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- PDB-6sen: TEAD4 bound to a FAM181A peptide -

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Basic information

Entry
Database: PDB / ID: 6sen
TitleTEAD4 bound to a FAM181A peptide
Components
  • Protein FAM181A
  • Transcriptional enhancer factor TEF-3
KeywordsTRANSCRIPTION / Complex / TEAD4 / FAM181A
Function / homology
Function and homology information


trophectodermal cell fate commitment / RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / hippo signaling / Formation of axial mesoderm / cell fate specification / muscle organ development / positive regulation of stem cell population maintenance / Zygotic genome activation (ZGA) / embryonic organ development ...trophectodermal cell fate commitment / RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / hippo signaling / Formation of axial mesoderm / cell fate specification / muscle organ development / positive regulation of stem cell population maintenance / Zygotic genome activation (ZGA) / embryonic organ development / embryo implantation / skeletal system development / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / 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 / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
FAM181 / FAM181 / 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. ...FAM181 / FAM181 / 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
Transcriptional enhancer factor TEF-3 / Protein FAM181A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsScheufler, C. / Villard, F.
CitationJournal: Protein Sci. / Year: 2020
Title: Identification of FAM181A and FAM181B as new interactors with the TEAD transcription factors.
Authors: Bokhovchuk, F. / Mesrouze, Y. / Delaunay, C. / Martin, T. / Villard, F. / Meyerhofer, M. / Fontana, P. / Zimmermann, C. / Erdmann, D. / Furet, P. / Scheufler, C. / Schmelzle, T. / Chene, P.
History
DepositionJul 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional enhancer factor TEF-3
B: Transcriptional enhancer factor TEF-3
L: Protein FAM181A
M: Protein FAM181A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0919
Polymers55,6114
Non-polymers4805
Water4,306239
1
A: Transcriptional enhancer factor TEF-3
L: Protein FAM181A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0945
Polymers27,8062
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-43 kcal/mol
Surface area11380 Å2
MethodPISA
2
B: Transcriptional enhancer factor TEF-3
M: Protein FAM181A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9984
Polymers27,8062
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-33 kcal/mol
Surface area11890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.490, 132.070, 62.020
Angle α, β, γ (deg.)90.000, 115.870, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Transcriptional enhancer factor TEF-3 / TEA domain family member 4 / TEAD-4 / Transcription factor 13-like 1 / Transcription factor RTEF-1


Mass: 25807.186 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TEAD4, RTEF1, TCF13L1, TEF3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15561
#2: Protein/peptide Protein FAM181A


Mass: 1998.352 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: FAM181A peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8N9Y4
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.3 Å3/Da / Density % sol: 46.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.59
Details: 200 mM Ammonium sulfate 100 mM Sodium acetate trihydrate pH 4.59 35% Pentaerythritol ethoxylate (15/4 EO/OH)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99982 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99982 Å / Relative weight: 1
ReflectionResolution: 1.614→50.224 Å / Num. obs: 47462 / % possible obs: 77 % / Redundancy: 3.4 % / Biso Wilson estimate: 31.43 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.038 / Rsym value: 0.038 / Net I/σ(I): 14.3
Reflection shellResolution: 1.614→1.732 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.835 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2373 / CC1/2: 0.579 / Rsym value: 0.835 / % possible all: 20.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
STARANISOdata scaling
PHASERphasing
BUSTER2.11.7refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GE3

6ge3


Resolution: 1.65→23.75 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / SU R Cruickshank DPI: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.121 / SU Rfree Blow DPI: 0.112 / SU Rfree Cruickshank DPI: 0.113
RfactorNum. reflection% reflectionSelection details
Rfree0.219 2362 5.01 %RANDOM
Rwork0.19 ---
obs0.191 47141 81.8 %-
Displacement parametersBiso max: 118.76 Å2 / Biso mean: 36.77 Å2 / Biso min: 18.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.0219 Å20 Å20.5574 Å2
2---2.024 Å20 Å2
3---2.0021 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: final / Resolution: 1.65→23.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3694 0 25 239 3958
Biso mean--40.39 42.17 -
Num. residues----454
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1356SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes670HARMONIC5
X-RAY DIFFRACTIONt_it3937HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion489SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4622SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3937HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5348HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion3.98
X-RAY DIFFRACTIONt_other_torsion16.7
LS refinement shellResolution: 1.65→1.7 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2417 58 6.15 %
Rwork0.2225 885 -
all0.2237 943 -
obs--20.57 %
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)
11.0240.2954-0.14861.5184-0.21681.08270.0092-0.1231-0.0530.02080.0278-0.13510.0761-0.0056-0.037-0.0807-0.02850.0063-0.0515-0.0191-0.00685.460216.409820.0174
21.23130.1526-0.13292.14890.26080.6407-0.12780.09690.1247-0.23230.0137-0.00270.0059-0.11020.1141-0.0365-0.0404-0.0392-0.0703-0.0074-0.064611.654649.010710.6583
33.07460.9056-1.22482.245-1.52737.48340.0411-0.1394-0.6704-0.3752-0.0771-0.33990.63040.43950.0360.0032-0.0658-0.0001-0.12050.01050.08041.8495-1.105812.9267
46.5783-0.55930.77612.5762-1.41242.2072-0.09840.54390.738-0.6453-0.0226-0.1536-0.26710.12040.1210.0217-0.0946-0.018-0.12870.07320.071424.844561.88415.5485
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A217 - 433
2X-RAY DIFFRACTION2{ B|* }B217 - 434
3X-RAY DIFFRACTION3{ L|* }L189 - 206
4X-RAY DIFFRACTION4{ M|* }M189 - 206

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