFRACTION	97
3.2585-3.7294	0.2067	159	0.1595	2542	X-RAY DIFFRACTION	99
3.7294-4.6967	0.1835	160	0.1366	2590	X-RAY DIFFRACTION	99
4.6967-33.7426	0.2386	163	0.2056	2644	X-RAY DIFFRACTION	98

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	0.0612	-0.118	0.0831	-0.0486	-0.1917	0.2992	0.041	-0.3405	0.0514	0.2549	0.1141	0.3199	-0.5942	0.5519	0.0014	0.2384	-0.0164	0.0319	0.5252	0.0154	0.2737	41.3757	51.2459	-7.1594
2	0.0857	-0.139	0.0487	0.1057	-0.0589	-0.0498	0.1724	0.151	0.1715	-0.184	-0.0942	0.7786	-0.0134	0.3283	0.0032	0.3227	-0.1156	0.1413	0.6889	-0.096	0.2511	53.5998	54.186	-11.4989
3	0.3829	0.0788	-0.0891	0.0752	-0.2669	0.1414	-0.2207	0.3187	-0.043	0.2133	0.4801	0.1885	0.1164	-0.1091	-0	0.5438	-0.0002	-0.0082	0.5109	0.0801	0.3466	32.0404	50.0132	-22.5143
4	0.1588	-0.1482	-0.0025	0.3447	0.1304	0.2184	-0.0686	-0.0812	-0.3575	-0.1483	0.1934	-0.0075	-0.2626	-0.3306	0.0001	0.2809	0.0396	0.0078	0.3076	0.0652	0.4237	28.5668	46.2572	-18.219
5	-0.0712	0.0313	-0.4321	-0.21	-0.0915	0.0447	0.1349	-0.3393	-0.173	0.1246	0.223	0.222	-0.4575	0.6928	-0.0002	0.3091	-0.0006	0.0438	0.4894	-0.0673	0.3281	49.7401	50.5427	-12.5193
6	0.3528	0.2766	0.0973	-0.0403	0.4022	0.1188	-0.2037	0.149	-0.1554	0.1165	0.0278	-0.0415	0.6619	-0.7056	-0.0014	0.3813	0.0636	-0.0002	0.2731	0.0333	0.3055	37.514	40.319	-11.804
7	-0.0976	-0.0241	-0.0235	0.0039	0.1328	0.0635	0.1787	-0.7607	0.0623	-0.3872	-0.1013	0.0007	0.286	0.6301	-0.0002	0.2962	0.0563	0.0198	0.4858	-0.0566	0.2454	38.1946	46.8838	4.8446
8	0.1447	-0.0559	-0.0023	-0.293	0.1922	0.0951	0.0095	-0.5447	-0.0818	0.1421	-0.115	0.0472	0.2431	0.5946	0	0.4098	0.0861	0.0429	0.4884	0.0766	0.3052	52.9311	43.2822	-17.8985
9	0.9586	-0.4252	0.7756	0.2485	0.4678	0.8029	-0.084	-0.02	0.2139	-0.1568	0.2123	0.1502	-0.0218	-0.0416	-0.0002	0.2749	0.0862	0.038	0.1169	0.0184	0.2733	41.0644	47.6084	-20.1469
10	-0.0323	-0.1179	0.0209	0.1687	-0.1102	0.2498	-0.3606	0.3836	0.3788	-0.1526	0.4009	0.2166	-0.8105	-0.2232	-0.0012	0.512	-0.0095	0.0627	0.1894	0.0318	0.3202	39.4255	59.0972	-19.8723
11	0.0365	-0.1338	-0.0978	0.001	0.1675	0.0757	0.5419	-0.3928	-0.1709	0.1004	-0.2868	-0.1069	0.1816	-0.2297	-0.0002	0.25	0.01	-0.155	0.4461	0.0161	0.2959	51.4124	16.9051	-4.5206
12	0.2279	-0.1558	-0.1505	0.2583	0.1848	0.3649	-0.0859	0.3285	0.2263	0.1917	0.1073	0.0553	0.8604	-0.3229	-0.008	0.2049	-0.1042	-0.049	0.374	-0.0442	0.2567	30.6267	13.7866	-16.357
13	0.2583	0.342	0.5155	0.0971	0.3097	0.1732	-0.0735	0.2845	-0.0662	-0.3089	0.384	0.1092	0.126	0.5766	-0.0001	0.3367	-0.0235	0.0445	0.5399	-0.0478	0.3805	59.3794	16.8597	-17.2437
14	0.5139	-0.1078	-0.1646	1.2195	-0.1213	0.3767	-0.2401	-0.2504	-0.1438	-0.7154	0.0682	-0.3854	0.0667	0.4923	-0.0016	0.259	0.0367	-0.0031	0.3633	0.0221	0.2936	59.6802	25.4509	-14.9036
15	0.1185	0.1228	-0.0717	0.3361	-0.4518	-0.0553	0.1284	-0.1355	0.0641	-0.0337	-0.0846	0.0751	0.3449	-0.1596	0.0001	0.3722	-0.0502	-0.0207	0.2507	-0.0313	0.2572	39.5525	16.5546	-15.707
16	0.267	0.6522	0.3792	0.7757	-0.0066	0.5442	0.2276	-0.1598	-0.0089	-0.2244	0.0948	-0.0237	-0.6424	0.7149	0.0147	0.3307	0.0438	0.0005	0.2626	-0.029	0.2196	48.2263	29.1359	-13.2525
17	0.1966	0.1379	-0.01	0.1277	-0.2129	0.1264	-0.1272	-0.5286	-0.067	0.0219	-0.146	-0.0093	-0.3102	-0.744	-0.0001	0.2803	-0.0629	0.0349	0.5436	-0.0278	0.2763	41.3397	23.1966	1.0725
18	0.0048	-0.1632	0.05	-0.0464	-0.0413	0.0712	0.0855	0.1068	0.0054	0.2863	-0.33	0.072	-0.1536	-0.1569	-0.0001	0.3637	0.0028	0.0271	0.3217	-0.0209	0.271	37.3068	22.0987	-26.9183
19	0.9241	0.2447	-0.3132	0.2091	-0.6766	0.3935	0.0125	-0.0886	-0.0386	-0.2348	0.0042	-0.1664	-0.0824	-0.0618	0.0001	0.2283	0.0532	-0.0114	0.2174	0.0037	0.2872	50.0559	22.0977	-20.028
20	0.0329	0.0553	-0.3628	-0.0019	-0.2213	0.5989	-0.301	0.0581	-0.0913	-0.3572	0.2089	-0.0342	0.456	0.1404	-0.0001	0.364	0.0322	0.0117	0.1879	0.0031	0.3442	51.3454	11.4788	-19.8413

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 222:239)
2	X-RAY DIFFRACTION	2	(chain A and resid 247:253)
3	X-RAY DIFFRACTION	3	(chain A and resid 254:281)
4	X-RAY DIFFRACTION	4	(chain A and resid 282:302)
5	X-RAY DIFFRACTION	5	(chain A and resid 303:334)
6	X-RAY DIFFRACTION	6	(chain A and resid 335:359)
7	X-RAY DIFFRACTION	7	(chain A and resid 360:373)
8	X-RAY DIFFRACTION	8	(chain A and resid 374:392)
9	X-RAY DIFFRACTION	9	(chain A and resid 393:431)
10	X-RAY DIFFRACTION	10	(chain A and resid 432:446)
11	X-RAY DIFFRACTION	11	(chain B and resid 221:233)
12	X-RAY DIFFRACTION	12	(chain B and resid 234:253)
13	X-RAY DIFFRACTION	13	(chain B and resid 254:279)
14	X-RAY DIFFRACTION	14	(chain B and resid 280:302)
15	X-RAY DIFFRACTION	15	(chain B and resid 303:335)
16	X-RAY DIFFRACTION	16	(chain B and resid 336:359)
17	X-RAY DIFFRACTION	17	(chain B and resid 360:376)
18	X-RAY DIFFRACTION	18	(chain B and resid 377:393)
19	X-RAY DIFFRACTION	19	(chain B and resid 394:424)
20	X-RAY DIFFRACTION	20	(chain B and resid 425:446)

-
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://pdbjlvh1.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

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

+
Jul 12, 2017. Major update of PDB

-
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

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

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

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi