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- PDB-6l9f: Crystal structure of TEAD4 in complex with a novel FAM181A peptide -

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Basic information

Entry
Database: PDB / ID: 6l9f
TitleCrystal structure of TEAD4 in complex with a novel FAM181A peptide
Components
  • Protein FAM181A
  • Transcriptional enhancer factor TEF-3
KeywordsPROTEIN BINDING / Transcription factor / Suppressor / Complex
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 / embryonic organ development / cell fate commitment / embryo implantation ...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 / embryonic organ development / cell fate commitment / 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
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
ACETATE ION / Transcriptional enhancer factor TEF-3 / Protein FAM181A
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.555 Å
AuthorsChen, M. / Zhou, Z.
CitationJournal: To be published
Title: Crystal structure of TEAD4 in complex with a novel FAM181A peptide
Authors: Chen, M. / Zhou, Z.
History
DepositionNov 9, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2019Provider: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional enhancer factor TEF-3
C: Protein FAM181A
B: Transcriptional enhancer factor TEF-3
D: Protein FAM181A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4669
Polymers57,1714
Non-polymers2955
Water2,720151
1
A: Transcriptional enhancer factor TEF-3
C: Protein FAM181A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7635
Polymers28,5862
Non-polymers1773
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-8 kcal/mol
Surface area11280 Å2
MethodPISA
2
B: Transcriptional enhancer factor TEF-3
D: Protein FAM181A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7044
Polymers28,5862
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-5 kcal/mol
Surface area11360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.009, 110.009, 182.711
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11B-650-

HOH

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Components

#1: 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: 26171.732 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tead4, Tcf13r1, Tef3, Tefr1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): CodonPlus / References: UniProt: Q62296
#2: Protein/peptide Protein FAM181A


Mass: 2413.796 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8N9Y4
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.81 Å3/Da / Density % sol: 56.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 2.5 M Ammonium nitrate, 0.1 M Sodium acetate trihydrate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1.00928 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00928 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 21907 / % possible obs: 99.8 % / Redundancy: 14.6 % / Rmerge(I) obs: 0.185 / Rpim(I) all: 0.05 / Rrim(I) all: 0.191 / Χ2: 1.418 / Net I/σ(I): 6.3 / Num. measured all: 320535
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.55-2.59150.90110640.9070.2390.9331.02100
2.59-2.64150.85810680.9110.2280.8881.047100
2.64-2.6915.10.77610730.9240.2050.8041.046100
2.69-2.75150.65110690.9410.1730.6741.099100
2.75-2.81150.57110630.9470.1520.5911.10399.9
2.81-2.8715.10.47610710.9660.1260.4931.139100
2.87-2.9414.90.41110710.9730.1090.4251.187100
2.94-3.02150.35210780.9790.0930.3641.244100
3.02-3.11150.30710770.9820.0810.3181.273100
3.11-3.2114.90.25210800.9870.0670.2611.387100
3.21-3.3314.90.20311030.9910.0540.211.536100
3.33-3.4614.80.16910780.9940.0450.1751.615100
3.46-3.6214.80.15610790.9940.0420.1621.676100
3.62-3.8114.60.15111050.9930.0410.1561.954100
3.81-4.0514.50.13710920.9930.0370.1421.882100
4.05-4.3614.30.12611030.9950.0340.131.965100
4.36-4.814.10.11311190.9960.0310.1171.921100
4.8-5.49140.08911360.9970.0240.0921.6100
5.49-6.9213.80.08211450.9980.0220.0851.28799.6
6.92-50130.05212330.9990.0150.0541.40597.8

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JUA

3jua


Resolution: 2.555→46.094 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2528 1999 9.14 %
Rwork0.1901 19875 -
obs0.1959 21874 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.7 Å2 / Biso mean: 28.7292 Å2 / Biso min: 9.88 Å2
Refinement stepCycle: final / Resolution: 2.555→46.094 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3667 0 20 151 3838
Biso mean--25.52 31.84 -
Num. residues----451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073789
X-RAY DIFFRACTIONf_angle_d0.975122
X-RAY DIFFRACTIONf_chiral_restr0.052550
X-RAY DIFFRACTIONf_plane_restr0.006649
X-RAY DIFFRACTIONf_dihedral_angle_d4.312601
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.555-2.61850.32191390.22871388100
2.6185-2.68930.32391400.24071377100
2.6893-2.76840.31981390.24281391100
2.7684-2.85780.35721380.22871376100
2.8578-2.95990.31011420.22361405100
2.9599-3.07840.29141410.21471394100
3.0784-3.21840.25721390.20951395100
3.2184-3.38810.25461420.1921407100
3.3881-3.60030.26981410.17781407100
3.6003-3.87810.24891430.17741425100
3.8781-4.26810.22821440.16061426100
4.2681-4.88520.17011440.13631438100
4.8852-6.15250.23241490.17491481100
6.1525-46.0940.22361580.2121156599

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