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- PDB-2dze: Crystal structure of histone chaperone Asf1 in complex with a C-t... -

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Basic information

Entry
Database: PDB / ID: 2dze
TitleCrystal structure of histone chaperone Asf1 in complex with a C-terminus of histone H3
Components
  • 10-mer peptide from Histone H3.1/H3.2
  • Histone chaperone cia1
KeywordsCHAPERONE / Immunoglobulin fold / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / Oxidative Stress Induced Senescence / Factors involved in megakaryocyte development and platelet production / Estrogen-dependent gene expression / RNA Polymerase I Promoter Escape / nucleolar peripheral inclusion body / subtelomeric heterochromatin ...Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / Oxidative Stress Induced Senescence / Factors involved in megakaryocyte development and platelet production / Estrogen-dependent gene expression / RNA Polymerase I Promoter Escape / nucleolar peripheral inclusion body / subtelomeric heterochromatin / Transcriptional regulation by small RNAs / mating-type region heterochromatin / heterochromatin boundary formation / H3-H4 histone complex chaperone activity / mitotic sister chromatid biorientation / histone chaperone activity / pericentric heterochromatin formation / DNA replication-dependent chromatin assembly / chromatin-protein adaptor activity / nucleosome disassembly / pericentric heterochromatin / heterochromatin / transcription initiation-coupled chromatin remodeling / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / chromatin organization / histone binding / protein heterodimerization activity / DNA damage response / chromatin / DNA binding / nucleus
Similarity search - Function
Histone chaperone ASF1-like / Histone deposition protein Asf1 / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 ...Histone chaperone ASF1-like / Histone deposition protein Asf1 / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Histone chaperone cia1 / Histone H3.1/H3.2
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPadmanabhan, B. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of histone chaperone Asf1 in complex with a C-terminus of histone H3
Authors: Padmanabhan, B. / Yokoyama, S.
History
DepositionSep 28, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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

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Assembly

Deposited unit
A: Histone chaperone cia1
B: Histone chaperone cia1
X: 10-mer peptide from Histone H3.1/H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2875
Polymers37,9863
Non-polymers3002
Water3,945219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.155, 52.130, 60.654
Angle α, β, γ (deg.)107.35, 105.94, 93.95
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILELYSLYSAA3 - 353 - 35
21ILEILELYSLYSBB3 - 353 - 35
32LEULEUILEILEAA42 - 5642 - 56
42LEULEUILEILEBB42 - 5642 - 56
53ILEILEPHEPHEAA67 - 7267 - 72
63ILEILEPHEPHEBB67 - 7267 - 72
74PROPROASNASNAA79 - 15679 - 156
84PROPROASNASNBB79 - 15679 - 156

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Components

#1: Protein Histone chaperone cia1 / spCia1/Asf1


Mass: 18347.934 Da / Num. of mol.: 2 / Fragment: N-termianl region, residues 1-162
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: cia1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: O74515
#2: Protein/peptide 10-mer peptide from Histone H3.1/H3.2


Mass: 1290.582 Da / Num. of mol.: 1 / Fragment: C-terminal H3 peptide / Source method: obtained synthetically / Details: Synthetic peptide / References: UniProt: P09988
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 3.02 Å3/Da / Density % sol: 59.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG6000, AS, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 14, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 41187 / Num. obs: 38738 / % possible obs: 94.1 % / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Rmerge(I) obs: 0.056
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2 % / Rmerge(I) obs: 0.191 / Num. unique all: 3746 / % possible all: 91.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
BL26B1Beamline softwaredata collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 2CU9

2cu9


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.63 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24352 1956 5 %RANDOM
Rwork0.21364 ---
obs0.21514 36782 93.8 %-
all-39213 --
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: 27.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å2-0.27 Å2-0.28 Å2
2---0.69 Å2-1.66 Å2
3----1.03 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2619 0 20 219 2858
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222690
X-RAY DIFFRACTIONr_angle_refined_deg1.751.9753652
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3885323
X-RAY DIFFRACTIONr_chiral_restr0.1360.2422
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022005
X-RAY DIFFRACTIONr_nbd_refined0.2050.21008
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2187
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.226
X-RAY DIFFRACTIONr_mcbond_it1.2181.51635
X-RAY DIFFRACTIONr_mcangle_it2.12622675
X-RAY DIFFRACTIONr_scbond_it3.25331055
X-RAY DIFFRACTIONr_scangle_it5.3044.5977
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
528medium positional0.080.5
529loose positional0.235
528medium thermal0.782
529loose thermal1.3110
LS refinement shellResolution: 1.799→1.846 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.3 145
Rwork0.265 2501

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