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- PDB-5vna: Crystal structure of human YEATS domain -

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Basic information

Entry
Database: PDB / ID: 5vna
TitleCrystal structure of human YEATS domain
ComponentsYEATS domain-containing protein 4
KeywordsTRANSCRIPTION / Histone reader / YEATS domain
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 / nuclear membrane / regulation of apoptotic process / histone binding / 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 domain / YEATS / : / YEATS superfamily / YEATS family / YEATS domain profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
YEATS domain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCho, H.J. / Cierpicki, T.
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: GAS41 Recognizes Diacetylated Histone H3 through a Bivalent Binding Mode.
Authors: Cho, H.J. / Li, H. / Linhares, B.M. / Kim, E. / Ndoj, J. / Miao, H. / Grembecka, J. / Cierpicki, T.
History
DepositionApr 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 4, 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
A: YEATS domain-containing protein 4
B: 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)70,48017
Polymers69,3244
Non-polymers1,15613
Water7,080393
1
A: YEATS domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4272
Polymers17,3311
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YEATS domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8959
Polymers17,3311
Non-polymers5658
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: YEATS domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5233
Polymers17,3311
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: YEATS domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6343
Polymers17,3311
Non-polymers3032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.158, 79.926, 121.643
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 17330.924 Da / Num. of mol.: 4 / Fragment: UNP residues 1-148
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YEATS4, GAS41 / Plasmid: pGST-parallel / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O95619
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#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-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 9.4 / Details: 1.24 M ammonium sulfate, 100 mM CHES pH 9.4

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 24, 2016
RadiationMonochromator: KOHZU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 40747 / % possible obs: 99.6 % / Redundancy: 7.2 % / Net I/σ(I): 27.12
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 3 / Num. unique obs: 4052 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QRL

3qrl


Resolution: 2.1→48.4 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.713 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22228 2083 5.1 %RANDOM
Rwork0.17381 ---
obs0.17631 38396 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.951 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å2-0 Å2
2---0.14 Å20 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.1→48.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4205 0 67 393 4665
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0194390
X-RAY DIFFRACTIONr_bond_other_d0.0020.024138
X-RAY DIFFRACTIONr_angle_refined_deg1.9571.9595943
X-RAY DIFFRACTIONr_angle_other_deg1.03839535
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9255505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.28123.756205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.42215743
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1221518
X-RAY DIFFRACTIONr_chiral_restr0.1190.2636
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214786
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021032
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_it3.5073.6892029
X-RAY DIFFRACTIONr_mcbond_other3.5083.6882028
X-RAY DIFFRACTIONr_mcangle_it5.0415.5032528
X-RAY DIFFRACTIONr_mcangle_other5.0415.5042529
X-RAY DIFFRACTIONr_scbond_it4.5624.1062361
X-RAY DIFFRACTIONr_scbond_other4.5614.1062362
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3615.9623415
X-RAY DIFFRACTIONr_long_range_B_refined8.94630.7124988
X-RAY DIFFRACTIONr_long_range_B_other8.85530.1624827
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 167 -
Rwork0.239 2775 -
obs--99.9 %

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