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- PDB-2ygv: Conserved N-terminal domain of the yeast Histone Chaperone Asf1 i... -

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Basic information

Entry
Database: PDB / ID: 2ygv
TitleConserved N-terminal domain of the yeast Histone Chaperone Asf1 in complex with the C-terminal fragment of Rad53
Components
  • HISTONE CHAPERONE ASF1
  • SERINE/THREONINE-PROTEIN KINASE RAD53
KeywordsCHAPERONE/TRANSFERASE / CHAPERONE-TRANSFERASE COMPLEX / CHECKPOINT / DNA DAMAGE / CHROMATIN
Function / homology
Function and homology information


deoxyribonucleoside triphosphate biosynthetic process / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / H3 histone acetyltransferase complex / meiotic recombination checkpoint signaling / acetyltransferase activator activity / DNA replication-dependent chromatin assembly / negative regulation of phosphorylation / dual-specificity kinase / nucleosome disassembly / silent mating-type cassette heterochromatin formation ...deoxyribonucleoside triphosphate biosynthetic process / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / H3 histone acetyltransferase complex / meiotic recombination checkpoint signaling / acetyltransferase activator activity / DNA replication-dependent chromatin assembly / negative regulation of phosphorylation / dual-specificity kinase / nucleosome disassembly / silent mating-type cassette heterochromatin formation / DNA replication origin binding / telomere maintenance in response to DNA damage / negative regulation of DNA damage checkpoint / DNA replication initiation / subtelomeric heterochromatin formation / regulation of DNA repair / protein serine/threonine/tyrosine kinase activity / DNA damage checkpoint signaling / positive regulation of transcription elongation by RNA polymerase II / regulation of protein phosphorylation / protein modification process / protein localization / nucleosome assembly / chromatin organization / histone binding / regulation of gene expression / protein tyrosine kinase activity / chromosome, telomeric region / protein kinase activity / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / chromatin / regulation of transcription by RNA polymerase II / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase Rad53 / Histone chaperone ASF1-like / Histone deposition protein Asf1 / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain ...Serine/threonine-protein kinase Rad53 / Histone chaperone ASF1-like / Histone deposition protein Asf1 / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase RAD53 / Histone chaperone ASF1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.94 Å
AuthorsJiao, Y. / Seeger, K. / Murciano, B. / Ledu, M.H. / Charbonnier, J.B. / Legrand, P. / Lautrette, A. / Gaubert, A. / Mousson, F. / Guerois, R. ...Jiao, Y. / Seeger, K. / Murciano, B. / Ledu, M.H. / Charbonnier, J.B. / Legrand, P. / Lautrette, A. / Gaubert, A. / Mousson, F. / Guerois, R. / Mann, C. / Ochsenbein, F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Surprising Complexity of the Asf1 Histone Chaperone-Rad53 Kinase Interaction
Authors: Jiao, Y. / Seeger, K. / Lautrette, A. / Gaubert, A. / Mousson, F. / Guerois, R. / Mann, C. / Ochsenbein, F.
History
DepositionApr 21, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2012Group: Other
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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 CHAPERONE ASF1
B: HISTONE CHAPERONE ASF1
C: HISTONE CHAPERONE ASF1
D: HISTONE CHAPERONE ASF1
E: SERINE/THREONINE-PROTEIN KINASE RAD53
F: SERINE/THREONINE-PROTEIN KINASE RAD53
G: SERINE/THREONINE-PROTEIN KINASE RAD53
H: SERINE/THREONINE-PROTEIN KINASE RAD53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,95613
Polymers81,4808
Non-polymers4765
Water30617
1
A: HISTONE CHAPERONE ASF1
E: SERINE/THREONINE-PROTEIN KINASE RAD53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4663
Polymers20,3702
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-16.7 kcal/mol
Surface area10160 Å2
MethodPISA
2
B: HISTONE CHAPERONE ASF1
F: SERINE/THREONINE-PROTEIN KINASE RAD53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5584
Polymers20,3702
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-21.7 kcal/mol
Surface area9270 Å2
MethodPISA
3
C: HISTONE CHAPERONE ASF1
G: SERINE/THREONINE-PROTEIN KINASE RAD53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4663
Polymers20,3702
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-20.2 kcal/mol
Surface area9350 Å2
MethodPISA
4
D: HISTONE CHAPERONE ASF1
H: SERINE/THREONINE-PROTEIN KINASE RAD53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4663
Polymers20,3702
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-16.2 kcal/mol
Surface area9480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.240, 98.180, 86.490
Angle α, β, γ (deg.)90.00, 132.49, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
HISTONE CHAPERONE ASF1 / ASF1 / ANTI-SILENCING FUNCTION PROTEIN 1 / YASF1


Mass: 17874.141 Da / Num. of mol.: 4 / Fragment: CONSERVED N-TERMINAL DOMAIN, RESIDUES 1-156
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: W303 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P32447
#2: Protein/peptide
SERINE/THREONINE-PROTEIN KINASE RAD53 / RAD53 / CHK2 HOMOLOG / SERINE-PROTEIN KINASE 1


Mass: 2495.872 Da / Num. of mol.: 4 / Fragment: C-TERMINAL, RESIDUES 800-821 / Source method: obtained synthetically / Source: (synth.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: P22216, non-specific serine/threonine protein kinase
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.41 Å3/Da / Density % sol: 48.88 % / Description: NONE
Crystal growpH: 6 / Details: 5% PEG 8000, 0.1M NACACO PH 6, 0.2M MG ACETATE

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.94→38.9 Å / Num. obs: 16378 / % possible obs: 98.7 % / Observed criterion σ(I): 2.36 / Redundancy: 3.96 % / Biso Wilson estimate: 61.41 Å2 / Rmerge(I) obs: 0.02 / Net I/σ(I): 10.59
Reflection shellResolution: 2.94→3.12 Å / Redundancy: 3.82 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 2.36 / % possible all: 97.5

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ROC

1roc


Resolution: 2.94→38.9 Å / Cor.coef. Fo:Fc: 0.867 / Cor.coef. Fo:Fc free: 0.8082 / Cross valid method: THROUGHOUT / σ(F): 0
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.
RfactorNum. reflection% reflectionSelection details
Rfree0.257 809 4.94 %RANDOM
Rwork0.1875 ---
obs0.1908 16377 --
Displacement parametersBiso mean: 54.12 Å2
Baniso -1Baniso -2Baniso -3
1-25.2695 Å20 Å25.2244 Å2
2---34.9154 Å20 Å2
3---9.6459 Å2
Refine analyzeLuzzati coordinate error obs: 0.367 Å
Refinement stepCycle: LAST / Resolution: 2.94→38.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5357 0 26 17 5400
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015490HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.337461HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1877SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes151HARMONIC2
X-RAY DIFFRACTIONt_gen_planes767HARMONIC5
X-RAY DIFFRACTIONt_it5490HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.2
X-RAY DIFFRACTIONt_other_torsion22.32
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion704SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5887SEMIHARMONIC4
LS refinement shellResolution: 2.94→3.14 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3298 133 4.69 %
Rwork0.2306 2704 -
all0.2352 2837 -

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