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- PDB-2z3f: Crystal structure of spCia1/Asf1 complexed with Cac2 peptide -

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Basic information

Entry
Database: PDB / ID: 2z3f
TitleCrystal structure of spCia1/Asf1 complexed with Cac2 peptide
Components
  • Histone chaperone cia1
  • SPAC26H5.03 protein
KeywordsCHAPERONE / Histone chaperone / nucleosome diassembly/assembly / chromatin regulation / Chromatin regulator / Coiled coil / Nucleus / Transcription / Transcription regulation / 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


H3-H4 histone complex chaperone activity / mitotic recombination-dependent replication fork processing / CAF-1 complex / histone chaperone activity / DNA replication-dependent chromatin assembly / nucleosome disassembly / nuclear replication fork / nucleosome assembly / chromatin organization / histone binding ...H3-H4 histone complex chaperone activity / mitotic recombination-dependent replication fork processing / CAF-1 complex / histone chaperone activity / DNA replication-dependent chromatin assembly / nucleosome disassembly / nuclear replication fork / nucleosome assembly / chromatin organization / histone binding / chromatin remodeling / chromatin / nucleus / cytosol
Similarity search - Function
Histone deposition protein Asf1 / Histone chaperone ASF1-like / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / : / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / WD domain, G-beta repeat / WD40 repeats ...Histone deposition protein Asf1 / Histone chaperone ASF1-like / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / : / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / 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
Uncharacterized WD repeat-containing protein C26H5.03 / Histone chaperone cia1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 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
DepositionJun 4, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 9, 2018Group: Data collection / Derived calculations / Source and taxonomy
Category: pdbx_entity_src_syn / pdbx_struct_assembly ...pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_biol
Item: _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.3Nov 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 / struct_ncs_dom_lim
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone chaperone cia1
I: SPAC26H5.03 protein
B: Histone chaperone cia1
J: SPAC26H5.03 protein
C: Histone chaperone cia1
K: SPAC26H5.03 protein
D: Histone chaperone cia1
L: SPAC26H5.03 protein
E: Histone chaperone cia1
M: SPAC26H5.03 protein
F: Histone chaperone cia1
N: SPAC26H5.03 protein
G: Histone chaperone cia1
O: SPAC26H5.03 protein
H: Histone chaperone cia1
P: SPAC26H5.03 protein
Q: SPAC26H5.03 protein
R: SPAC26H5.03 protein
T: SPAC26H5.03 protein


Theoretical massNumber of molelcules
Total (without water)171,82719
Polymers171,82719
Non-polymers00
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24150 Å2
ΔGint-129 kcal/mol
Surface area62760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.512, 151.512, 144.206
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21F
12B
22E
13C
23D
14G
24H

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: TRP / End label comp-ID: TRP / Refine code: 1 / Auth seq-ID: 3 - 159 / Label seq-ID: 3 - 159

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21FK
12BC
22EI
13CE
23DG
14GM
24HO

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein
Histone chaperone cia1 / Anti-silencing function protein 1 / Cia1/Asf1


Mass: 18347.934 Da / Num. of mol.: 8 / Fragment: Cia1/Asf1 N-terminal domain, residues 1-162
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
SPAC26H5.03 protein / Cac2


Mass: 2276.719 Da / Num. of mol.: 11 / Fragment: cac2 C-terminal domain, residues 493-512 / Source method: obtained synthetically / Source: (synth.) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O13985
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 48.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.8M Na/K phosphate pH 8.0, 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: Sep 1, 2006 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 50157 / Num. obs: 50092 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Rmerge(I) obs: 0.072
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 6 % / Rmerge(I) obs: 0.48 / Num. unique all: 5054 / % possible all: 100

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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: PDB ENTRY 2CU9

2cu9


Resolution: 2.7→31.6 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.888 / SU B: 12.854 / SU ML: 0.259 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26319 2252 5.1 %RANDOM
Rwork0.20829 ---
obs0.21103 42342 99.84 %-
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: 38.992 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å20 Å20 Å2
2---0.96 Å20 Å2
3---1.93 Å2
Refinement stepCycle: LAST / Resolution: 2.7→31.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10996 0 0 312 11308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.02211240
X-RAY DIFFRACTIONr_bond_other_d0.0030.0210264
X-RAY DIFFRACTIONr_angle_refined_deg1.7491.97315321
X-RAY DIFFRACTIONr_angle_other_deg1.011324032
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.49951351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0970.21776
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212223
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022045
X-RAY DIFFRACTIONr_nbd_refined0.190.21831
X-RAY DIFFRACTIONr_nbd_other0.2460.211273
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.090.26852
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2406
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2690.2105
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2460.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9491.56899
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.766211328
X-RAY DIFFRACTIONr_scbond_it1.94734341
X-RAY DIFFRACTIONr_scangle_it3.3864.53993
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2441tight positional0.060.05
2B2442tight positional0.060.05
3C2442tight positional0.050.05
4G2442tight positional0.050.05
1A2441tight thermal0.160.5
2B2442tight thermal0.130.5
3C2442tight thermal0.130.5
4G2442tight thermal0.150.5
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.344 149
Rwork0.267 3136

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