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- PDB-3kys: Crystal structure of human YAP and TEAD complex -

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Basic information

Entry
Database: PDB / ID: 3kys
TitleCrystal structure of human YAP and TEAD complex
Components
  • 65 kDa Yes-associated protein
  • Transcriptional enhancer factor TEF-1
KeywordsTRANSCRIPTION/PROTEIN BINDING / immunoglobulin-like fold / Activator / Disease mutation / DNA-binding / Nucleus / Phosphoprotein / Transcription / Transcription regulation / TRANSCRIPTION-PROTEIN BINDING complex
Function / homology
Function and homology information


enterocyte differentiation / regulation of keratinocyte proliferation / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / glandular epithelial cell differentiation / TEAD-YAP complex / lateral mesoderm development / polarized epithelial cell differentiation / bud elongation involved in lung branching / RUNX3 regulates YAP1-mediated transcription ...enterocyte differentiation / regulation of keratinocyte proliferation / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / glandular epithelial cell differentiation / TEAD-YAP complex / lateral mesoderm development / polarized epithelial cell differentiation / bud elongation involved in lung branching / RUNX3 regulates YAP1-mediated transcription / notochord development / negative regulation of cilium assembly / lung epithelial cell differentiation / YAP1- and WWTR1 (TAZ)-stimulated gene expression / heart process / trophectodermal cell differentiation / paraxial mesoderm development / hippo signaling / regulation of stem cell proliferation / EGR2 and SOX10-mediated initiation of Schwann cell myelination / negative regulation of epithelial cell apoptotic process / intestinal epithelial cell development / tissue homeostasis / Formation of axial mesoderm / negative regulation of stem cell differentiation / embryonic heart tube morphogenesis / female germ cell nucleus / proline-rich region binding / Signaling by Hippo / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / organ growth / negative regulation of epithelial cell differentiation / interleukin-6-mediated signaling pathway / positive regulation of Notch signaling pathway / negative regulation of fat cell differentiation / RUNX2 regulates osteoblast differentiation / positive regulation of stem cell population maintenance / Zygotic genome activation (ZGA) / regulation of neurogenesis / somatic stem cell population maintenance / bicellular tight junction / canonical Wnt signaling pathway / embryonic organ development / positive regulation of osteoblast differentiation / vasculogenesis / Nuclear signaling by ERBB4 / keratinocyte differentiation / positive regulation of cardiac muscle cell proliferation / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / response to progesterone / positive regulation of epithelial cell proliferation / epithelial cell proliferation / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / negative regulation of extrinsic apoptotic signaling pathway / transcription coregulator activity / wound healing / cellular response to gamma radiation / cell morphogenesis / positive regulation of miRNA transcription / positive regulation of protein localization to nucleus / transcription corepressor activity / sequence-specific double-stranded DNA binding / cell junction / positive regulation of canonical Wnt signaling pathway / cell-cell junction / RUNX1 regulates transcription of genes involved in differentiation of HSCs / positive regulation of cell growth / protein-containing complex assembly / DNA-binding transcription factor binding / transcription regulator complex / transcription coactivator activity / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / DNA damage response / chromatin binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Virus Scaffolding Protein; Chain A / Virus Scaffolding Protein; Chain A - #10 / : / Omega loop, TEAD interating region 3 / : / Coagulation Factor XIII; Chain A, domain 1 - #80 / TEA/ATTS domain / Transcriptional enhancer factor, metazoa / TEA/ATTS domain superfamily / TEA/ATTS domain ...Virus Scaffolding Protein; Chain A / Virus Scaffolding Protein; Chain A - #10 / : / Omega loop, TEAD interating region 3 / : / 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 / Other non-globular / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Special / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Transcriptional enhancer factor TEF-1 / Transcriptional coactivator YAP1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsLi, Z. / Zhao, B. / Wang, P. / Chen, F. / Dong, Z. / Yang, H. / Guan, K.L. / Xu, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)30870493 China
CitationJournal: Genes Dev. / Year: 2010
Title: Structural insights into the YAP and TEAD complex
Authors: Li, Z. / Zhao, B. / Wang, P. / Chen, F. / Dong, Z. / Yang, H. / Guan, K.L. / Xu, Y.
History
DepositionDec 7, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Oct 7, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / diffrn / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_mod_residue / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / software / struct / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _diffrn.pdbx_serial_crystal_experiment / _entity_name_com.name / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_database_status.SG_entry / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_all / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_all / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.occupancy_max / _refine.occupancy_min / _refine.overall_FOM_work_R_set / _refine.overall_SU_ML / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_ls_sigma_F / _refine.pdbx_ls_sigma_I / _refine.pdbx_overall_phase_error / _refine.solvent_model_param_bsol / _refine.solvent_model_param_ksol / _refine_hist.cycle_id / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _reflns.pdbx_netI_over_sigmaI / _reflns_shell.meanI_over_sigI_obs / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_diffrn_id / _software.classification / _software.name / _software.version / _struct.pdbx_CASP_flag / _struct_ref_seq_dif.details / _struct_sheet.id / _struct_sheet.number_strands
Description: Model completeness / Provider: author / Type: Coordinate replacement
Revision 2.1Mar 26, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional enhancer factor TEF-1
B: 65 kDa Yes-associated protein
C: Transcriptional enhancer factor TEF-1
D: 65 kDa Yes-associated protein


Theoretical massNumber of molelcules
Total (without water)77,6824
Polymers77,6824
Non-polymers00
Water93752
1
A: Transcriptional enhancer factor TEF-1
B: 65 kDa Yes-associated protein


Theoretical massNumber of molelcules
Total (without water)38,8412
Polymers38,8412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-20 kcal/mol
Surface area12880 Å2
MethodPISA
2
C: Transcriptional enhancer factor TEF-1
D: 65 kDa Yes-associated protein


Theoretical massNumber of molelcules
Total (without water)38,8412
Polymers38,8412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-20 kcal/mol
Surface area13200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.643, 110.503, 165.695
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 25676.406 Da / Num. of mol.: 2 / Fragment: YAP binding domain
Source method: isolated from a genetically manipulated source
Details: X=P1L / Source: (gene. exp.) Homo sapiens (human) / Gene: TEAD1, TCF13, TEF1 / Plasmid: pRSFDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P28347
#2: Protein 65 kDa Yes-associated protein / ranscriptional coactivator YAP1 / Yes-associated protein 1 / Protein yorkie homolog / Yes- ...ranscriptional coactivator YAP1 / Yes-associated protein 1 / Protein yorkie homolog / Yes-associated protein YAP65 homolog


Mass: 13164.702 Da / Num. of mol.: 2 / Fragment: TEAD binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YAP1, YAP65 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P46937
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M sodium acetate, 2M sodium formate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97869 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 6, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97869 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 20593 / % possible obs: 97.9 % / Redundancy: 13.8 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 44.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 3.91 / Num. unique obs: 20593 / % possible all: 83.6

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
MAR345dtbdata collection
SOLVEphasing
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.8→40.16 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2658 1050 5.12 %
Rwork0.2277 19457 -
obs0.2296 20507 97.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 190.68 Å2 / Biso mean: 71.2349 Å2 / Biso min: 29.29 Å2
Refinement stepCycle: final / Resolution: 2.8→40.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4234 0 0 52 4286
Biso mean---64.77 -
Num. residues----518
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.930.3533960.31082058215485
2.93-3.080.35381290.29312412254198
3.08-3.270.36131420.273824272569100
3.28-3.530.29931280.256124702598100
3.53-3.880.28831360.220224452581100
3.88-4.440.26341210.199125252646100
4.44-5.60.19071440.187724972641100
5.6-40.160.25931540.23582623277799
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)
13.4279-0.285-0.78592.41750.06564.8506-0.0815-0.00580.0398-0.07140.0646-0.1590.20140.25310.02070.3532-0.0931-0.08980.34220.07140.3591-12.79499.899918.753
23.39640.2805-1.2824.56630.57482.3333-0.2285-0.6405-1.01420.16880.0546-0.72590.67260.61610.09730.72450.0114-0.17020.63840.16160.6002-8.6757-1.285227.4797
32.46360.7516-0.60483.51870.27584.78540.0016-0.00860.1009-0.12430.05580.19620.1063-0.3846-0.01240.21170.0496-0.02220.3678-0.05550.3663-11.329611.2843-23.6735
43.2285-0.0115-0.76283.80130.31141.9668-0.38970.3414-0.8008-0.2120.30410.56420.5191-0.44660.07260.6428-0.0205-0.08350.6103-0.09080.5507-13.3367-0.555-32.8117
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 195:411)A195 - 411
2X-RAY DIFFRACTION2(chain B and resseq 51:100)B51 - 100
3X-RAY DIFFRACTION3(chain C and resseq 194:411)C194 - 411
4X-RAY DIFFRACTION4(chain D and resseq 52:100)D52 - 100

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