8a8q

Crystal structure of Protein Scalloped in complex with YAP peptide

Method: X-RAY DIFFRACTION D_max: 82.4 Å Quality: EXCELLENT

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Protein scalloped

Drosophila melanogaster

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 222–440 Chain B； UniProt 222–440	Non-standard monomer：Yes (specific site not provided by mmCIF)	Isoform 7 of Transcriptional coactivator YAP1 × 2 （P46937） ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M MES pH 6 20 % PEG8000 0.2 M sodium acetate trihydrate	Resolution 1.47 Å R-free 0.234

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 8A8Q	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6Y20 Crystal structure of Protein Scalloped (222-440) bound to Protein Vestigial (298-337) Deposited 2020-02-14	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 222–440（219 aa） Chain B 222–440（219 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	MYR MYRISTIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2 M Magnesium chloride, 0.1 M Bis-Tris pH 6.5, 25% PEG3350	Resolution 1.85 Å R-free 0.222

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SCAL_DROME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–219； UniProt 222–440 Author chain B； PDBConstruct 1–219； UniProt 222–440

Isoform 7 of Transcriptional coactivator YAP1

OrganismNot specified

UniProt P46937

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 51–99 Chain D； UniProt 51–99	Non-standard monomer：Yes (specific site not provided by mmCIF)	Protein scalloped × 2 （P30052） ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M MES pH 6 20 % PEG8000 0.2 M sodium acetate trihydrate	Resolution 1.47 Å R-free 0.234

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 8A8Q	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1JMQ YAP65 (L30K mutant) WW domain in Complex with GTPPPPYTVG peptide Deposited 2001-07-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 165–210（46 aa）	Mutation：L30K	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；288 K；Ionic strength (raw mmCIF value) 100mM NaCl；Pressure 1 NMR measurement conditions pH 6；288 K；Ionic strength (raw mmCIF value) 100mM NaCl；Pressure 1 NMR sample composition 1.2 mM WW domain; 2.4 mM peptide GTPPPPYTVG; 10mM potassium phosphate buffer pH6; 100mM NaCl; 0.1 mM DTT; 0.1 mM EDTA, \| 90% H20, 10% D20 NMR sample composition 1.2 mM WW domain; 2.4 mM peptide GTPPPPYTVG; 10mM potassium phosphate buffer pH6; 100mM NaCl; 0.1 mM DTT; 0.1 mM EDTA, \| 100%D20	Resolution not provided
1K5R YAP65 WW domain S24-Amino-Ethylsulfanyl-Acetic Acid mutant Deposited 2001-10-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 165–204（40 aa） Fragment：WW domain, residues 5-44	Mutation：S24/Amino-ethyl-sulfanyl-acetic acid Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；288 K；Ionic strength (raw mmCIF value) 100 mM NaCl；Pressure 1 NMR measurement conditions pH 6；288 K；Ionic strength (raw mmCIF value) 100 mM NaCl；Pressure 1 NMR sample composition phosphate buffer 10 mM, Nacl 100mM, DTT 0.1mM, EDTA 0.1 mM, pH 6, WW domain 1.2 mM Ligand 2.4 mM \| H20 (10% D20) NMR sample composition phosphate buffer 10 mM, Nacl 100mM, DTT 0.1mM, EDTA 0.1 mM, pH 6 WW domain, 1.2 mM Ligand 2.4 mM \| D2O	Resolution not provided
1K9Q YAP65 WW domain complexed to N-(n-octyl)-GPPPY-NH2 Deposited 2001-10-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 165–204（40 aa） Fragment：Wild type WW domain	Not recorded	OCT N-OCTANE × 1	SOLUTION NMR NMR measurement conditions pH 6；288 K；Ionic strength (raw mmCIF value) 100mM NaCl；Pressure 1 NMR measurement conditions pH 6；288 K；Ionic strength (raw mmCIF value) 100mM NaCl；Pressure 1 NMR sample composition phosphate buffer 10mM, NaCl 100mM, DTT 0.1mM, EDTA 0.1mM, pH 6, WW domain 1.2mM, ligand 2.4mM \| H2O (10% D2O) NMR sample composition phosphate buffer 10mM, NaCl 100mM, DTT 0.1mM, EDTA 0.1mM, pH 6, WW domain 1.2mM, ligand 2.4mM \| D2O	Resolution not provided
1K9R YAP65 WW domain complexed to Acetyl-PLPPY Deposited 2001-10-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 165–204（40 aa） Fragment：Wild type WW domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；288 K；Ionic strength (raw mmCIF value) 100mM NaCl；Pressure 1 NMR measurement conditions pH 6；288 K；Ionic strength (raw mmCIF value) 100mM NaCl；Pressure 1 NMR sample composition phosphate buffer 10mM, NaCl 100mM, DTT 0.1mM, EDTA 0.1mM, pH 6, WW domain 1.2mM, ligand 2.4mM \| H2O (10% D2O) NMR sample composition phosphate buffer 10mM, NaCl 100mM, DTT 0.1mM, EDTA 0.1mM, pH 6, WW domain 1.2mM, ligand 2.4mM \| D2O	Resolution not provided
2LAW Structure of the second WW domain from human YAP in complex with a human Smad1 derived peptide Deposited 2011-03-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 230–263（34 aa） Fragment：second WW domain, residues 230-263	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；285 K；Ionic strength (raw mmCIF value) 0.420；Pressure ambient NMR sample composition 1 mM NEDD4LWW3, 3 mM SMAD3, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 15N] NEDD4LWW3, 3 mM SMAD3, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N] NEDD4LWW3, 3 mM SMAD3, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2LAX Structure of first WW domain of human YAP in complex with a human Smad1 doubly-phosphorilated derived peptide. Deposited 2011-03-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 170–205（36 aa） Fragment：first WW domain, residues 170-205	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；285 K；Ionic strength (raw mmCIF value) 0.420；Pressure ambient NMR sample composition 1 mM NEDD4LWW3, 3 mM SMAD3, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 15N] NEDD4LWW3, 3 mM SMAD3, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N] NEDD4LWW3, 3 mM SMAD3, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2LAY Structure of the first WW domain of human YAP in complex with a phosphorylated human Smad1 derived peptide Deposited 2011-03-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 170–205（36 aa） Fragment：residues 170-205	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；285 K；Ionic strength (raw mmCIF value) 0.420；Pressure ambient NMR sample composition 1 mM NEDD4LWW3, 3 mM SMAD3, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 15N] NEDD4LWW3, 3 mM SMAD3, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N] NEDD4LWW3, 3 mM SMAD3, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2LTV YAP WW2 in complex with a Smad7 derived peptide Deposited 2012-06-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 230–265（36 aa） Fragment：WW2 domain (UNP residues 230-265)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.2；285 K；Pressure ambient NMR sample composition 1 mM YAPWW2, 2 mM SMAD7, 20 mM [U-100% 2H] TRIS, 100 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N] YAPWW2, 3 mM SMAD7, 20 mM [U-100% 2H] TRIS, 100 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2LTW YAP WW1 in complex with a Smad7 derived peptide Deposited 2012-06-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 170–205（36 aa） Fragment：WW1 domain (UNP residues 170-205)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.2；285 K；Pressure ambient NMR sample composition 1 mM YAPWW1, 2 mM SMAD7, 20 mM [U-100% 2H] TRIS, 100 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N] YAPWW1, 3 mM SMAD7, 20 mM [U-100% 2H] TRIS, 100 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3KYS Crystal structure of human YAP and TEAD complex Deposited 2009-12-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 50–171（122 aa） Fragment：TEAD binding domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；0.1M sodium acetate, 2M sodium formate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.266
3KYS Crystal structure of human YAP and TEAD complex Deposited 2009-12-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 50–171（122 aa） Fragment：TEAD binding domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；0.1M sodium acetate, 2M sodium formate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.266
4RE1 Crystal structure of human TEAD1 and disulfide-engineered YAP Deposited 2014-09-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 50–171（122 aa） Fragment：TEAD BINDING DOMAIN (UNP RESIDUES 50-171)	Mutation：R87C, D93A, F96C, E100R	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；0.1M sodium acetate, 1.8M sodium formate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.20 Å R-free 0.248
4RE1 Crystal structure of human TEAD1 and disulfide-engineered YAP Deposited 2014-09-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 50–171（122 aa） Fragment：TEAD BINDING DOMAIN (UNP RESIDUES 50-171)	Mutation：R87C, D93A, F96C, E100R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；0.1M sodium acetate, 1.8M sodium formate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.20 Å R-free 0.248
4REX Crystal structure of the first WW domain of human YAP2 isoform Deposited 2014-09-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 165–209（45 aa） Fragment：WW domain (UNP residues 165-209)	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；293 K；1.5 M ammonium sulphate, 0.1 M sodium acetate, 100 mM proline, 5 mM NDSB-201 and 5mM MBCD, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.60 Å R-free 0.194
5OAQ TEAD4 COMPLEXED WITH YAP PEPTIDE AND MYRISTATE (COVALENTLY BOUND) Deposited 2017-06-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 60–100（41 aa）	Not recorded	GOL GLYCEROL × 1 MYR MYRISTIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；15% PEG 3350,2% tacsimate, 0.1M NaCitrate	Resolution 1.95 Å R-free 0.252
6G6X 14-3-3sigma in complex with a P129beta3P mutated YAP pS127 phosphopeptide Deposited 2018-04-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain P 124–133（10 aa）	Mutation：Proline 129 to beta3-proline Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 8 NA SODIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.095 M HEPES, pH 7.1, 29% PEG 400, 0.19 M CaCl2, 5% glycerol	Resolution 1.13 Å R-free 0.168
6G8P 14-3-3sigma in complex with a P129beta3P and L132beta3L mutated YAP pS127 phosphopeptide Deposited 2018-04-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain P 124–133（10 aa） Fragment：UNP residues 124-133	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 4 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.095 M HEPES, pH 7.1, 29% PEG 400, 0.19 M CaCl2, 5% glycerol	Resolution 1.90 Å R-free 0.159
6G8Q 14-3-3sigma in complex with a A130beta3A and Q133beta3Q mutated YAP pS127 phosphopeptide Deposited 2018-04-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain P 124–133（10 aa） Fragment：UNP residues 124-133	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 2 CL CHLORIDE ION × 4 NA SODIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.095 M HEPES, pH 7.1, 29% PEG 400, 0.19 M CaCl2, 5% glycerol	Resolution 1.85 Å R-free 0.175
6GE3 X-ray structure of TEAD4 (wildtype) complexed with YAP (wildtype): The role of residual flexibility and water molecules in the adaptation of a bound intrinsically disordered protein to mutations at a binding interface Deposited 2018-04-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 60–100（41 aa）	Not recorded	MYR MYRISTIC ACID × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；16% PEG 3350,2% tacsimate, 0.1M NaCit, pH 5.6	Resolution 1.85 Å R-free 0.242
6GE4 TEAD4 (216-434);E263A COMPLEXED WITH YAP PEPTIDE (60-100) AND MYRISTOATE (COVALENTLY BOUND) AT 1.97A (P41212 CRYSTAL FORM); MYRISTOYLATION WAS DONE BY ADDING MYR-COA Deposited 2018-04-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 60–100（41 aa）	Not recorded	MYR MYRISTIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；20% PEG 3350, 0.2M MgNitrate	Resolution 1.97 Å R-free 0.241
6GE5 TEAD4 (216-434);Y429F COMPLEXED WITH YAP PEPTIDE (60-100) AND MYRISTOATE (COVALENTLY BOUND) AT 2.05A (P41212 CRYSTAL FORM); MYRISTOYLATION WAS DONE BY ADDING MYR-COA Deposited 2018-04-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 60–100（41 aa）	Not recorded	MYR MYRISTIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；298 K；20% PEG 3350, 8% Tacsimate	Resolution 2.05 Å R-free 0.238
6GE6 X-ray structure of TEAD4(E263A+Y429F mutant) complexed with YAP(wildtype): The role of residual flexibility and water molecules in the adaptation of a bound intrinsically disordered protein to mutations at a binding interface Deposited 2018-04-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 60–100（41 aa）	Not recorded	MYR MYRISTIC ACID × 1 PO4 PHOSPHATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；2M ammonium sulfate, 0.1M Bis-TRIS	Resolution 1.80 Å R-free 0.238
6GEC TEAD4 (216-434) COMPLEXED WITH YAP PEPTIDE (60-100);S94A AND MYRISTOATE (COVALENTLY BOUND) AT 1.70A (P41212 CRYSTAL FORM); MYRISTOYLATION WAS DONE BY ADDING MYR-COA Deposited 2018-04-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 60–99（40 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	MYR MYRISTIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；20% PEG 3350, 0.2M NaTartrate	Resolution 1.70 Å R-free 0.242
6GEE TEAD4 (216-434);E263A COMPLEXED WITH YAP PEPTIDE (60-100); S94A AND MYRISTOATE (COVALENTLY BOUND) AT 1.96A (P41212 CRYSTAL FORM); MYRISTOYLATION WAS DONE BY ADDING MYR-COA Deposited 2018-04-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 60–99（40 aa）	Mutation：S94A Non-standard monomer：Yes (specific site not provided by mmCIF)	MYR MYRISTIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；17% PEG 10000, 0.1M ammonium acetate, 0.1M Bis-TRIS	Resolution 1.96 Å R-free 0.245
6GEG TEAD4 (216-434);Y429F COMPLEXED WITH YAP PEPTIDE (60-100); S94A AND MYRISTOATE (COVALENTLY BOUND) AT 2.23A (P41212 CRYSTAL FORM); MYRISTOYLATION WAS DONE BY ADDING MYR-COA Deposited 2018-04-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 60–99（40 aa）	Mutation：S94A Non-standard monomer：Yes (specific site not provided by mmCIF)	MYR MYRISTIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；20% PEG 3350, 0.2M Na tartrate	Resolution 2.23 Å R-free 0.236
6GEI TEAD4 (216-434);E263A+Y429F COMPLEXED WITH YAP PEPTIDE (60- 100);S94A AND MYRISTOATE (COVALENTLY BOUND TO LYS344, NOT CYS367!) AT 1.65A (P41212 CRYSTAL FORM); MYRISTOYLATION WAS DONE BY ADDING MYR-COA Deposited 2018-04-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 60–100（41 aa）	Mutation：S94A Non-standard monomer：Yes (specific site not provided by mmCIF)	MYR MYRISTIC ACID × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；20% PEG 3350, 0.2M Na acetate	Resolution 1.65 Å R-free 0.248
6GEK TEAD4 (216-434);Y429F COMPLEXED WITH YAP PEPTIDE (60-100) AND MYRISTOATE (COVALENTLY BOUND) AT 2.28A (P212121 CRYSTAL FORM); MYRISTOYLATION WAS DONE BY ADDING MYR-COA Deposited 2018-04-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 60–100（41 aa）	Not recorded	MYR MYRISTIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；25% PEG 3350, 0.2M MgCl2, 0.1M Bis-TRIS	Resolution 2.28 Å R-free 0.246
6GEK TEAD4 (216-434);Y429F COMPLEXED WITH YAP PEPTIDE (60-100) AND MYRISTOATE (COVALENTLY BOUND) AT 2.28A (P212121 CRYSTAL FORM); MYRISTOYLATION WAS DONE BY ADDING MYR-COA Deposited 2018-04-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain M 60–100（41 aa）	Not recorded	MYR MYRISTIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；25% PEG 3350, 0.2M MgCl2, 0.1M Bis-TRIS	Resolution 2.28 Å R-free 0.246
6HIK X-ray structure of TEAD4(Y429H) mutant) complexed with YAP (wildtype): Molecular and structural characterization of a TEAD mutation at the origin of Sveinsson's chorioretinal atrophy Deposited 2018-08-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 60–99（40 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	MYR MYRISTIC ACID × 1 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；1.4M Na/K PO4	Resolution 1.65 Å R-free 0.237
6HIL X-ray structure of TEAD1(Y421H mutant) complexed with YAP(wildtype): Molecular and structural characterization of a TEAD mutation at the origin of Sveinsson's chorioretinal atrophy Deposited 2018-08-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 60–100（41 aa）	Not recorded	MYR MYRISTIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；22% (w/v) PEG3350, 0.2M Na Malonate	Resolution 2.30 Å R-free 0.267
6HIL X-ray structure of TEAD1(Y421H mutant) complexed with YAP(wildtype): Molecular and structural characterization of a TEAD mutation at the origin of Sveinsson's chorioretinal atrophy Deposited 2018-08-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain O 60–100（41 aa）	Not recorded	MYR MYRISTIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；22% (w/v) PEG3350, 0.2M Na Malonate	Resolution 2.30 Å R-free 0.267
6HIL X-ray structure of TEAD1(Y421H mutant) complexed with YAP(wildtype): Molecular and structural characterization of a TEAD mutation at the origin of Sveinsson's chorioretinal atrophy Deposited 2018-08-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain M 60–100（41 aa）	Not recorded	MYR MYRISTIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；22% (w/v) PEG3350, 0.2M Na Malonate	Resolution 2.30 Å R-free 0.267
6HIL X-ray structure of TEAD1(Y421H mutant) complexed with YAP(wildtype): Molecular and structural characterization of a TEAD mutation at the origin of Sveinsson's chorioretinal atrophy Deposited 2018-08-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain N 60–100（41 aa）	Not recorded	MYR MYRISTIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；22% (w/v) PEG3350, 0.2M Na Malonate	Resolution 2.30 Å R-free 0.267
6Q2X TEAD4 (216-434) COMPLEXED WITH YAP PEPTIDE (60-100) AND MYRISTOATE (COVALENTLY BOUND) AT 2.1A (P41212 CRYSTAL FORM) Deposited 2018-12-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 60–100（41 aa）	Not recorded	GOL GLYCEROL × 1 MYR MYRISTIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；16% PEG 3350,2% tacsimate, 0.1M NaCit	Resolution 2.10 Å R-free 0.253
8A8R Crystal structure of TEAD4 in complex with YAP peptide Deposited 2022-06-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain L 50–100（51 aa） Chain M 50–100（51 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	MYR MYRISTIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；50 mM sodium acetate trihydrate pH 4.6 50 mM magnesium acetate tetrahydrate 25% PEG400	Resolution 1.70 Å R-free 0.243
8WRG Solution structure of the TAD domain (450-504) of human transcriptional coactivator YAP1 Deposited 2023-10-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 450–504（55 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120；Pressure 1 NMR sample composition 0.95 mM [U-99% 13C; U-99% 15N] YAP-TAD, 20 mM HEPES, 100 mM sodium chloride, 5 % v/v [U-99% 2H] D2O, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
9FZA TEAD1/YAP in complex with a reversible inhibitor N-[(4-phenoxyphenyl)methyl]imidazo[1,2-a]pyridine-3-carboxamide Deposited 2024-07-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 51–110（60 aa）	Not recorded	CL CHLORIDE ION × 1 A1IHH ~{N}-[(4-phenoxyphenyl)methyl]imidazo[1,2-a]pyridine-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；2M Sodium Formate, 0.1M Sodium Acetate pH 4.6	Resolution 2.21 Å R-free 0.262
9FZA TEAD1/YAP in complex with a reversible inhibitor N-[(4-phenoxyphenyl)methyl]imidazo[1,2-a]pyridine-3-carboxamide Deposited 2024-07-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 51–110（60 aa）	Not recorded	CL CHLORIDE ION × 1 A1IHH ~{N}-[(4-phenoxyphenyl)methyl]imidazo[1,2-a]pyridine-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；2M Sodium Formate, 0.1M Sodium Acetate pH 4.6	Resolution 2.21 Å R-free 0.262

31 other PDB entries and 38 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	YAP1_HUMAN
Isoform	P46937-7
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 2–50； UniProt 51–99 Author chain D； PDBConstruct 2–50； UniProt 51–99

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	8a8q
Deposition date deposition_date	2022-06-23
Structure title title	Crystal structure of Protein Scalloped in complex with YAP peptide
Keywords keywords	Complex, TRANSCRIPTION; TRANSCRIPTION
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	26.38 Å
Radius of gyration Rg (electron density) rg_electron	25.52 Å
Forward intensity I(0) i0	49311100.00
Molecular weight molecular_weight	56206.0 kDa
Excluded volume excluded_volume	71110 Å³
Envelope volume envelope_volume	86795 Å³
Hydration-shell volume shell_volume	28512 Å³
Envelope diameter envelope_diameter	85.6 Å
Shell Rg shell_rg	32.82 Å
Envelope Rg envelope_rg	25.63 Å
Shape Rg shape_rg	25.55 Å
Total Rg total_rg	26.31 Å
Total atoms total_atoms	3964
Residues n_residues	487
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	82.4 Å
Rg (real space) rg_real	26.38 Å
Rg uncertainty (real space) rg_real_error	0.61 Å
I(0) (real space) i0_real	4.9310e+07
I(0) uncertainty (real space) i0_real_error	7.6690e+05
Rg (reciprocal space) rg_reciprocal	26.38 Å
I(0) (reciprocal space) i0_reciprocal	49310000.0000
Solution quality estimate total_estimate	0.9016
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.9 Å
Skewness Skewness skewness	0.355
Kurtosis Kurtosis kurtosis	-0.405
Angular range angular_range	— – 0.3000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10480000.0000
Real-space data points n_real_points	61
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.921; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.958

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Protein scalloped
Molecular weight formula_weight	25757.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4211

GRAIATHKFRLLEFTAFMEIQRDEIYHRHLFVQLGGKPSFSDPLLETVDIRQIFDKFPEKSGGLKDLYEKGPQNAFYLVKCWADLNTDLTTGSETGDFYGVTSQYESNENVVLVCSTIVCSFGKQVVEXVESEYSRLENNRYVYRIQRSPMCEYMINFIQKLKNLPERYMMNSVLENFTILQVMRARETQETLLCIAYVFEVAAQNSGTTHHIYRLIKE

来源 Source

来源生物 organism	Drosophila melanogaster
通用名 common_name	fruit fly
NCBI Class编号 ncbi_taxonomy_id	7227
宿主生物 host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 polymer

Description description	Isoform 7 of Transcriptional coactivator YAP1
Molecular weight formula_weight	5496.3 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

XGHQIVHVRGDSETDLEALFNAVLNPKTANVPQTVPLRLRKLPDSFFKPPX

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	235

▶

8. Citations (1)

▶

Unit-cell length a length_a	42.772 Å
Unit-cell length b length_b	85.700 Å
Unit-cell length c length_c	76.227 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.62 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.465 Å
Low-resolution limit resolution_low	29.090 Å
R factor r_factor	0.2119
R_work r_work	0.2108
R_free r_free	0.2337

fit	/app/data/saxs_computation/a8/8a8q/8a8q.fit
pddf	/app/data/pr_computation/a8/8a8q/8a8q.pr.out
profile	/app/data/saxs_computation/a8/8a8q/8a8q.dat

Crystal structure of Protein Scalloped in complex with YAP peptide

1. Protein Identity and Related Structures Protein Identity & Related Structures

Protein scalloped

State in the Current Structure

Other States of the Same Protein in the Database

Isoform 7 of Transcriptional coactivator YAP1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)