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- PDB-4wnn: SPT16-H2A-H2B FACT HISTONE Complex -

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Basic information

Entry
Database: PDB / ID: 4wnn
TitleSPT16-H2A-H2B FACT HISTONE Complex
Components
  • Histone H2A.1
  • Histone H2B.1
  • SPT16
KeywordsDNA BINDING PROTEIN / FACT / SPT16 / Histone / POB3 / H2A / H2B
Function / homology
Function and homology information


Regulation of TP53 Activity through Phosphorylation / regulation of sister chromatid cohesion / FACT complex / Condensation of Prophase Chromosomes / regulation of chromatin organization / nucleosome organization / replication fork protection complex / RMTs methylate histone arginines / postreplication repair / TP53 Regulates Transcription of DNA Repair Genes ...Regulation of TP53 Activity through Phosphorylation / regulation of sister chromatid cohesion / FACT complex / Condensation of Prophase Chromosomes / regulation of chromatin organization / nucleosome organization / replication fork protection complex / RMTs methylate histone arginines / postreplication repair / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Pre-transcription Events / positive regulation of transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly / transcription elongation by RNA polymerase II / DNA-templated DNA replication / nucleosome assembly / structural constituent of chromatin / nucleosome / chromatin organization / protein heterodimerization activity / DNA repair / chromatin / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
: / FACT complex subunit SPT16, C-terminal domain / FACT complex subunit Spt16, peptidase M24-like domain / FACT complex subunit Spt16 domain / FACT complex subunit (SPT16/CDC68) / FACT complex subunit (SPT16/CDC68) / FACT complex subunit Spt16, N-terminal lobe domain / FACT complex subunit Spt16 / FACT complex subunit SPT16 N-terminal lobe domain / FACT complex subunit SPT16 N-terminal lobe domain ...: / FACT complex subunit SPT16, C-terminal domain / FACT complex subunit Spt16, peptidase M24-like domain / FACT complex subunit Spt16 domain / FACT complex subunit (SPT16/CDC68) / FACT complex subunit (SPT16/CDC68) / FACT complex subunit Spt16, N-terminal lobe domain / FACT complex subunit Spt16 / FACT complex subunit SPT16 N-terminal lobe domain / FACT complex subunit SPT16 N-terminal lobe domain / Histone chaperone RTT106/FACT complex subunit SPT16-like, middle domain / Histone chaperone Rttp106-like, middle domain / Histone chaperone Rttp106-like / Creatinase/Aminopeptidase P/Spt16, N-terminal / Histone, subunit A / Histone, subunit A / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / PH-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Histone H2B.1 / Histone H2A.1 / FACT complex subunit SPT16
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKemble, D.J. / Hill, C.P. / Whitby, F.G. / Formosa, T. / McCullough, L.L.
Funding support United States, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P50GM082545 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1GM059135 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1GM064649 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA042014 United States
Department of Energy (DOE, United States)DE-AC02-76SF00515 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103393 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)P41RR001209 United States
CitationJournal: Mol.Cell / Year: 2015
Title: FACT Disrupts Nucleosome Structure by Binding H2A-H2B with Conserved Peptide Motifs.
Authors: Kemble, D.J. / McCullough, L.L. / Whitby, F.G. / Formosa, T. / Hill, C.P.
History
DepositionOct 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H2A.1
B: Histone H2B.1
C: Histone H2A.1
D: Histone H2B.1
E: Histone H2A.1
F: Histone H2B.1
G: Histone H2A.1
H: Histone H2B.1
T: SPT16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,00911
Polymers103,8199
Non-polymers1902
Water6,990388
1
A: Histone H2A.1
B: Histone H2B.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4843
Polymers25,3892
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-49 kcal/mol
Surface area10100 Å2
MethodPISA
2
E: Histone H2A.1
F: Histone H2B.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4843
Polymers25,3892
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-48 kcal/mol
Surface area10120 Å2
MethodPISA
3
G: Histone H2A.1
H: Histone H2B.1


Theoretical massNumber of molelcules
Total (without water)25,3892
Polymers25,3892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-43 kcal/mol
Surface area10230 Å2
MethodPISA
4
C: Histone H2A.1
D: Histone H2B.1
T: SPT16


Theoretical massNumber of molelcules
Total (without water)27,6513
Polymers27,6513
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.667, 109.667, 187.470
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
Histone H2A.1


Mass: 14013.177 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: HTA1, H2A1, SPT11, YDR225W, YD9934.10 / Production host: Escherichia coli (E. coli) / References: UniProt: P04911
#2: Protein
Histone H2B.1 / Suppressor of Ty protein 12


Mass: 11376.043 Da / Num. of mol.: 4 / Fragment: UNP residues 31-131
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: HTB1, H2B1, SPT12, YDR224C, YD9934.09C / Production host: Escherichia coli (E. coli) / References: UniProt: P02293
#3: Protein/peptide SPT16


Mass: 2262.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P32558*PLUS
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 2.05 Å3/Da / Density % sol: 40.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Crystals of ~ 60 x 60 mm formed within 10 days in 0.1M SPG (succinic acid:sodium dihydrogen phosphate:glycine ) pH 7, 25 % PEG 1500 (A4 of the PACT suite commercial screen (Qiagen).

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: single wavelength
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.12709 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12709 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 77661 / % possible obs: 98.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 34.58 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 20.2
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.928 / % possible all: 95.6

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
Blu-Icedata collection
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ID3

1id3


Resolution: 1.8→21.22 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 24.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.225 3900 5.03 %
Rwork0.179 --
obs0.181 77580 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.02 Å2
Refinement stepCycle: LAST / Resolution: 1.8→21.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5729 0 10 388 6127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075853
X-RAY DIFFRACTIONf_angle_d0.9527871
X-RAY DIFFRACTIONf_dihedral_angle_d13.6632256
X-RAY DIFFRACTIONf_chiral_restr0.039906
X-RAY DIFFRACTIONf_plane_restr0.005997
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.81420.34091320.28322264X-RAY DIFFRACTION84
1.8142-1.83710.28411410.27192497X-RAY DIFFRACTION95
1.8371-1.86130.29951240.27482642X-RAY DIFFRACTION97
1.8613-1.88680.39911550.32822607X-RAY DIFFRACTION98
1.8868-1.91370.35231260.30012623X-RAY DIFFRACTION100
1.9137-1.94220.31171440.25342701X-RAY DIFFRACTION100
1.9422-1.97260.32591590.25162661X-RAY DIFFRACTION100
1.9726-2.00490.30071510.2152656X-RAY DIFFRACTION100
2.0049-2.03940.24841200.19952673X-RAY DIFFRACTION100
2.0394-2.07650.20381380.19642719X-RAY DIFFRACTION100
2.0765-2.11640.21861250.18642683X-RAY DIFFRACTION100
2.1164-2.15950.24141390.18632655X-RAY DIFFRACTION100
2.1595-2.20650.22991400.17962689X-RAY DIFFRACTION100
2.2065-2.25770.23261260.19872685X-RAY DIFFRACTION100
2.2577-2.31410.24131520.19112630X-RAY DIFFRACTION100
2.3141-2.37660.25361230.18842702X-RAY DIFFRACTION100
2.3766-2.44640.24481620.18672654X-RAY DIFFRACTION100
2.4464-2.52530.22331410.17842682X-RAY DIFFRACTION100
2.5253-2.61540.20661530.17972678X-RAY DIFFRACTION100
2.6154-2.71990.21971380.18082638X-RAY DIFFRACTION100
2.7199-2.84340.21631250.1832661X-RAY DIFFRACTION100
2.8434-2.99290.22971670.18862654X-RAY DIFFRACTION100
2.9929-3.17990.24481430.19752679X-RAY DIFFRACTION100
3.1799-3.42450.29581370.18922688X-RAY DIFFRACTION100
3.4245-3.76730.19991320.16062623X-RAY DIFFRACTION99
3.7673-4.30850.1941250.1532650X-RAY DIFFRACTION98
4.3085-5.41330.18031450.14132637X-RAY DIFFRACTION98
5.4133-21.22430.20191370.16572349X-RAY DIFFRACTION88
Refinement TLS params.Method: refined / Origin x: 28.6745 Å / Origin y: -6.7327 Å / Origin z: -32.1876 Å
111213212223313233
T0.2261 Å20.0215 Å2-0.0037 Å2-0.2678 Å2-0.0175 Å2--0.2556 Å2
L0.586 °20.1995 °20.0803 °2-0.6357 °20.2432 °2--0.7295 °2
S0.0486 Å °0.1093 Å °-0.0999 Å °-0.0332 Å °-0.036 Å °-0.1065 Å °0.0889 Å °-0.0423 Å °0.0001 Å °
Refinement TLS groupSelection details: ALL

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