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- PDB-2nqb: Drosophila Nucleosome Structure -

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Basic information

Entry
Database: PDB / ID: 2nqb
TitleDrosophila Nucleosome Structure
Components
  • Histone H2A
  • Histone H2B
  • Histone H3
  • Histone H4
  • alpha-satellite DNA
KeywordsSTRUCTURAL PROTEIN/DNA / Nucleosome / NCP / chromatin / histone / STRUCTURAL PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


HDMs demethylate histones / PKMTs methylate histone lysines / Interleukin-7 signaling / Chromatin modifying enzymes / Condensation of Prophase Chromosomes / SUMOylation of chromatin organization proteins / Metalloprotease DUBs / E3 ubiquitin ligases ubiquitinate target proteins / Factors involved in megakaryocyte development and platelet production / RCAF complex ...HDMs demethylate histones / PKMTs methylate histone lysines / Interleukin-7 signaling / Chromatin modifying enzymes / Condensation of Prophase Chromosomes / SUMOylation of chromatin organization proteins / Metalloprotease DUBs / E3 ubiquitin ligases ubiquitinate target proteins / Factors involved in megakaryocyte development and platelet production / RCAF complex / RMTs methylate histone arginines / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / polytene chromosome band / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / HDACs deacetylate histones / Ub-specific processing proteases / RNA Polymerase I Promoter Escape / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Regulation of endogenous retroelements by KRAB-ZFP proteins / larval somatic muscle development / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Senescence-Associated Secretory Phenotype (SASP) / Transcriptional regulation by small RNAs / Estrogen-dependent gene expression / HATs acetylate histones / UCH proteinases / Assembly of the ORC complex at the origin of replication / Oxidative Stress Induced Senescence / polytene chromosome / nucleosomal DNA binding / nuclear chromosome / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / chromosome / chromatin organization / protein heterodimerization activity / chromatin / protein-containing complex binding / DNA binding / nucleus
Similarity search - Function
Histone, subunit A / Histone, subunit A / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A ...Histone, subunit A / Histone, subunit A / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / 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 domain / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H2B / Histone H3 / Histone H4 / Histone H2A
Similarity search - Component
Biological speciesHomo sapiens (human)
Drosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLuger, K. / Chakravarthy, S.
CitationJournal: To be Published
Title: Comparative analysis of nucleosome structures from different species.
Authors: Chakravarthy, S. / Luger, K.
History
DepositionOct 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: alpha-satellite DNA
J: alpha-satellite DNA
A: Histone H3
B: Histone H4
C: Histone H2A
D: Histone H2B
E: Histone H3
F: Histone H4
G: Histone H2A
H: Histone H2B


Theoretical massNumber of molelcules
Total (without water)197,34710
Polymers197,34710
Non-polymers00
Water4,756264
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.143, 109.581, 182.045
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsEach nucleosome has two copies each of histones H2A, H2B, H3 and H4, and a 146 base pairs long palindromic strand of DNA derived from human alpha-satellite sequence.

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Components

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Protein , 4 types, 8 molecules AEBFCGDH

#2: Protein Histone H3


Mass: 15289.904 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: His4 / Production host: Escherichia coli (E. coli) / References: UniProt: P02299
#3: Protein Histone H4


Mass: 11390.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: His2A / Production host: Escherichia coli (E. coli) / References: UniProt: P84040
#4: Protein Histone H2A


Mass: 13257.529 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: His2B / Production host: Escherichia coli (E. coli) / References: UniProt: P84051
#5: Protein Histone H2B


Mass: 13680.951 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Escherichia coli (E. coli) / References: UniProt: P02283

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DNA chain / Non-polymers , 2 types, 266 molecules IJ

#1: DNA chain alpha-satellite DNA


Mass: 45054.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: His3 / Production host: Escherichia coli (E. coli)
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.64 Å3/Da / Density % sol: 53.37 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Constituents of the crystallization buffer: Potassium Chloride, Manganese Chloride, and Potassium Cacodylate., pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Components of the solutions
IDNameCrystal-IDSol-ID
1Potassium Chloride11
2Manganese Chloride11
3Potassium Cacodylate11
4H2O11
5Potassium Chloride12
6Manganese Chloride12
7Potassium Cacodylate12
8H2O12

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.3→99 Å / Num. all: 94877 / Num. obs: 93949 / % possible obs: 98.2 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 22
Reflection shellResolution: 2.3→2.35 Å / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 3 / Num. unique all: 5358 / % possible all: 85

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Processing

Software
NameClassification
CrystalCleardata collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1AOI

1aoi


Resolution: 2.3→99 Å
RfactorNum. reflection% reflection
Rfree0.254 2267 -
Rwork0.2233 --
all-94877 -
obs-91209 96.1 %
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.473 Å20 Å20 Å2
2--5.934 Å20 Å2
3----2.461 Å2
Refinement stepCycle: LAST / Resolution: 2.3→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6050 5980 0 264 12294
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005735
X-RAY DIFFRACTIONc_angle_deg0.95646
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param

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