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- PDB-2idc: Structure of the Histone H3-Asf1 Chaperone Interaction -

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Basic information

Entry
Database: PDB / ID: 2idc
TitleStructure of the Histone H3-Asf1 Chaperone Interaction
ComponentsANTI-SILENCING PROTEIN 1 AND HISTONE H3 CHIMERA
KeywordsReplication/Chaperone / Ig-like fold / Asf1 / H3 / histone / chaperone / chromatin / Replication-Chaperone COMPLEX
Function / homology
Function and homology information


Formation of Senescence-Associated Heterochromatin Foci (SAHF) / CENP-A containing nucleosome / H3 histone acetyltransferase complex / global genome nucleotide-excision repair / sexual sporulation resulting in formation of a cellular spore / histone H2B ubiquitination / : / regulation of transcription from RNA polymerase II promoter in response to stress / histone H3-K56 acetylation / histone exchange ...Formation of Senescence-Associated Heterochromatin Foci (SAHF) / CENP-A containing nucleosome / H3 histone acetyltransferase complex / global genome nucleotide-excision repair / sexual sporulation resulting in formation of a cellular spore / histone H2B ubiquitination / : / regulation of transcription from RNA polymerase II promoter in response to stress / histone H3-K56 acetylation / histone exchange / acetyltransferase activator activity / nucleosome disassembly / chromatin assembly or disassembly / replication fork protection complex / silent mating-type cassette heterochromatin assembly / subtelomeric heterochromatin assembly => GO:0031509 / rRNA transcription / DNA replication-independent chromatin assembly / histone acetylation / DNA replication-dependent chromatin assembly / positive regulation of histone acetylation / positive regulation of transcription elongation from RNA polymerase II promoter / regulation of protein phosphorylation / nucleosome / regulation of gene expression / histone binding / chromosome, telomeric region / protein heterodimerization activity / DNA binding / nucleus / cytosol
Similarity search - Function
Histone chaperone ASF1-like / Histone deposition protein Asf1 / ASF1 like histone chaperone / Histone chaperone ASF1-like superfamily / Histone chaperone ASF1-like / 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 / ASF1 like histone chaperone / Histone chaperone ASF1-like superfamily / Histone chaperone ASF1-like / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Histone chaperone ASF1 / Histone H3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsAntczak, A.J. / Tsubota, T. / Kaufman, P.D. / Berger, J.M.
CitationJournal: Bmc Struct.Biol. / Year: 2006
Title: Structure of the yeast histone H3-ASF1 interaction: implications for chaperone mechanism, species-specific interactions, and epigenetics.
Authors: Antczak, A.J. / Tsubota, T. / Kaufman, P.D. / Berger, J.M.
History
DepositionSep 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jun 14, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _struct_ref.pdbx_align_begin ..._entity.pdbx_description / _struct_ref.pdbx_align_begin / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_seq_num
Remark 999SEQUENCE The yeast ASF1 gene was genetically modified in a pET28b (novagen) derivative plasmid that ...SEQUENCE The yeast ASF1 gene was genetically modified in a pET28b (novagen) derivative plasmid that contains a hepta-his tag, Maltose Binding Protein tag, and is tethered to Asf1 via a TEV protease cleavable linker. Ala A 1 is therefore a reminant of the TEV cleavage reaction. Ala A 156 and Ala A 157 are part of an Ala/Gly/Thr linker which connects Asf1 and H3, however, no density was seen for the other six residues in this linker region.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ANTI-SILENCING PROTEIN 1 AND HISTONE H3 CHIMERA


Theoretical massNumber of molelcules
Total (without water)20,0851
Polymers20,0851
Non-polymers00
Water1,63991
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)44.431, 52.094, 86.676
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ANTI-SILENCING PROTEIN 1 AND HISTONE H3 CHIMERA / Histone chaperone ASF1 / Anti-silencing function protein 1 / yASF1


Mass: 20084.734 Da / Num. of mol.: 1 / Fragment: Asf1, residues 2-155 and H3, residues 121-134
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Strain: ATCC 204508 / S288c
Gene: ASF1, CIA1, YJL115W, J0755, HHT1, YBR010W, YBR0201, HHT2, SIN2, YNL031C, N2749
Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P32447, UniProt: P61830
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.5 Å3/Da / Density % sol: 50.72 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Tris-HCl, Li2SO4, PEG 4000, glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 30, 2005
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.1→44.687 Å / Num. all: 12061 / Num. obs: 12061 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 9.1
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2 / Rsym value: 0.362 / % possible all: 98.8

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.25 Å44.65 Å
Translation2.25 Å44.65 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
Blu-Icedata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1ROC
Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.92 / SU B: 10.866 / SU ML: 0.141 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.252 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2394 500 4.8 %RANDOM
Rwork0.194 ---
obs0.19605 9995 98.02 %-
all-10495 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 56.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20 Å20 Å2
2---1.47 Å20 Å2
3---0.5 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1338 0 0 91 1429
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221366
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6141.9741857
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6585165
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.83724.15465
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.10615234
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.551510
X-RAY DIFFRACTIONr_chiral_restr0.1260.2213
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021033
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.2523
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.2924
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2101
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.227
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2820.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1491.5862
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.78121366
X-RAY DIFFRACTIONr_scbond_it2.4973572
X-RAY DIFFRACTIONr_scangle_it3.764.5491
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 42 -
Rwork0.257 720 -
obs--98.58 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.13080.35120.73761.42590.42433.5815-0.0520.0306-0.0183-0.33190.0960.1188-0.03960.1047-0.0440.00540.0106-0.0348-0.11370.0096-0.01932.612910.944422.7905
225.0552-7.4913-3.816114.95228.14245.7095-0.2738-0.31661.0752-0.35660.1851.6197-1.036-3.49290.0888-0.0002-0.0020.0013-0.00030.00020-11.352516.673220.9251
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
111 - 873 - 89
2188 - 15790 - 159
32165 - 169167 - 171
42170 - 174172 - 176

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