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- PDB-1tzy: Crystal Structure of the Core-Histone Octamer to 1.90 Angstrom Re... -

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Basic information

Entry
Database: PDB / ID: 1tzy
TitleCrystal Structure of the Core-Histone Octamer to 1.90 Angstrom Resolution
Components
  • HISTONE H3
  • HISTONE H4-VI
  • Histone H2A-IV
  • Histone H2B
KeywordsDNA BINDING PROTEIN / Histone-fold / tetramer-dimer-dimer
Function / homology
Function and homology information


PKMTs methylate histone lysines / HDMs demethylate histones / RMTs methylate histone arginines / SUMOylation of chromatin organization proteins / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint / Processing of DNA double-strand break ends / Condensation of Prophase Chromosomes / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Metalloprotease DUBs ...PKMTs methylate histone lysines / HDMs demethylate histones / RMTs methylate histone arginines / SUMOylation of chromatin organization proteins / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint / Processing of DNA double-strand break ends / Condensation of Prophase Chromosomes / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Metalloprotease DUBs / Interleukin-7 signaling / Chromatin modifying enzymes / UCH proteinases / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / Oxidative Stress Induced Senescence / HDACs deacetylate histones / HATs acetylate histones / B-WICH complex positively regulates rRNA expression / Transcriptional regulation by small RNAs / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Ub-specific processing proteases / Assembly of the ORC complex at the origin of replication / RNA Polymerase I Promoter Opening / RNA Polymerase I Promoter Escape / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Estrogen-dependent gene expression / Deposition of new CENPA-containing nucleosomes at the centromere / Factors involved in megakaryocyte development and platelet production / heterochromatin organization / nucleosomal DNA binding / structural constituent of chromatin / nucleosome / nucleosome assembly / gene expression / protein heterodimerization activity / chromatin binding / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Histone, subunit A / Histone, subunit A / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A ...Histone, subunit A / Histone, subunit A / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Histone H2A-IV / Histone H2B 5 / Histone H2B 7 / Histone H4 / Histone H3.2
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWood, C.M. / Nicholson, J.M. / Chantalat, L. / Reynolds, C.D. / Lambert, S.J. / Baldwin, J.P.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2005
Title: High-resolution structure of the native histone octamer.
Authors: Wood, C.M. / Nicholson, J.M. / Lambert, S.J. / Chantalat, L. / Reynolds, C.D. / Baldwin, J.P.
History
DepositionJul 12, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H2A-IV
B: Histone H2B
C: HISTONE H3
D: HISTONE H4-VI
E: Histone H2A-IV
F: Histone H2B
G: HISTONE H3
H: HISTONE H4-VI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,76736
Polymers109,4768
Non-polymers1,29028
Water11,025612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34270 Å2
ΔGint-478 kcal/mol
Surface area33000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.351, 158.351, 103.576
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Protein , 4 types, 8 molecules AEBFCGDH

#1: Protein Histone H2A-IV


Mass: 13969.363 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P02263
#2: Protein Histone H2B


Mass: 13953.251 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P02279, UniProt: P0C1H5*PLUS
#3: Protein HISTONE H3


Mass: 15421.101 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P84229
#4: Protein HISTONE H4-VI


Mass: 11394.426 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P62801

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Non-polymers , 3 types, 640 molecules

#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#6: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 612 / 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: 3.45 Å3/Da / Density % sol: 64.4 %
Crystal growTemperature: 277 K / Method: microdialysis / pH: 6.7
Details: 2.0M KCL, 1.35M PHOSPHATE, pH 6.7, MICRODIALYSIS, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 20, 2002 / Details: Plane Mirror, vertically focussing
RadiationMonochromator: Si 111, horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→14.96 Å / Num. obs: 109956 / % possible obs: 99.86 % / Observed criterion σ(F): 4.1 / Observed criterion σ(I): 25.7 / Redundancy: 6.3 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 25.7
Reflection shellResolution: 1.9→1.948 Å / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
PXGENdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→14.96 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.19 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.102 / ESU R Free: 0.105
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22152 5809 5 %RANDOM
Rwork0.18667 ---
all0.18984 ---
obs0.18844 109956 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.325 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→14.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5965 0 48 612 6625
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0226063
X-RAY DIFFRACTIONr_bond_other_d0.0020.025890
X-RAY DIFFRACTIONr_angle_refined_deg1.9231.9758149
X-RAY DIFFRACTIONr_angle_other_deg1.062313577
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8895747
X-RAY DIFFRACTIONr_chiral_restr0.1940.2936
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026607
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021285
X-RAY DIFFRACTIONr_nbd_refined0.2470.21475
X-RAY DIFFRACTIONr_nbd_other0.2630.26963
X-RAY DIFFRACTIONr_nbtor_other0.0910.23929
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2386
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3230.280
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1970.220
X-RAY DIFFRACTIONr_mcbond_it1.4091.53742
X-RAY DIFFRACTIONr_mcangle_it2.58426007
X-RAY DIFFRACTIONr_scbond_it3.80832321
X-RAY DIFFRACTIONr_scangle_it6.1864.52142
LS refinement shellResolution: 1.899→1.948 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.331 411
Rwork0.311 8049

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