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- PDB-2z34: Crystal structure of SpCia1/Asf1 complex with Hip1 -

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Basic information

Entry
Database: PDB / ID: 2z34
TitleCrystal structure of SpCia1/Asf1 complex with Hip1
Components
  • Histone chaperone cia1
  • Protein hir1
KeywordsCHAPERONE / histone chaperone / nucleosome disassmebly/assembly / chromatin regulation / Chromatin regulator / Coiled coil / Nucleus / Transcription / Transcription regulation / Cytoplasm / Repressor / WD repeat / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


HIR complex / : / chromatin organization => GO:0006325 / H3-H4 histone complex chaperone activity / histone chaperone activity / chromatin => GO:0000785 / nucleosome organization / DNA replication-dependent chromatin assembly / nucleosome disassembly / mitotic sister chromatid segregation ...HIR complex / : / chromatin organization => GO:0006325 / H3-H4 histone complex chaperone activity / histone chaperone activity / chromatin => GO:0000785 / nucleosome organization / DNA replication-dependent chromatin assembly / nucleosome disassembly / mitotic sister chromatid segregation / nucleosome assembly / transcription corepressor activity / chromatin organization / histone binding / chromatin remodeling / DNA-templated transcription / chromatin / nucleus / cytosol
Similarity search - Function
HIRA B motif / HIRA B motif / TUP1-like enhancer of split / WD repeat HIR1 / TUP1-like enhancer of split / Histone deposition protein Asf1 / Histone chaperone ASF1-like / WD40-like beta propeller / WD40-like Beta Propeller Repeat / Histone chaperone ASF1-like ...HIRA B motif / HIRA B motif / TUP1-like enhancer of split / WD repeat HIR1 / TUP1-like enhancer of split / Histone deposition protein Asf1 / Histone chaperone ASF1-like / WD40-like beta propeller / WD40-like Beta Propeller Repeat / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / : / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Histone chaperone cia1 / Protein hir1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMalay, A.D. / Padmanabhan, B. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Crystal structures of fission yeast histone chaperone Asf1 complexed with the Hip1 B-domain or the Cac2 C terminus
Authors: Malay, A.D. / Umehara, T. / Matsubara-Malay, K. / Padmanabhan, B. / Yokoyama, S.
History
DepositionMay 31, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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

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Assembly

Deposited unit
A: Histone chaperone cia1
B: Histone chaperone cia1
C: Protein hir1
D: Protein hir1


Theoretical massNumber of molelcules
Total (without water)43,1024
Polymers43,1024
Non-polymers00
Water2,324129
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-28.9 kcal/mol
Surface area18390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.013, 48.086, 63.247
Angle α, β, γ (deg.)90.00, 99.25, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN

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Components

#1: Protein Histone chaperone cia1 / SpCia1/Asf1 / Anti-silencing function protein 1


Mass: 18347.934 Da / Num. of mol.: 2 / Fragment: N-terminal region 1-161
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: cia1, asf1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: O74515
#2: Protein/peptide Protein hir1 / Hip1 / Histone transcription regulator 1 homolog


Mass: 3202.869 Da / Num. of mol.: 2 / Fragment: Hip1 B domain peptide / Source method: obtained synthetically
Details: Synthetic peptide: The sequence corresponding to 469-497 in HIR1_SCHPO
References: UniProt: P87314
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.16 Å3/Da / Density % sol: 43.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 25% PEG3350, 0.18M Ammonium Fluoride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 15, 2006 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 16590 / Num. obs: 16188 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.062
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.237 / Num. unique all: 1621 / % possible all: 98.7

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Processing

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

2cu9


Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.891 / SU B: 8.425 / SU ML: 0.199 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.59 / ESU R Free: 0.29 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25408 736 5.2 %RANDOM
Rwork0.19445 ---
obs0.19756 13543 97.56 %-
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: 29.602 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å20 Å2-1.12 Å2
2---0.48 Å20 Å2
3---0.77 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2778 0 0 129 2907
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222830
X-RAY DIFFRACTIONr_bond_other_d0.0020.022636
X-RAY DIFFRACTIONr_angle_refined_deg1.7391.9743845
X-RAY DIFFRACTIONr_angle_other_deg0.8736172
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1045341
X-RAY DIFFRACTIONr_chiral_restr0.1020.2458
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023023
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02509
X-RAY DIFFRACTIONr_nbd_refined0.2050.2460
X-RAY DIFFRACTIONr_nbd_other0.2440.23035
X-RAY DIFFRACTIONr_nbtor_other0.0890.21806
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2148
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.231
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2440.2115
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.210
X-RAY DIFFRACTIONr_mcbond_it0.9811.51736
X-RAY DIFFRACTIONr_mcangle_it1.79422852
X-RAY DIFFRACTIONr_scbond_it2.34231094
X-RAY DIFFRACTIONr_scangle_it3.8674.5993
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.439 56
Rwork0.245 1020

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