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- PDB-8iiy: Crystal structure of MBP fused GAS41 YEATS domain in complex with... -

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Basic information

Entry
Database: PDB / ID: 8iiy
TitleCrystal structure of MBP fused GAS41 YEATS domain in complex with H3K14ac peptide
Components
  • Histone H3.1Histone H3
  • Maltodextrin-binding protein,YEATS domain-containing protein 4
KeywordsNUCLEAR PROTEIN / YEATS domain / Transcription / Complex / Histone modification
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 / carbohydrate transmembrane transporter activity / Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening ...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 / carbohydrate transmembrane transporter activity / Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / lysine-acetylated histone binding / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / structural constituent of cytoskeleton / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nuclear matrix / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / mitotic cell cycle / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / outer membrane-bounded periplasmic space / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / histone binding / Senescence-Associated Secretory Phenotype (SASP) / regulation of apoptotic process / Oxidative Stress Induced Senescence / nuclear membrane / Estrogen-dependent gene expression / regulation of cell cycle / chromatin remodeling / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus
Similarity search - Function
YEATS / YEATS superfamily / YEATS family / YEATS domain profile. / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Histone H3 signature 1. ...YEATS / YEATS superfamily / YEATS family / YEATS domain profile. / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
alpha-maltotetraose / Maltodextrin-binding protein / YEATS domain-containing protein 4 / Histone H3.1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsKikuchi, M. / Umehara, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: GAS41 promotes H2A.Z deposition through recognition of the N terminus of histone H3 by the YEATS domain.
Authors: Kikuchi, M. / Takase, S. / Konuma, T. / Noritsugu, K. / Sekine, S. / Ikegami, T. / Ito, A. / Umehara, T.
History
DepositionFeb 24, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltodextrin-binding protein,YEATS domain-containing protein 4
B: Histone H3.1
C: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3016
Polymers61,4503
Non-polymers8513
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint6 kcal/mol
Surface area22850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.241, 66.241, 248.821
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 57212.938 Da / Num. of mol.: 1 / Mutation: D108A, K109A, E198A, N199A, K265A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Gene: YEATS4, GAS41 / Production host: Escherichia coli (E. coli) / References: UniProt: C3SHQ8, UniProt: O95619
#2: Protein/peptide Histone H3.1 / Histone H3 / Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone ...Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone H3/i / Histone H3/j / Histone H3/k / Histone H3/l


Mass: 2118.444 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotetraose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.56 Å3/Da / Density % sol: 52.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM Tris buffer (pH 8.5) containing 20% (w/v) PEG monomethyl ether 2000, 200 mM trimethylamine N-oxide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Aug 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 35680 / % possible obs: 100 % / Redundancy: 11 % / Rsym value: 0.093 / Net I/σ(I): 14.5
Reflection shellResolution: 2.15→2.22 Å / Num. unique obs: 3067 / Rsym value: 1.433

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→45 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.94 / SU B: 14.555 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24671 1853 5.2 %RANDOM
Rwork0.16975 ---
obs0.17359 33750 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20.21 Å20 Å2
2--0.41 Å2-0 Å2
3----1.33 Å2
Refinement stepCycle: 1 / Resolution: 2.15→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4088 0 57 145 4290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0134293
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174054
X-RAY DIFFRACTIONr_angle_refined_deg1.1741.6635839
X-RAY DIFFRACTIONr_angle_other_deg1.1791.5959377
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9715530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.18324.213197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.91215700
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4731512
X-RAY DIFFRACTIONr_chiral_restr0.0460.2575
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024821
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02931
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_it4.6595.6432117
X-RAY DIFFRACTIONr_mcbond_other4.6662116
X-RAY DIFFRACTIONr_mcangle_it5.9788.4542648
X-RAY DIFFRACTIONr_mcangle_other5.98338.4212649
X-RAY DIFFRACTIONr_scbond_it5.5952176
X-RAY DIFFRACTIONr_scbond_other5.5952176
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7013192
X-RAY DIFFRACTIONr_long_range_B_refined7.6074758
X-RAY DIFFRACTIONr_long_range_B_other7.6064759
X-RAY DIFFRACTIONr_rigid_bond_restr1.50834232
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 126 -
Rwork0.275 2476 -
obs--100 %

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