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- PDB-5z2q: Vgll1-TEAD4 core complex -

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Basic information

Entry
Database: PDB / ID: 5z2q
TitleVgll1-TEAD4 core complex
Components
  • (Transcription cofactor vestigial-like protein ...) x 2
  • (Transcriptional enhancer factor TEF- ...) x 2
KeywordsTRANSCRIPTION / TEAD / Transcription factor / co-regulator / Vgll1 / Vestigial
Function / homology
Function and homology information


RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / trophectodermal cell fate commitment / : / hippo signaling / blastocyst formation / cell fate specification / positive regulation of stem cell population maintenance / cell fate commitment / embryonic organ development ...RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / trophectodermal cell fate commitment / : / hippo signaling / blastocyst formation / cell fate specification / positive regulation of stem cell population maintenance / cell fate commitment / embryonic organ development / embryo implantation / protein-DNA complex / DNA-binding transcription activator activity, RNA polymerase II-specific / in utero embryonic development / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Vestigial family / Vestigial/Tondu family / Transcriptional enhancer factor TEF-3 (TEAD4) / 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. ...Vestigial family / Vestigial/Tondu family / Transcriptional enhancer factor TEF-3 (TEAD4) / 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 / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Transcriptional enhancer factor TEF-3 / Transcription cofactor vestigial-like protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsPobbati, A.V. / Song, H.
CitationJournal: Structure / Year: 2012
Title: Structural and functional similarity between the Vgll1-TEAD and the YAP-TEAD complexes.
Authors: Pobbati, A.V. / Chan, S.W. / Lee, I. / Song, H. / Hong, W.
History
DepositionJan 3, 2018Deposition site: PDBJ / Processing site: PDBJ
SupersessionJan 31, 2018ID: 4EAZ
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Transcription cofactor vestigial-like protein 1
D: Transcription cofactor vestigial-like protein 1
A: Transcriptional enhancer factor TEF-3
B: Transcriptional enhancer factor TEF-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6615
Polymers64,5664
Non-polymers951
Water1629
1
C: Transcription cofactor vestigial-like protein 1
B: Transcriptional enhancer factor TEF-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4133
Polymers32,3182
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-19 kcal/mol
Surface area12730 Å2
MethodPISA
2
D: Transcription cofactor vestigial-like protein 1
A: Transcriptional enhancer factor TEF-3


Theoretical massNumber of molelcules
Total (without water)32,2472
Polymers32,2472
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-16 kcal/mol
Surface area13180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.931, 113.931, 144.357
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21D
12A
22B

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROLEULEUCA19 - 5214 - 47
21PROPROLEULEUDB19 - 5214 - 47
12ILEILELYSLYSAC207 - 4267 - 226
22ILEILELYSLYSBD207 - 4269 - 228

NCS ensembles :
ID
1
2

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Components

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Transcription cofactor vestigial-like protein ... , 2 types, 2 molecules CD

#1: Protein/peptide Transcription cofactor vestigial-like protein 1 / Vgl-1 / Vestigial-related factor


Mass: 5600.120 Da / Num. of mol.: 1 / Fragment: UNP residues 20-53
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Vgll1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99NC0
#2: Protein/peptide Transcription cofactor vestigial-like protein 1 / Vgl-1 / Vestigial-related factor


Mass: 5757.314 Da / Num. of mol.: 1 / Fragment: UNP residues 20-54
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Vgll1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99NC0

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Transcriptional enhancer factor TEF- ... , 2 types, 2 molecules AB

#3: Protein Transcriptional enhancer factor TEF-3 / ETF-related factor 2 / ETFR-2 / TEA domain family member 4 / TEAD-4 / TEF-1-related factor 1 / TEF- ...ETF-related factor 2 / ETFR-2 / TEA domain family member 4 / TEAD-4 / TEF-1-related factor 1 / TEF-1-related factor FR-19 / RTEF-1


Mass: 26490.045 Da / Num. of mol.: 1 / Fragment: UNP residues 210-426
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tead4, Tcf13r1, Tef3, Tefr1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q62296
#4: Protein Transcriptional enhancer factor TEF-3 / ETF-related factor 2 / ETFR-2 / TEA domain family member 4 / TEAD-4 / TEF-1-related factor 1 / TEF- ...ETF-related factor 2 / ETFR-2 / TEA domain family member 4 / TEAD-4 / TEF-1-related factor 1 / TEF-1-related factor FR-19 / RTEF-1


Mass: 26718.291 Da / Num. of mol.: 1 / Fragment: UNP residues 210-426
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tead4, Tcf13r1, Tef3, Tefr1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q62296

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Non-polymers , 2 types, 10 molecules

#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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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: 4.46 Å3/Da / Density % sol: 72.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.9 / Details: 1M phosphate buffer

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.99 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 3, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.74→98.67 Å / Num. obs: 28983 / % possible obs: 99.7 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 2.7
Reflection shellResolution: 2.74→2.81 Å / Rmerge(I) obs: 0.58 / Num. unique obs: 1974 / % possible all: 98.87

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TEAD4 in 3JUA

3jua


Resolution: 2.74→98.67 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.923 / SU B: 23.465 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.348 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24617 1472 5.1 %RANDOM
Rwork0.20079 ---
obs0.20303 27472 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 84.267 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.74→98.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4134 0 5 9 4148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0194267
X-RAY DIFFRACTIONr_bond_other_d0.0020.023832
X-RAY DIFFRACTIONr_angle_refined_deg1.8541.9395755
X-RAY DIFFRACTIONr_angle_other_deg1.04538898
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9375496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.39823.796216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.99515741
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1431523
X-RAY DIFFRACTIONr_chiral_restr0.1140.2612
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024667
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02932
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1015.742005
X-RAY DIFFRACTIONr_mcbond_other3.1015.742004
X-RAY DIFFRACTIONr_mcangle_it4.7578.6072494
X-RAY DIFFRACTIONr_mcangle_other4.7568.6072495
X-RAY DIFFRACTIONr_scbond_it3.7766.1022261
X-RAY DIFFRACTIONr_scbond_other3.6786.0742253
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6648.9663249
X-RAY DIFFRACTIONr_long_range_B_refined7.80863.1134411
X-RAY DIFFRACTIONr_long_range_B_other7.80763.1214412
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11C18340.1
12D18340.1
21A126140.13
22B126140.13
LS refinement shellResolution: 2.74→2.811 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 117 -
Rwork0.351 1974 -
obs--98.87 %
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)
19.85414.5759-2.67532.6469-0.9621.342-0.56050.6702-0.6945-0.30550.3456-0.17040.3091-0.21290.21490.4668-0.1045-0.07790.19890.00730.1607-45.1746.0098.714
29.1319-0.7329-3.77471.79830.71533.68260.0752-0.53010.87390.22850.0308-0.4026-0.13760.3296-0.1060.18540.0065-0.04720.401-0.05290.2062-10.10740.88856.056
33.83111.0039-0.90372.5543-0.14112.87440.0003-0.5027-0.19680.322-0.09880.13040.388-0.12340.09850.18750.01860.03180.25580.00630.0276-21.69427.03955.942
42.87081.92580.79882.17470.36162.75280.0201-0.14060.0781-0.1663-0.04390.10740.2551-0.31640.02380.2603-0.0496-0.01810.11830.03270.0207-39.33316.41123.17
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C19 - 53
2X-RAY DIFFRACTION2D19 - 54
3X-RAY DIFFRACTION3A207 - 426
4X-RAY DIFFRACTION4B203 - 426

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