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

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Basic information

Entry
Database: PDB / ID: 8iiz
TitleCrystal structure of MBP fused GAS41 YEATS domain in complex with H3K27ac peptide
Components
  • Histone H3.1
  • 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 / carbohydrate transmembrane transporter activity / positive regulation of double-strand break repair via homologous recombination / maltose binding / maltose transport / maltodextrin transmembrane transport / Chromatin modifying enzymes ...modification-dependent protein binding / regulation of double-strand break repair / Activation of the TFAP2 (AP-2) family of transcription factors / NuA4 histone acetyltransferase complex / carbohydrate transmembrane transporter activity / positive regulation of double-strand break repair via homologous recombination / maltose binding / maltose transport / maltodextrin transmembrane transport / Chromatin modifying enzymes / epigenetic regulation of gene expression / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / 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 / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / 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 / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / structural constituent of cytoskeleton / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / nuclear matrix / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / mitotic cell cycle / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / gene expression / histone binding / Senescence-Associated Secretory Phenotype (SASP) / outer membrane-bounded periplasmic space / regulation of apoptotic process / nuclear membrane / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / regulation of cell cycle / chromatin remodeling / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / 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-maltose / 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: 2.1 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)64,6097
Polymers63,9913
Non-polymers6194
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-4 kcal/mol
Surface area22860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.200, 66.200, 248.583
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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/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: 3388.944 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


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.46 Å3/Da / Density % sol: 49.94 %
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: Apr 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 34835 / % possible obs: 91.1 % / Redundancy: 10.9 % / Rsym value: 0.118 / Net I/σ(I): 9.9
Reflection shellResolution: 2.1→2.17 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3093 / Rsym value: 1.502

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→45.004 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.907 / SU B: 8.117 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.288 / ESU R Free: 0.24
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3009 1617 4.753 %
Rwork0.2496 32405 -
all0.252 --
obs-34022 89.308 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 48.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.002 Å2-0.001 Å2-0 Å2
2---0.002 Å20 Å2
3---0.007 Å2
Refinement stepCycle: LAST / Resolution: 2.1→45.004 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4055 0 41 104 4200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0134204
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173940
X-RAY DIFFRACTIONr_angle_refined_deg1.3081.6545717
X-RAY DIFFRACTIONr_angle_other_deg1.1731.5879098
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.785523
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.63924.574188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.31315664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.81159
X-RAY DIFFRACTIONr_chiral_restr0.0530.2565
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024738
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02904
X-RAY DIFFRACTIONr_nbd_refined0.190.2898
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1720.23782
X-RAY DIFFRACTIONr_nbtor_refined0.1630.22038
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.21869
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2159
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2020.211
X-RAY DIFFRACTIONr_nbd_other0.1510.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1360.210
X-RAY DIFFRACTIONr_mcbond_it2.7945.0992101
X-RAY DIFFRACTIONr_mcbond_other2.7945.0962100
X-RAY DIFFRACTIONr_mcangle_it4.3027.6372620
X-RAY DIFFRACTIONr_mcangle_other4.3017.642621
X-RAY DIFFRACTIONr_scbond_it2.7045.2722103
X-RAY DIFFRACTIONr_scbond_other2.7035.2732104
X-RAY DIFFRACTIONr_scangle_it4.3087.7883096
X-RAY DIFFRACTIONr_scangle_other4.3077.7893097
X-RAY DIFFRACTIONr_lrange_it6.32959.554696
X-RAY DIFFRACTIONr_lrange_other6.32859.5594697
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.1-2.1540.6421300.65426440.65327910.6590.66499.39090.7
2.154-2.2130.569940.5718840.5726960.1650.22973.3680.606
2.213-2.2770.818100.8451910.84426010.0220.0247.72780.842
2.277-2.3470.3761060.322710.30325430.7440.82993.47230.274
2.347-2.4240.321910.28223700.28424610.8290.8391000.256
2.424-2.5090.3271080.26422830.26623910.8350.8761000.236
2.509-2.6030.3491280.24921870.25423150.840.8891000.223
2.603-2.7090.361140.26321140.26822280.8330.8751000.239
2.709-2.8290.332840.26520550.26821390.8240.8631000.244
2.829-2.9670.277970.22319610.22520580.8910.9141000.21
2.967-3.1260.3161070.23318660.23719730.8770.9131000.223
3.126-3.3150.274980.23417770.23618750.8940.9121000.231
3.315-3.5430.301700.22316550.22617250.8890.9211000.228
3.543-3.8240.24620.22511700.22616640.9150.9374.03850.229
3.824-4.1860.222550.19211350.19415220.9450.95278.18660.211
4.186-4.6750.249880.17813090.18213970.9370.9541000.206
4.675-5.3890.205590.16811750.1712340.960.9671000.194
5.389-6.5770.331510.20610290.21110800.9070.9391000.232
6.577-9.2030.22360.1878180.1898540.9330.9541000.222
9.203-45.0040.25290.2125110.2145400.9440.9661000.247

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