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- PDB-2io5: Crystal structure of the CIA- histone H3-H4 complex -

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Basic information

Entry
Database: PDB / ID: 2io5
TitleCrystal structure of the CIA- histone H3-H4 complex
Components
  • ASF1A protein
  • Histone H3.1
  • Histone H4
KeywordsCHAPERONE/STRUCTURAL PROTEIN / HISTONE / CHAPERONE / CHAPERONE-STRUCTURAL PROTEIN COMPLEX
Function / homology
Function and homology information


histone chaperone activity / muscle cell differentiation / DNA replication-dependent chromatin assembly / DNA repair-dependent chromatin remodeling / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / replication fork processing / osteoblast differentiation / structural constituent of chromatin / nucleosome / nucleosome assembly ...histone chaperone activity / muscle cell differentiation / DNA replication-dependent chromatin assembly / DNA repair-dependent chromatin remodeling / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / replication fork processing / osteoblast differentiation / structural constituent of chromatin / nucleosome / nucleosome assembly / site of double-strand break / histone binding / protein heterodimerization activity / DNA repair / chromatin binding / chromatin / protein-containing complex / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Histone chaperone ASF1-like / 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. / Histone H4 / Histone H4 ...Histone chaperone ASF1-like / 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. / Histone H4 / Histone H4 / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / 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 H4 / Histone H3.2 / Histone chaperone ASF1A / Histone chaperone ASF1A
Similarity search - Component
Biological speciesHomo sapiens (human)
Xenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsNatsume, R. / Akai, Y. / Horikoshi, M. / Senda, T.
CitationJournal: Nature / Year: 2007
Title: Structure and function of the histone chaperone CIA/ASF1 complexed with histones H3 and H4.
Authors: Natsume, R. / Eitoku, M. / Akai, Y. / Sano, N. / Horikoshi, M. / Senda, T.
History
DepositionOct 10, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 25, 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: ASF1A protein
B: Histone H3.1
C: Histone H4


Theoretical massNumber of molelcules
Total (without water)46,3803
Polymers46,3803
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6840 Å2
ΔGint-44 kcal/mol
Surface area15720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.361, 104.780, 86.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a hetero trimer of CIA-H3-H4 obsereved in the asymmetric unit.

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Components

#1: Protein ASF1A protein / CIA / CCG1-Interacting factor A / Anti Silencing Function 1 Homolog A


Mass: 19826.939 Da / Num. of mol.: 1 / Fragment: Residues 1-172
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: asf1a / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus -RIL / References: UniProt: Q6IA08, UniProt: Q9Y294*PLUS
#2: Protein Histone H3.1


Mass: 15289.904 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: Histone H3.1 / Plasmid: pET3d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P84233
#3: Protein Histone H4


Mass: 11263.231 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: Histone H4 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P62799

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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: 2.38 Å3/Da / Density % sol: 48.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 0.05M cadmium sulfate hydrate, 1.0M sodium acetate tryhydrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 21, 2006
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→29.19 Å / Num. all: 12485 / Num. obs: 12148 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2.5 / Redundancy: 5.4 % / Biso Wilson estimate: 51.732 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 7.1
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 1.8 / Num. measured all: 9916 / Num. unique all: 1779 / Rsym value: 0.413 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TEY, PDB ENTRY 1KX3 chain A and B

1tey

1kx3


Resolution: 2.7→29.19 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.873 / SU B: 28.822 / SU ML: 0.276 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.81 / ESU R Free: 0.377 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29331 604 5 %RANDOM
Rwork0.23761 ---
all0.245 12461 --
obs0.24041 11529 97.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.349 Å2
Baniso -1Baniso -2Baniso -3
1--2.78 Å20 Å20 Å2
2--2.49 Å20 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 2.7→29.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2474 0 0 0 2474
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222521
X-RAY DIFFRACTIONr_bond_other_d0.0010.021750
X-RAY DIFFRACTIONr_angle_refined_deg1.3261.9643415
X-RAY DIFFRACTIONr_angle_other_deg0.83534235
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7865304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.53723.2125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.87815440
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4051526
X-RAY DIFFRACTIONr_chiral_restr0.0750.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022786
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02534
X-RAY DIFFRACTIONr_nbd_refined0.2130.2467
X-RAY DIFFRACTIONr_nbd_other0.1950.21668
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21180
X-RAY DIFFRACTIONr_nbtor_other0.0850.21536
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0970.239
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2420.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9311.51987
X-RAY DIFFRACTIONr_mcbond_other0.0871.5612
X-RAY DIFFRACTIONr_mcangle_it1.01222492
X-RAY DIFFRACTIONr_scbond_it1.18331141
X-RAY DIFFRACTIONr_scangle_it1.8444.5923
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.452 50 -
Rwork0.305 859 -
obs-909 100 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0643-0.7037-0.01432.79440.30351.1081-0.0716-0.05130.0329-0.05890.04540.0685-0.0528-0.02650.0261-0.0113-0.0162-0.03820.024-0.0087-0.0325-13.4446-33.090910.9294
23.42640.9699-1.13551.5922-1.17131.89750.05260.08930.1849-0.0761-0.00660.06920.0186-0.0127-0.0460.0311-0.01470.0646-0.0567-0.04490.01169.9025-25.80792.2475
32.34940.5351-0.68690.56510.24991.46660.0220.33850.3174-0.0776-0.0235-0.0792-0.08-0.13640.00160.04160.00590.03570.03980.0254-0.02029.0995-22.58361.6137
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1544 - 157
2X-RAY DIFFRACTION2BB60 - 13560 - 135
3X-RAY DIFFRACTION3CC24 - 10024 - 100

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