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- PDB-5wcu: Crystal structure of 167 bp nucleosome bound to the globular doma... -

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Basic information

Entry
Database: PDB / ID: 5wcu
TitleCrystal structure of 167 bp nucleosome bound to the globular domain of linker histone H5
Components
  • (DNA (167-MER)) x 2
  • Histone H2A
  • Histone H2B
  • Histone H3
  • Histone H4
  • Histone H5Histone H1
KeywordsCHROMATIN BINDING PROTEIN/DNA / NUCLEOSOME CORE PARTICLE / HISTONE FOLD / CHROMOSOME / CHROMATIN / GLOBULAR DOMAIN / HISTONE H5 / GH5 / 167 BP NUCLEOSOME / CHROMATOSOME / NUCLEOSOME PACKING / 30 NM CHROMATIN FIBER / LINKER HISTONE H5 / LINKER DNA / NUCLEOSOME BINDING PROTEIN / PROTEIN DNA COMPLEXES / DNA BINDING / CHROMATIN HIGHER ORDER STRUCTURE / CHROMATIN FOLDING / CHROMATIN BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


Interleukin-7 signaling / Chromatin modifying enzymes / RCAF complex / Factors involved in megakaryocyte development and platelet production / E3 ubiquitin ligases ubiquitinate target proteins / polytene chromosome band / HATs acetylate histones / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Ub-specific processing proteases / larval somatic muscle development ...Interleukin-7 signaling / Chromatin modifying enzymes / RCAF complex / Factors involved in megakaryocyte development and platelet production / E3 ubiquitin ligases ubiquitinate target proteins / polytene chromosome band / HATs acetylate histones / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Ub-specific processing proteases / larval somatic muscle development / polytene chromosome / negative regulation of DNA recombination / chromosome condensation / nucleosomal DNA binding / nuclear chromosome / nucleosome assembly / structural constituent of chromatin / nucleosome / chromosome / chromatin organization / double-stranded DNA binding / nucleic acid binding / protein heterodimerization activity / chromatin / protein-containing complex binding / DNA binding / nucleus
Similarity search - Function
Linker histone H1/H5 / linker histone H1 and H5 family / Linker histone H1/H5, domain H15 / Linker histone H1/H5 globular (H15) domain profile. / Domain in histone families 1 and 5 / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. ...Linker histone H1/H5 / linker histone H1 and H5 family / Linker histone H1/H5, domain H15 / Linker histone H1/H5 globular (H15) domain profile. / Domain in histone families 1 and 5 / 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 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / 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 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H5 / Histone H2B / Histone H3 / Histone H4 / Histone H2A
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Gallus gallus (chicken)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.53 Å
AuthorsJiang, J.S. / Zhou, B.R.
CitationJournal: J. Mol. Biol. / Year: 2018
Title: Revisit of Reconstituted 30-nm Nucleosome Arrays Reveals an Ensemble of Dynamic Structures.
Authors: Zhou, B.R. / Jiang, J. / Ghirlando, R. / Norouzi, D. / Sathish Yadav, K.N. / Feng, H. / Wang, R. / Zhang, P. / Zhurkin, V. / Bai, Y.
History
DepositionJul 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 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: Histone H3
B: Histone H4
C: Histone H2A
D: Histone H2B
E: Histone H3
F: Histone H4
G: Histone H2A
H: Histone H2B
I: DNA (167-MER)
J: DNA (167-MER)
K: Histone H3
L: Histone H4
M: Histone H2A
N: Histone H2B
O: Histone H3
P: Histone H4
Q: Histone H2A
R: Histone H2B
S: DNA (167-MER)
T: DNA (167-MER)
U: Histone H5
V: Histone H5


Theoretical massNumber of molelcules
Total (without water)393,46722
Polymers393,46722
Non-polymers00
Water0
1
A: Histone H3
B: Histone H4
C: Histone H2A
D: Histone H2B
E: Histone H3
F: Histone H4
G: Histone H2A
H: Histone H2B
I: DNA (167-MER)
J: DNA (167-MER)
U: Histone H5


Theoretical massNumber of molelcules
Total (without water)196,73411
Polymers196,73411
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area62380 Å2
ΔGint-404 kcal/mol
Surface area82510 Å2
MethodPISA
2
K: Histone H3
L: Histone H4
M: Histone H2A
N: Histone H2B
O: Histone H3
P: Histone H4
Q: Histone H2A
R: Histone H2B
S: DNA (167-MER)
T: DNA (167-MER)
V: Histone H5


Theoretical massNumber of molelcules
Total (without water)196,73411
Polymers196,73411
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area61970 Å2
ΔGint-384 kcal/mol
Surface area83250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.926, 108.543, 180.770
Angle α, β, γ (deg.)100.79, 90.08, 89.94
Int Tables number1
Space group name H-MP1

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Components

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Protein , 5 types, 18 molecules AEKOBFLPCGMQDHNRUV

#1: Protein
Histone H3 /


Mass: 11488.410 Da / Num. of mol.: 4 / Fragment: UNP residues 39-136
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: His3, His3:CG31613, CG31613, His3:CG33803, CG33803, His3:CG33806, CG33806, His3:CG33809, CG33809, His3:CG33812, CG33812, His3:CG33815, CG33815, His3:CG33818, CG33818, His3:CG33821, CG33821, ...Gene: His3, His3:CG31613, CG31613, His3:CG33803, CG33803, His3:CG33806, CG33806, His3:CG33809, CG33809, His3:CG33812, CG33812, His3:CG33815, CG33815, His3:CG33818, CG33818, His3:CG33821, CG33821, His3:CG33824, CG33824, His3:CG33827, CG33827, His3:CG33830, CG33830, His3:CG33833, CG33833, His3:CG33836, CG33836, His3:CG33839, CG33839, His3:CG33842, CG33842, His3:CG33845, CG33845, His3:CG33848, CG33848, His3:CG33851, CG33851, His3:CG33854, CG33854, His3:CG33857, CG33857, His3:CG33860, CG33860, His3:CG33863, CG33863, His3:CG33866, CG33866
Production host: Escherichia coli (E. coli) / References: UniProt: P02299
#2: Protein
Histone H4 /


Mass: 9279.875 Da / Num. of mol.: 4 / Fragment: UNP residues 22-103
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: His4, H4, His4r, H4r, CG3379, His4:CG31611, CG31611, His4:CG33869, CG33869, His4:CG33871, CG33871, His4:CG33873, CG33873, His4:CG33875, CG33875, His4:CG33877, CG33877, His4:CG33879, CG33879, ...Gene: His4, H4, His4r, H4r, CG3379, His4:CG31611, CG31611, His4:CG33869, CG33869, His4:CG33871, CG33871, His4:CG33873, CG33873, His4:CG33875, CG33875, His4:CG33877, CG33877, His4:CG33879, CG33879, His4:CG33881, CG33881, His4:CG33883, CG33883, His4:CG33885, CG33885, His4:CG33887, CG33887, His4:CG33889, CG33889, His4:CG33891, CG33891, His4:CG33893, CG33893, His4:CG33895, CG33895, His4:CG33897, CG33897, His4:CG33899, CG33899, His4:CG33901, CG33901, His4:CG33903, CG33903, His4:CG33905, CG33905, His4:CG33907, CG33907, His4:CG33909, CG33909
Production host: Escherichia coli (E. coli) / References: UniProt: P84040
#3: Protein
Histone H2A /


Mass: 11352.236 Da / Num. of mol.: 4 / Fragment: UNP residues 15-118
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: His2A, H2a, His2A:CG31618, CG31618, His2A:CG33808, CG33808, His2A:CG33814, CG33814, His2A:CG33817, CG33817, His2A:CG33820, CG33820, His2A:CG33823, CG33823, His2A:CG33826, CG33826, His2A: ...Gene: His2A, H2a, His2A:CG31618, CG31618, His2A:CG33808, CG33808, His2A:CG33814, CG33814, His2A:CG33817, CG33817, His2A:CG33820, CG33820, His2A:CG33823, CG33823, His2A:CG33826, CG33826, His2A:CG33829, CG33829, His2A:CG33832, CG33832, His2A:CG33835, CG33835, His2A:CG33838, CG33838, His2A:CG33841, CG33841, His2A:CG33844, CG33844, His2A:CG33847, CG33847, His2A:CG33850, CG33850, His2A:CG33862, CG33862, His2A:CG33865, CG33865
Production host: Escherichia coli (E. coli) / References: UniProt: P84051
#4: Protein
Histone H2B /


Mass: 10592.202 Da / Num. of mol.: 4 / Fragment: UNP residues 29-122
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: His2B, His2B:CG17949, CG17949, His2B:CG33868, CG33868, His2B:CG33870, CG33870, His2B:CG33872, CG33872, His2B:CG33874, CG33874, His2B:CG33876, CG33876, His2B:CG33878, CG33878, His2B:CG33880, ...Gene: His2B, His2B:CG17949, CG17949, His2B:CG33868, CG33868, His2B:CG33870, CG33870, His2B:CG33872, CG33872, His2B:CG33874, CG33874, His2B:CG33876, CG33876, His2B:CG33878, CG33878, His2B:CG33880, CG33880, His2B:CG33882, CG33882, His2B:CG33884, CG33884, His2B:CG33886, CG33886, His2B:CG33888, CG33888, His2B:CG33890, CG33890, His2B:CG33892, CG33892, His2B:CG33894, CG33894, His2B:CG33896, CG33896, His2B:CG33898, CG33898, His2B:CG33900, CG33900, His2B:CG33902, CG33902, His2B:CG33904, CG33904, His2B:CG33906, CG33906, His2B:CG33908, CG33908, His2B:CG33910, CG33910
Production host: Escherichia coli (E. coli) / References: UniProt: P02283
#7: Protein Histone H5 / Histone H1


Mass: 8199.485 Da / Num. of mol.: 2 / Fragment: UNP residues 23-98
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Escherichia coli (E. coli) / References: UniProt: P02259

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DNA chain , 2 types, 4 molecules ISJT

#5: DNA chain DNA (167-MER)


Mass: 51318.695 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: 167 BP WIDOM 601 DNA / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (167-MER)


Mass: 51789.977 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: 167 BP WIDOM 601 DNA / Source: (synth.) synthetic construct (others)

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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: 3.23 Å3/Da / Density % sol: 61.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 0.1 M NH4NO3, 10% MPD (v/v)

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 18, 2016
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 5.53→49.63 Å / Num. obs: 15268 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 176.6 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 7.3
Reflection shellResolution: 5.53→5.73 Å / Redundancy: 2.2 % / Rmerge(I) obs: 1.706 / Mean I/σ(I) obs: 0.7 / % possible all: 95.7

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QLC

4qlc


Resolution: 5.53→48.62 Å / Cross valid method: THROUGHOUT / σ(F): 1.93 / Phase error: 29.56 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1548 10.14 %Random
Rwork0.189 ---
obs0.195 15266 97.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 5.53→48.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13051 13568 0 0 26619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00528441
X-RAY DIFFRACTIONf_angle_d0.75141235
X-RAY DIFFRACTIONf_dihedral_angle_d24.50414822
X-RAY DIFFRACTIONf_chiral_restr0.0414678
X-RAY DIFFRACTIONf_plane_restr0.0042928
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
5.5376-5.71610.35451360.33271220X-RAY DIFFRACTION87
5.7161-5.91990.37891370.30031229X-RAY DIFFRACTION87
5.9199-6.15640.40271360.28541260X-RAY DIFFRACTION89
6.1564-6.43590.3731420.26831278X-RAY DIFFRACTION89
6.4359-6.77410.35351350.22391237X-RAY DIFFRACTION88
6.7741-7.1970.28621430.2241263X-RAY DIFFRACTION88
7.197-7.75020.281370.20241252X-RAY DIFFRACTION88
7.7502-8.52550.2221380.17221247X-RAY DIFFRACTION88
8.5255-9.74850.20091410.15961268X-RAY DIFFRACTION88
9.7485-12.24220.13921360.13731241X-RAY DIFFRACTION88
12.2422-45.44390.17251400.13631238X-RAY DIFFRACTION87

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