PDB-8s6y: Co-crystal structure of TEAD1 with OPN-9652

ID or keywords:

Entry

Database: PDB / ID: 8s6y

Title

Co-crystal structure of TEAD1 with OPN-9652

Components

Transcriptional enhancer factor TEF-1

Keywords

TRANSCRIPTION / TEAD inhibitor / TEAD1 / auto-palmitoylation pocket

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 ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.031 Å

Authors

Aplin, A.E.

Funding support

1items

Citation

Journal: To Be Published
Title: Targeting TAZ-TEAD in minimal residual disease enhances the duration of targeted therapy in melanoma models
Authors: Aplin, A.E.

History

Deposition	Feb 28, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 30, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8s6y.cif.gz	222.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8s6y.ent.gz		Display	PDB format
PDBx/mmJSON format	8s6y.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8s6y_validation.pdf.gz	2.4 MB	Display	wwPDB validaton report
Full document	8s6y_full_validation.pdf.gz	2.4 MB	Display
Data in XML	8s6y_validation.xml.gz	49.8 KB	Display
Data in CIF	8s6y_validation.cif.gz	65.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s6/8s6y ftp://data.pdbj.org/pub/pdb/validation_reports/s6/8s6y	HTTPS FTP

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#247 - Jul 2020 Myelin-associated Glycoprotein similarity (1) #96 - Dec 2007 Oxidosqualene Cyclase similarity (1)

Deposited unit

AAA: Transcriptional enhancer factor TEF-1

BBB: Transcriptional enhancer factor TEF-1

CCC: Transcriptional enhancer factor TEF-1

DDD: Transcriptional enhancer factor TEF-1

hetero molecules

105 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	120.957, 120.957, 155.520
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	154
Space group name H-M	P3₂21

Components on special symmetry positions

ID	Model	Components
1	1	CCC-757- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	AAA
2	1	BBB
3	2	AAA
4	2	CCC
5	3	AAA
6	3	DDD
7	4	BBB
8	4	CCC
9	5	BBB
10	5	DDD
11	6	CCC
12	6	DDD

NCS domain segments:

Beg auth comp-ID: ARG / Beg label comp-ID: ARG

Dom-ID	Component-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	ASP	ASP	AAA	A	209 - 426	2 - 217
2	2	1	ASP	ASP	BBB	B	209 - 426	2 - 217
3	3	2	LYS	LYS	AAA	A	209 - 425	2 - 216
4	4	2	LYS	LYS	CCC	C	209 - 425	2 - 216
5	5	3	ASP	ASP	AAA	A	209 - 426	2 - 217
6	6	3	ASP	ASP	DDD	D	209 - 426	2 - 217
7	7	4	VAL	VAL	BBB	B	209 - 424	2 - 215
8	8	4	VAL	VAL	CCC	C	209 - 424	2 - 215
9	9	5	ASP	ASP	BBB	B	209 - 426	2 - 217
10	10	5	ASP	ASP	DDD	D	209 - 426	2 - 217
11	11	6	LYS	LYS	CCC	C	209 - 425	2 - 216
12	12	6	LYS	LYS	DDD	D	209 - 425	2 - 216

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

-
Protein , 1 types, 4 molecules AAABBBCCCDDD

#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: 25068.627 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

#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: 25068.627 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

-
Non-polymers , 6 types, 633 molecules

#2: Chemical	ChemComp-A1H5I / 1-[7-[3-fluoranyl-4-(trifluoromethyl)phenoxy]-3,4-dihydro-1~{H}-isoquinolin-2-yl]propan-1-one Mass: 367.337 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₉H₁₇F₄NO₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 591 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.31 Å³/Da / Density % sol: 62.81 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / Details: buffer, salt and precipitant

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.885603 Å
Detector	Type: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Jan 26, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.885603 Å / Relative weight: 1
Reflection	Resolution: 2.031→104.752 Å / Num. obs: 81249 / % possible obs: 95.4 % / Redundancy: 12.6 % / CC_1/2: 0.99 / Net I/σ(I): 6.5
Reflection shell	Resolution: 2.031→2.066 Å / Num. unique obs: 3241 / CC_1/2: 0.664

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
autoPROC		data reduction
autoPROC		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.031→104.752 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.912 / SU B: 5.396 / SU ML: 0.142 / Cross valid method: FREE R-VALUE / ESU R: 0.188 / ESU R Free: 0.169
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2581	647	0.798 %
R_work	0.2233	80456	-
all	0.224	-	-
obs	-	81103	95.156 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 39.692 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.609 Å²	0.304 Å²	0 Å²
2-	-	0.609 Å²	-0 Å²
3-	-	-	-1.975 Å²

Refinement step

Cycle: LAST / Resolution: 2.031→104.752 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6959	0	276	591	7826

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.003	0.013	7607
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.017	6900
X-RAY DIFFRACTION	r_angle_refined_deg	1.336	1.679	10323
X-RAY DIFFRACTION	r_angle_other_deg	1.099	1.586	15878
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.146	5	928
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.784	22.98	396
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.767	15.145	1243
X-RAY DIFFRACTION	r_dihedral_angle_other_3_deg	4.424	20	4
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.153	15	33
X-RAY DIFFRACTION	r_chiral_restr	0.046	0.2	945
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	8698
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1816
X-RAY DIFFRACTION	r_nbd_refined	0.144	0.2	1081
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.144	0.2	6013
X-RAY DIFFRACTION	r_nbtor_refined	0.149	0.2	3213
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.065	0.2	3184
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.11	0.2	434
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.138	0.2	34
X-RAY DIFFRACTION	r_nbd_other	0.13	0.2	106
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.094	0.2	20
X-RAY DIFFRACTION	r_mcbond_it	1.787	4.202	3622
X-RAY DIFFRACTION	r_mcbond_other	1.787	4.201	3621
X-RAY DIFFRACTION	r_mcangle_it	3.152	6.265	4584
X-RAY DIFFRACTION	r_mcangle_other	3.153	6.268	4581
X-RAY DIFFRACTION	r_scbond_it	1.575	4.377	3984
X-RAY DIFFRACTION	r_scbond_other	1.575	4.378	3985
X-RAY DIFFRACTION	r_scangle_it	2.732	6.475	5739
X-RAY DIFFRACTION	r_scangle_other	2.731	6.476	5740
X-RAY DIFFRACTION	r_lrange_it	5.894	47.093	7756
X-RAY DIFFRACTION	r_lrange_other	5.832	46.78	7665
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.045	0.05	2358
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.05	0.05	2339
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.046	0.05	2332
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.042	0.05	2346
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.044	0.05	2309
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.043	0.05	2352

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	AAA	X-RAY DIFFRACTION	Local ncs	0.04548	0.05
1	2	BBB	X-RAY DIFFRACTION	Local ncs	0.04548	0.05
2	3	AAA	X-RAY DIFFRACTION	Local ncs	0.04994	0.05
2	4	CCC	X-RAY DIFFRACTION	Local ncs	0.04994	0.05
3	5	AAA	X-RAY DIFFRACTION	Local ncs	0.04565	0.05
3	6	DDD	X-RAY DIFFRACTION	Local ncs	0.04565	0.05
4	7	BBB	X-RAY DIFFRACTION	Local ncs	0.04166	0.05
4	8	CCC	X-RAY DIFFRACTION	Local ncs	0.04166	0.05
5	9	BBB	X-RAY DIFFRACTION	Local ncs	0.0438	0.05
5	10	DDD	X-RAY DIFFRACTION	Local ncs	0.0438	0.05
6	11	CCC	X-RAY DIFFRACTION	Local ncs	0.04254	0.05
6	12	DDD	X-RAY DIFFRACTION	Local ncs	0.04254	0.05

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.031-2.084	0.238	37	0.312	4637	0.311	6253	0.81	0.77	74.7481	0.314
2.084-2.141	0.28	49	0.287	6029	0.287	6078	0.855	0.813	100	0.289
2.141-2.203	0.314	47	0.267	5839	0.268	5886	0.838	0.849	100	0.267
2.203-2.271	0.245	36	0.272	4634	0.271	5771	0.864	0.853	80.9219	0.268
2.271-2.345	0.304	44	0.248	5503	0.249	5547	0.868	0.873	100	0.245
2.345-2.427	0.313	44	0.259	5363	0.259	5407	0.838	0.871	100	0.252
2.427-2.519	0.355	41	0.254	5184	0.255	5225	0.836	0.878	100	0.248
2.519-2.622	0.254	40	0.235	4979	0.235	5019	0.891	0.905	100	0.229
2.622-2.738	0.305	32	0.233	3892	0.233	4831	0.896	0.911	81.2254	0.227
2.738-2.872	0.276	37	0.229	4561	0.229	4598	0.901	0.912	100	0.226
2.872-3.027	0.327	35	0.222	4391	0.223	4426	0.878	0.92	100	0.223
3.027-3.21	0.212	33	0.222	4099	0.222	4132	0.938	0.934	100	0.228
3.21-3.432	0.205	31	0.219	3838	0.219	3943	0.937	0.945	98.1233	0.231
3.432-3.706	0.233	27	0.207	3407	0.208	3659	0.943	0.951	93.8508	0.224
3.706-4.06	0.227	25	0.197	3134	0.197	3377	0.933	0.951	93.5446	0.223
4.06-4.538	0.246	25	0.172	3046	0.173	3071	0.916	0.96	100	0.211
4.538-5.238	0.224	22	0.171	2727	0.172	2749	0.955	0.963	100	0.224
5.238-6.412	0.3	18	0.237	2301	0.238	2319	0.902	0.936	100	0.293
6.412-9.05	0.156	15	0.262	1819	0.261	1834	0.916	0.919	100	0.323
9.05-104.752	0.359	9	0.254	1073	0.254	1085	0.86	0.931	99.7235	0.426

-
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

+
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

-
Protein , 1 types, 4 molecules AAABBBCCCDDD

-
Non-polymers , 6 types, 633 molecules

-
Details

-
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

-Protein , 1 types, 4 molecules AAABBBCCCDDD

-Non-polymers , 6 types, 633 molecules

-Details

-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

-
Protein , 1 types, 4 molecules AAABBBCCCDDD

-
Non-polymers , 6 types, 633 molecules

-
Details

-
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