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- PDB-2i32: Structure of a human ASF1a-HIRA complex and insights into specifi... -

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Basic information

Entry
Database: PDB / ID: 2i32
TitleStructure of a human ASF1a-HIRA complex and insights into specificity of histone chaperone complex assembly
Components
  • Anti-Silencing Factor 1 paralog a
  • Histone Regulatory homolog A
KeywordsREPLICATION CHAPERONE / Histone Deposition / Chromatin Regulation / Histone Chaperones / ASF1 / HIRA / CAF-1
Function / homology
Function and homology information


HIR complex / muscle cell differentiation / histone chaperone activity / DNA replication-dependent chromatin assembly / DNA repair-dependent chromatin remodeling / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / replication fork processing / gastrulation / anatomical structure morphogenesis / Replacement of protamines by nucleosomes in the male pronucleus ...HIR complex / muscle cell differentiation / histone chaperone activity / DNA replication-dependent chromatin assembly / DNA repair-dependent chromatin remodeling / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / replication fork processing / gastrulation / anatomical structure morphogenesis / Replacement of protamines by nucleosomes in the male pronucleus / PML body / osteoblast differentiation / nucleosome assembly / transcription corepressor activity / site of double-strand break / histone binding / RNA polymerase II-specific DNA-binding transcription factor binding / chromatin remodeling / DNA repair / DNA-templated transcription / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / protein-containing complex / extracellular exosome / nucleoplasm / nucleus
Similarity search - Function
TUP1-like enhancer of split / WD repeat HIR1 / TUP1-like enhancer of split / Histone chaperone ASF1-like / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats ...TUP1-like enhancer of split / WD repeat HIR1 / TUP1-like enhancer of split / Histone chaperone ASF1-like / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / 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
Protein HIRA / Histone chaperone ASF1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMarmorstein, R. / Tang, Y.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Structure of a human ASF1a-HIRA complex and insights into specificity of histone chaperone complex assembly.
Authors: Tang, Y. / Poustovoitov, M.V. / Zhao, K. / Garfinkel, M. / Canutescu, A. / Dunbrack, R. / Adams, P.D. / Marmorstein, R.
History
DepositionAug 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Anti-Silencing Factor 1 paralog a
B: Anti-Silencing Factor 1 paralog a
E: Histone Regulatory homolog A
F: Histone Regulatory homolog A


Theoretical massNumber of molelcules
Total (without water)54,1064
Polymers54,1064
Non-polymers00
Water2,342130
1
A: Anti-Silencing Factor 1 paralog a
E: Histone Regulatory homolog A


Theoretical massNumber of molelcules
Total (without water)27,0532
Polymers27,0532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-4 kcal/mol
Surface area9290 Å2
MethodPISA
2
B: Anti-Silencing Factor 1 paralog a
F: Histone Regulatory homolog A


Theoretical massNumber of molelcules
Total (without water)27,0532
Polymers27,0532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.226, 116.226, 167.599
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Anti-Silencing Factor 1 paralog a / ASF1a protein / ASF1 anti-silencing function 1 homolog A / Hypothetical protein FLJ22085 / Anti- ...ASF1a protein / ASF1 anti-silencing function 1 homolog A / Hypothetical protein FLJ22085 / Anti-silencing function 1A / CGI-98 protein / CIA


Mass: 20837.066 Da / Num. of mol.: 2 / Fragment: Residues 1-157
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASF1A, DKFZp564E2182 / Plasmid: modified pET_Duet (Novagen) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21_Gold (DE3) / References: UniProt: Q9Y294
#2: Protein Histone Regulatory homolog A / HIRA protein / TUP1-like enhancer of split protein 1


Mass: 6215.963 Da / Num. of mol.: 2 / Fragment: Residues 425-472
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIRA, DGCR1, HIR, TUPLE1 / Plasmid: modified pCDF_Duet vector (Novagen) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21_Gold(DE3) / References: UniProt: P54198
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 59.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: CRYSTALS OF THE HUMAN ASF1AN-HIRA(425-472) COMPLEX WERE GROWN BY HANGING DROP VAPOR DIFFUSION AT ROOM TEMPERATURE AND WERE OBTAINED BY MIXING 2 UL OF A 0.5 MM PROTEIN COMPLEX SOLUTION (IN 20 ...Details: CRYSTALS OF THE HUMAN ASF1AN-HIRA(425-472) COMPLEX WERE GROWN BY HANGING DROP VAPOR DIFFUSION AT ROOM TEMPERATURE AND WERE OBTAINED BY MIXING 2 UL OF A 0.5 MM PROTEIN COMPLEX SOLUTION (IN 20 MM HEPES PH 7.0, 150 MM NACL AND 5 MM BETA-ME) WITH 2 UL OF RESERVOIR SOLUTION CONTAINING 1.44 M NAH2PO4 AND 0.16 M K2HPO4 AT PH 5.6, AND EQUILIBRATING OVER 1.0 ML OF RESERVOIR SOLUTION. CRYSTALS WERE FULLY GROWN WITHIN TWO WEEKS TO A TYPICAL SIZE OF 0.3MMX0.3MMX0.2MM, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298.0K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 1, 2005 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionAv σ(I) over netI: 12.8 / Number: 200485 / Rmerge(I) obs: 0.058 / Χ2: 1.01 / D res high: 2.5 Å / D res low: 50 Å / Num. obs: 23857 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
5.385099.810.0251.007
4.275.3810010.0280.994
3.734.2710010.0391
3.393.7310010.061.014
3.153.3910010.0911.009
2.963.1510010.1510.996
2.822.9610010.2680.983
2.692.8210010.3851.021
2.592.6910010.5891.045
2.52.5999.610.6411.014
ReflectionResolution: 2.5→50 Å / Num. obs: 43841 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.5 / Rmerge(I) obs: 0.058 / Χ2: 1.008 / Net I/σ(I): 12.8
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.641 / Num. unique all: 2322 / Χ2: 1.014 / % possible all: 99.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ROC

1roc


Resolution: 2.7→25 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1813 9.6 %RANDOM
Rwork0.229 ---
all-19106 --
obs-43841 95.7 %-
Solvent computationBsol: 41.493 Å2
Displacement parametersBiso mean: 52.923 Å2
Baniso -1Baniso -2Baniso -3
1--8.451 Å2-8.556 Å20 Å2
2---8.451 Å20 Å2
3---16.901 Å2
Refinement stepCycle: LAST / Resolution: 2.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2780 0 0 130 2910
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.421
X-RAY DIFFRACTIONc_mcbond_it1.4641.5
X-RAY DIFFRACTIONc_scbond_it2.1332
X-RAY DIFFRACTIONc_mcangle_it2.5612
X-RAY DIFFRACTIONc_scangle_it3.2752.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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