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- PDB-7jfy: GAS41 YEATS domain in complex with 5 -

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Basic information

Entry
Database: PDB / ID: 7jfy
TitleGAS41 YEATS domain in complex with 5
ComponentsYEATS domain-containing protein 4
KeywordsPROTEIN BINDING / Protein-inhibitor complex
Function / homology
Function and homology information


modification-dependent protein binding / regulation of double-strand break repair / Activation of the TFAP2 (AP-2) family of transcription factors / NuA4 histone acetyltransferase complex / positive regulation of double-strand break repair via homologous recombination / lysine-acetylated histone binding / structural constituent of cytoskeleton / nuclear matrix / nucleosome / mitotic cell cycle ...modification-dependent protein binding / regulation of double-strand break repair / Activation of the TFAP2 (AP-2) family of transcription factors / NuA4 histone acetyltransferase complex / positive regulation of double-strand break repair via homologous recombination / lysine-acetylated histone binding / structural constituent of cytoskeleton / nuclear matrix / nucleosome / mitotic cell cycle / HATs acetylate histones / histone binding / regulation of apoptotic process / nuclear membrane / regulation of cell cycle / chromatin remodeling / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / nucleoplasm / nucleus
Similarity search - Function
YEATS / YEATS superfamily / YEATS family / YEATS domain profile.
Similarity search - Domain/homology
Chem-V91 / YEATS domain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.10055713817 Å
AuthorsLinhares, B.M. / Listunov, D. / Winkler, A. / Grembecka, J. / Cierpicki, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA240514 United States
CitationJournal: To Be Published
Title: GAS41 YEATS domain in complex with 5
Authors: Linhares, B.M. / Listunov, D. / Winkler, A. / Grembecka, J. / Cierpicki, T.
History
DepositionJul 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

Downloads & links

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Assembly

Deposited unit
B: YEATS domain-containing protein 4
A: YEATS domain-containing protein 4
C: YEATS domain-containing protein 4
D: YEATS domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,11015
Polymers71,2104
Non-polymers1,90011
Water13,115728
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6630 Å2
ΔGint0 kcal/mol
Surface area25320 Å2
Unit cell
Length a, b, c (Å)117.266, 112.503, 63.222
Angle α, β, γ (deg.)90.000, 116.743, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-339-

HOH

21B-486-

HOH

31B-499-

HOH

41A-383-

HOH

51A-472-

HOH

61C-454-

HOH

71D-447-

HOH

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Components

#1: Protein
YEATS domain-containing protein 4 / Glioma-amplified sequence 41 / Gas41 / NuMA-binding protein 1 / NuBI1


Mass: 17802.453 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YEATS4, GAS41 / Production host: Escherichia coli (E. coli) / References: UniProt: O95619
#2: Chemical
ChemComp-V91 / N-(5-{3-[(2S)-1,3-thiazolidin-2-yl]azetidine-1-carbonyl}thiophen-2-yl)-L-prolinamide


Mass: 362.470 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H18N4O2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 728 / 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: 2.62 Å3/Da / Density % sol: 52.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 0.1 M Tris, pH 7.3, 0.2 M magnesium chloride, 2.2 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Oct 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.1→39.85 Å / Num. obs: 42637 / % possible obs: 98.13 % / Redundancy: 3.9 % / Biso Wilson estimate: 30.2473095888 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.09119 / Rpim(I) all: 0.05365 / Rrim(I) all: 0.1059 / Net I/σ(I): 11.74
Reflection shellResolution: 2.101→2.176 Å / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.49 / Num. unique obs: 4184 / CC1/2: 0.809 / Rpim(I) all: 0.2831 / Rrim(I) all: 0.5579

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Processing

Software
NameVersionClassification
HKL-20001.11.1_2575data scaling
PHENIX1.11.1_2575refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VNA

5vna


Resolution: 2.10055713817→39.8491142852 Å / SU ML: 0.304519619771 / Cross valid method: FREE R-VALUE / σ(F): 1.37232259317 / Phase error: 27.977092778
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.264217070077 2091 4.99462558223 %
Rwork0.207500426097 39774 -
obs0.210363055247 41865 98.1065310618 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.6552227129 Å2
Refinement stepCycle: LAST / Resolution: 2.10055713817→39.8491142852 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4089 0 124 728 4941
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001608440995454366
X-RAY DIFFRACTIONf_angle_d0.5091041979785938
X-RAY DIFFRACTIONf_chiral_restr0.0478023033928625
X-RAY DIFFRACTIONf_plane_restr0.00244489702597745
X-RAY DIFFRACTIONf_dihedral_angle_d15.05659974292524
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1006-2.14940.3175960164141490.2489978138242601X-RAY DIFFRACTION97.104519774
2.1494-2.20320.3172295712641350.2564178141892683X-RAY DIFFRACTION99.3302784632
2.2032-2.26270.3083628598811300.2511946329672686X-RAY DIFFRACTION99.1200281591
2.2627-2.32930.3040500460531110.2474463859122688X-RAY DIFFRACTION99.2905285562
2.3293-2.40450.303609110431330.2443124705192671X-RAY DIFFRACTION99.011299435
2.4045-2.49040.2979259086331640.2531199082182632X-RAY DIFFRACTION99.0084985836
2.4904-2.59010.3074127739461540.2516228183112645X-RAY DIFFRACTION98.8347457627
2.5901-2.7080.3570904363431260.2495474074172708X-RAY DIFFRACTION98.8145048815
2.708-2.85070.314598082741430.2491408331092653X-RAY DIFFRACTION98.6243386243
2.8507-3.02920.2642032432621370.2252266341562653X-RAY DIFFRACTION98.3086680761
3.0292-3.2630.2792098988811360.2111746655432653X-RAY DIFFRACTION98.2042253521
3.263-3.59120.2425865214581500.1799273410342626X-RAY DIFFRACTION97.5061468212
3.5912-4.11040.2128167804481390.166903613412640X-RAY DIFFRACTION97.577247191
4.1104-5.17690.2314923188821230.1551089306152635X-RAY DIFFRACTION96.0640891675
5.1769-39.840.236735823981610.2131787665912600X-RAY DIFFRACTION94.9449793673

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