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- PDB-2hue: Structure of the H3-H4 chaperone Asf1 bound to histones H3 and H4 -

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Basic information

Entry
Database: PDB / ID: 2hue
TitleStructure of the H3-H4 chaperone Asf1 bound to histones H3 and H4
Components
  • Anti-silencing protein 1
  • Histone H3
  • Histone H4
KeywordsDNA BINDING PROTEIN / mini beta sheet / elongated Beta sandwhich
Function / homology
Function and homology information


Formation of Senescence-Associated Heterochromatin Foci (SAHF) / H3 histone acetyltransferase complex / acetyltransferase activator activity / DNA replication-dependent chromatin assembly / nucleosome disassembly / silent mating-type cassette heterochromatin formation / negative regulation of DNA damage checkpoint / subtelomeric heterochromatin formation / regulation of DNA repair / positive regulation of transcription elongation by RNA polymerase II ...Formation of Senescence-Associated Heterochromatin Foci (SAHF) / H3 histone acetyltransferase complex / acetyltransferase activator activity / DNA replication-dependent chromatin assembly / nucleosome disassembly / silent mating-type cassette heterochromatin formation / negative regulation of DNA damage checkpoint / subtelomeric heterochromatin formation / regulation of DNA repair / positive regulation of transcription elongation by RNA polymerase II / regulation of protein phosphorylation / protein modification process / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / histone binding / regulation of gene expression / chromosome, telomeric region / protein heterodimerization activity / chromatin / regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytosol
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, subunit A / Histone, subunit A / Histone H4, conserved site / Histone H4 signature. / TATA box binding protein associated factor ...Histone chaperone ASF1-like / Histone deposition protein Asf1 / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / Histone, subunit A / Histone, subunit A / Histone H4, conserved site / Histone H4 signature. / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / 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 / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Histone chaperone ASF1 / Histone H4 / Histone H3.2 / Histone H3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Xenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsEnglish, C.M. / Churchill, M.E.A. / Tyler, J.K.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2006
Title: Structural basis for the histone chaperone activity of asf1.
Authors: English, C.M. / Adkins, M.W. / Carson, J.J. / Churchill, M.E. / Tyler, J.K.
History
DepositionJul 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE An Ala at position 102 agrees with the database reference GB P84233

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Structure visualization

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Assembly

Deposited unit
A: Anti-silencing protein 1
B: Histone H3
C: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5348
Polymers38,0933
Non-polymers4425
Water6,612367
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8100 Å2
ΔGint-85 kcal/mol
Surface area16220 Å2
MethodPISA
2
A: Anti-silencing protein 1
B: Histone H3
C: Histone H4
hetero molecules

A: Anti-silencing protein 1
B: Histone H3
C: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,06916
Polymers76,1856
Non-polymers88310
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area16770 Å2
ΔGint-271 kcal/mol
Surface area32060 Å2
MethodPISA
3
C: Histone H4
hetero molecules

C: Histone H4
hetero molecules

A: Anti-silencing protein 1
B: Histone H3
hetero molecules

A: Anti-silencing protein 1
B: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,06916
Polymers76,1856
Non-polymers88310
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation2_564-y,x-y+1,z-2/31
crystal symmetry operation6_445-x-1,-x+y-1,-z+1/31
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area7640 Å2
ΔGint-185 kcal/mol
Surface area41190 Å2
MethodPISA
4
A: Anti-silencing protein 1
hetero molecules

A: Anti-silencing protein 1
hetero molecules

B: Histone H3
C: Histone H4
hetero molecules

B: Histone H3
C: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,06916
Polymers76,1856
Non-polymers88310
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation3_455-x+y-1,-x,z+2/31
crystal symmetry operation6_455-x-1,-x+y,-z+1/31
identity operation1_555x,y,z1
crystal symmetry operation4_466y-1,x+1,-z+11
Buried area13930 Å2
ΔGint-233 kcal/mol
Surface area34900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.749, 95.749, 110.676
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-672-

HOH

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein Anti-silencing protein 1


Mass: 19663.973 Da / Num. of mol.: 1 / Fragment: residues 2-169
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ASF1 / Plasmid: PST39 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 PLys S / References: UniProt: P32447
#2: Protein Histone H3


Mass: 8888.460 Da / Num. of mol.: 1 / Fragment: residues 62-136 / Mutation: G103A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: H3l / Plasmid: PST39 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 Plys S / References: UniProt: Q92133, UniProt: P84233*PLUS
#3: Protein Histone H4


Mass: 9540.251 Da / Num. of mol.: 1 / Fragment: residues 20-102
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: PST39 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 Plys S / References: UniProt: P62799

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Non-polymers , 4 types, 372 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 3.9 Å3/Da / Density % sol: 68.44 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M potassium sulfate, 0.1M Tris-HCl, 14.5% PEG 4K, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.000, 1.23
DetectorType: NOIR-1 / Detector: CCD / Date: Sep 30, 2005
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.231
ReflectionResolution: 1.7→12 Å / Num. obs: 61200

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Processing

Software
NameClassification
PHASERphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→11.98 Å /
RfactorNum. reflection
Rfree0.239 -
Rwork0.209 -
obs-61200
Refinement stepCycle: LAST / Resolution: 1.7→11.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2560 0 23 367 2950
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.015
X-RAY DIFFRACTIONr_angle_refined_deg1.556
X-RAY DIFFRACTIONr_chiral_restr0.113
X-RAY DIFFRACTIONr_nbd_refined0.259
X-RAY DIFFRACTIONr_nbtor_refined0.317

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