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- PDB-5bs7: Structure of histone H3/H4 in complex with Spt2 -

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Basic information

Entry
Database: PDB / ID: 5bs7
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 / structural constituent of chromatin / nucleosome / heterochromatin formation / 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 / structural constituent of chromatin / nucleosome / heterochromatin formation / 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, subunit A / Histone, subunit A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site ...Chromatin SPT2 / : / SPT2 chromatin protein / SPT2 N-terminal domain / SPT2 chromatin protein / Histone, subunit A / Histone, subunit A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / 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 domain / Histone-fold / Orthogonal Bundle / Mainly Alpha
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: 3.3 Å
AuthorsChen, S. / Patel, D.J.
Funding support United States, 4items
OrganizationGrant numberCountry
Leukemia & Lymphoma SocietyLLS-SCOR 7132-08 United States
STARR Foundation grantI5-A554 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41 GM103403 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10 RR029205 United States
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 1.1Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / 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_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8167
Polymers76,7206
Non-polymers961
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12210 Å2
ΔGint-126 kcal/mol
Surface area20750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.205, 121.205, 118.503
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11C-301-

HOH

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Components

#1: Protein Histone H3.2


Mass: 12744.906 Da / Num. of mol.: 2 / Fragment: residues 26-136
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: 14351.676 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
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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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, 1.5 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 3.3→121.2 Å / Num. obs: 13876 / % possible obs: 99 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 21.6
Reflection shellResolution: 3.3→3.36 Å / Redundancy: 10.5 % / Mean I/σ(I) obs: 1.1 / % possible all: 82.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
PHASERphasing
HKL-2000data scaling
Cootmodel building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AOI

1aoi


Resolution: 3.3→121.2 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.826 / SU B: 20.36 / SU ML: 0.342 / Cross valid method: THROUGHOUT / ESU R Free: 0.533 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29025 565 5 %RANDOM
Rwork0.22994 ---
obs0.23282 10802 82.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.348 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å2-0 Å2-0 Å2
2--0.71 Å2-0 Å2
3----1.41 Å2
Refinement stepCycle: 1 / Resolution: 3.3→121.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2817 0 5 9 2831
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192852
X-RAY DIFFRACTIONr_bond_other_d0.0020.022740
X-RAY DIFFRACTIONr_angle_refined_deg1.761.9733844
X-RAY DIFFRACTIONr_angle_other_deg1.10436219
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.735374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.25622.411112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.11215483
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.781528
X-RAY DIFFRACTIONr_chiral_restr0.0950.2454
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023227
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02637
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.0935.7251514
X-RAY DIFFRACTIONr_mcbond_other4.0765.7241513
X-RAY DIFFRACTIONr_mcangle_it6.7098.5561882
X-RAY DIFFRACTIONr_mcangle_other6.7098.5581883
X-RAY DIFFRACTIONr_scbond_it4.4346.0011337
X-RAY DIFFRACTIONr_scbond_other4.43861331
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.5198.8741955
X-RAY DIFFRACTIONr_long_range_B_refined10.66143.5643347
X-RAY DIFFRACTIONr_long_range_B_other10.64343.5413345
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.303→3.389 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 12 -
Rwork0.288 239 -
obs--25.15 %

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