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- PDB-5bsa: Structure of histone H3/H4 in complex with Spt2 -

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Basic information

Entry
Database: PDB / ID: 5bsa
TitleStructure of histone H3/H4 in complex with Spt2
Components
  • Histone H3.2
  • Histone H4
  • Protein SPT2 homolog
KeywordsTRANSCRIPTION REGULATOR / chaperone / transcription
Function / homology
Function and homology information


histone chaperone activity / RNA polymerase I core binding / transcription by RNA polymerase I / heterochromatin formation / structural constituent of chromatin / nucleosome / nucleosome assembly / histone binding / protein heterodimerization activity / regulation of DNA-templated transcription ...histone chaperone activity / RNA polymerase I core binding / transcription by RNA polymerase I / heterochromatin formation / structural constituent of chromatin / nucleosome / nucleosome assembly / histone binding / protein heterodimerization activity / regulation of DNA-templated transcription / nucleolus / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Chromatin SPT2 / SPT2 chromatin protein / SPT2 N-terminal domain / SPT2 chromatin protein / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold ...Chromatin SPT2 / SPT2 chromatin protein / SPT2 N-terminal domain / SPT2 chromatin protein / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / 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
Similarity search - Domain/homology
Histone H4 / Histone H3.2 / Protein SPT2 homolog
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.611 Å
AuthorsChen, S. / Patel, D.J.
CitationJournal: Genes Dev. / Year: 2015
Title: Structure-function studies of histone H3/H4 tetramer maintenance during transcription by chaperone Spt2.
Authors: Chen, S. / Rufiange, A. / Huang, H. / Rajashankar, K.R. / Nourani, A. / Patel, D.J.
History
DepositionJun 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Sep 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H3.2
B: Histone H3.2
C: Histone H4
D: Histone H4
E: Protein SPT2 homolog
F: Protein SPT2 homolog


Theoretical massNumber of molelcules
Total (without water)77,1766
Polymers77,1766
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11420 Å2
ΔGint-97 kcal/mol
Surface area21250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.351, 128.351, 116.814
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein Histone H3.2


Mass: 12673.827 Da / Num. of mol.: 2 / Fragment: residues 27-136
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P84233
#2: Protein Histone H4


Mass: 11263.231 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799
#3: Protein Protein SPT2 homolog / Protein KU002155 / SPT2 domain-containing protein 1


Mass: 14651.086 Da / Num. of mol.: 2 / Fragment: residues 571-685
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPTY2D1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q68D10

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 0.02 M NaCl, 0.2 M HEPES 7.5, 1.6 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 4.6→50 Å / Num. obs: 5704 / % possible obs: 98.7 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 22.3
Reflection shellResolution: 4.6→4.68 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 1.3 / % possible all: 88.6

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data scaling
SHELXDEphasing
PHASERphasing
MOLREPphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AOI

1aoi


Resolution: 4.611→49.115 Å / SU ML: 0.89 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 38.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3289 375 4.68 %
Rwork0.2387 --
obs0.243 8005 77.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.611→49.115 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2733 0 0 0 2733
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132763
X-RAY DIFFRACTIONf_angle_d1.9723721
X-RAY DIFFRACTIONf_dihedral_angle_d18.053967
X-RAY DIFFRACTIONf_chiral_restr0.073443
X-RAY DIFFRACTIONf_plane_restr0.007483
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.6108-5.27730.3873710.28311363X-RAY DIFFRACTION42
5.2773-6.64620.38411390.31253004X-RAY DIFFRACTION92
6.6462-49.1180.27421650.18583263X-RAY DIFFRACTION100

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