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- PDB-4ld9: Crystal structure of the N-terminally acetylated BAH domain of Si... -

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Basic information

Entry
Database: PDB / ID: 4ld9
TitleCrystal structure of the N-terminally acetylated BAH domain of Sir3 bound to the nucleosome core particle
Components
  • (Widom 601 sequence ...) x 2
  • Histone H2A
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
  • Regulatory protein SIR3
KeywordsNUCLEAR PROTEIN/TRANSCRIPTION/DNA / BETA BARREL / PROTEIN-DNA COMPLEX / DOUBLE HELIX / alpha-helix / beta-sheet / double stranded DNA / chromatin binding / chromatin / N-terminal acetylation / nucleus / NUCLEAR PROTEIN-TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


establishment of protein-containing complex localization to telomere / nuclear-transcribed mRNA catabolic process, non-stop decay / telomere tethering at nuclear periphery / mitotic DNA replication checkpoint signaling / chromatin silencing complex / silent mating-type cassette heterochromatin formation / negative regulation of DNA replication / DNA replication origin binding / DNA replication initiation / subtelomeric heterochromatin formation ...establishment of protein-containing complex localization to telomere / nuclear-transcribed mRNA catabolic process, non-stop decay / telomere tethering at nuclear periphery / mitotic DNA replication checkpoint signaling / chromatin silencing complex / silent mating-type cassette heterochromatin formation / negative regulation of DNA replication / DNA replication origin binding / DNA replication initiation / subtelomeric heterochromatin formation / heterochromatin / nucleosome binding / double-strand break repair via nonhomologous end joining / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / single-stranded DNA binding / double-stranded DNA binding / nucleic acid binding / chromosome, telomeric region / protein heterodimerization activity / chromatin binding / nucleolus / mitochondrion / DNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
: / Regulatory protein SIR3, C-terminal domain / Bromo adjacent homology (BAH) domain / AAA lid domain / AAA lid domain / : / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily ...: / Regulatory protein SIR3, C-terminal domain / Bromo adjacent homology (BAH) domain / AAA lid domain / AAA lid domain / : / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. / 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 / SH3 type barrels. / 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 / Roll / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H2B 1.1 / Regulatory protein SIR3 / Histone H2A type 1 / Histone H4 / Histone H3.2 / Histone H2A
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.306 Å
AuthorsArnaudo, N. / Fernandez, I.S. / McLaughlin, S.H. / Peak-Chew, S.Y. / Rhodes, D. / Martino, F.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: The N-terminal acetylation of Sir3 stabilizes its binding to the nucleosome core particle.
Authors: Arnaudo, N. / Fernandez, I.S. / McLaughlin, S.H. / Peak-Chew, S.Y. / Rhodes, D. / Martino, F.
History
DepositionJun 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Sep 18, 2013Group: Database references
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H3.2
B: Histone H4
C: Histone H2A
D: Histone H2B 1.1
E: Histone H3.2
F: Histone H4
G: Histone H2A
H: Histone H2B 1.1
I: Widom 601 sequence reverse
J: Widom 601 sequence forward
K: Regulatory protein SIR3
L: Regulatory protein SIR3


Theoretical massNumber of molelcules
Total (without water)269,07912
Polymers269,07912
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.513, 105.513, 488.225
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein , 5 types, 10 molecules AEBFCGDHKL

#1: Protein Histone H3.2


Mass: 15421.101 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P84233
#2: Protein Histone H4


Mass: 11394.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799
#3: Protein Histone H2A


Mass: 14109.436 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC494591 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6AZJ8, UniProt: P06897*PLUS
#4: Protein Histone H2B 1.1 / H2B1.1


Mass: 13965.265 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281
#7: Protein Regulatory protein SIR3 / Silent information regulator 3


Mass: 28073.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SIR3, CMT1, MAR2, STE8, YLR442C, L9753.10 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P06701

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Widom 601 sequence ... , 2 types, 2 molecules IJ

#5: DNA chain Widom 601 sequence reverse


Mass: 51808.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence has been selected in vitro
#6: DNA chain Widom 601 sequence forward


Mass: 51341.676 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence has been selected in vitro

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Details

Has protein modificationY

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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: 2.9 Å3/Da / Density % sol: 57.55 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 6.5
Details: 50 mM MES pH 6.5, 12% PEG 400, 12 mM MnCl2, 100 mM NaCl, 10 mM EDTA, VAPOR DIFFUSION, temperature 293.15K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96863 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 25, 2013
RadiationMonochromator: don't know. / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. all: 44335 / Num. obs: 44335 / % possible obs: 90 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3

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Processing

Software
NameVersionClassification
PHASESphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
RefinementResolution: 3.306→19.997 Å / SU ML: 0.69 / σ(F): 1.99 / Phase error: 36.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2946 2217 5 %
Rwork0.2376 --
obs0.2405 44335 97.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.306→19.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9299 5841 0 0 15140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01116181
X-RAY DIFFRACTIONf_angle_d1.59723100
X-RAY DIFFRACTIONf_dihedral_angle_d28.4926531
X-RAY DIFFRACTIONf_chiral_restr0.0932607
X-RAY DIFFRACTIONf_plane_restr0.0061926
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3062-3.37770.42571230.40722371X-RAY DIFFRACTION89
3.3777-3.45590.41611400.36672661X-RAY DIFFRACTION99
3.4559-3.54190.39571380.35922616X-RAY DIFFRACTION97
3.5419-3.63710.36061400.32922667X-RAY DIFFRACTION98
3.6371-3.74340.36241430.32822659X-RAY DIFFRACTION98
3.7434-3.86340.37691400.32092636X-RAY DIFFRACTION99
3.8634-4.00040.39051390.29842669X-RAY DIFFRACTION99
4.0004-4.15920.32391390.28242677X-RAY DIFFRACTION99
4.1592-4.34670.33521440.27022663X-RAY DIFFRACTION99
4.3467-4.57330.34581390.24382704X-RAY DIFFRACTION99
4.5733-4.8560.27921400.2312630X-RAY DIFFRACTION99
4.856-5.22470.32291400.24212682X-RAY DIFFRACTION99
5.2247-5.73920.31761370.2372653X-RAY DIFFRACTION98
5.7392-6.5440.32061410.24622663X-RAY DIFFRACTION98
6.544-8.15080.25181400.21652620X-RAY DIFFRACTION97
8.1508-19.99690.19141340.14192547X-RAY DIFFRACTION94

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