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- PDB-4z2n: Crystal structure of human FACT SPT16 middle domain -

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Basic information

Entry
Database: PDB / ID: 4z2n
TitleCrystal structure of human FACT SPT16 middle domain
ComponentsFACT complex subunit SPT16
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


FACT complex / nucleosome disassembly / positive regulation of DNA-templated transcription, elongation / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat ...FACT complex / nucleosome disassembly / positive regulation of DNA-templated transcription, elongation / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / nucleosome binding / RNA Polymerase II Pre-transcription Events / transcription elongation by RNA polymerase II / TP53 Regulates Transcription of DNA Repair Genes / nucleosome assembly / DNA replication / Regulation of TP53 Activity through Phosphorylation / transcription by RNA polymerase II / DNA repair / RNA binding / nucleoplasm / nucleus
Similarity search - Function
PH-domain like - #150 / : / 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 ...PH-domain like - #150 / : / 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 / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
FACT complex subunit SPT16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.923 Å
AuthorsTsunaka, Y. / Fujiwara, Y. / Oyama, T. / Hirose, S. / Morikawa, K.
CitationJournal: Genes Dev / Year: 2016
Title: Integrated molecular mechanism directing nucleosome reorganization by human FACT.
Authors: Yasuo Tsunaka / Yoshie Fujiwara / Takuji Oyama / Susumu Hirose / Kosuke Morikawa /
Abstract: Facilitates chromatin transcription (FACT) plays essential roles in chromatin remodeling during DNA transcription, replication, and repair. Our structural and biochemical studies of human FACT- ...Facilitates chromatin transcription (FACT) plays essential roles in chromatin remodeling during DNA transcription, replication, and repair. Our structural and biochemical studies of human FACT-histone interactions present precise views of nucleosome reorganization, conducted by the FACT-SPT16 (suppressor of Ty 16) Mid domain and its adjacent acidic AID segment. AID accesses the H2B N-terminal basic region exposed by partial unwrapping of the nucleosomal DNA, thereby triggering the invasion of FACT into the nucleosome. The crystal structure of the Mid domain complexed with an H3-H4 tetramer exhibits two separate contact sites; the Mid domain forms a novel intermolecular β structure with H4. At the other site, the Mid-H2A steric collision on the H2A-docking surface of the H3-H4 tetramer within the nucleosome induces H2A-H2B displacement. This integrated mechanism results in disrupting the H3 αN helix, which is essential for retaining the nucleosomal DNA ends, and hence facilitates DNA stripping from histone.
History
DepositionMar 30, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Mar 30, 2016Group: Database references
Revision 1.3Feb 19, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 8, 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

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Assembly

Deposited unit
A: FACT complex subunit SPT16


Theoretical massNumber of molelcules
Total (without water)33,3721
Polymers33,3721
Non-polymers00
Water4,324240
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15220 Å2
Unit cell
Length a, b, c (Å)160.891, 49.748, 40.048
Angle α, β, γ (deg.)90.00, 95.18, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein FACT complex subunit SPT16 / Chromatin-specific transcription elongation factor 140 kDa subunit / FACT 140 kDa subunit / ...Chromatin-specific transcription elongation factor 140 kDa subunit / FACT 140 kDa subunit / FACTp140 / Facilitates chromatin transcription complex subunit SPT16 / hSPT16


Mass: 33372.195 Da / Num. of mol.: 1 / Fragment: UNP residues 644-930
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUPT16H, FACT140, FACTP140 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: Q9Y5B9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.39 Å3/Da / Density % sol: 48.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.4 / Details: 5% PEG1000, 100mM citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 23921 / % possible obs: 99.9 % / Redundancy: 3.7 % / Net I/σ(I): 33.4

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IOY

4ioy


Resolution: 1.923→34.485 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2164 1999 8.36 %
Rwork0.174 --
obs0.1776 23917 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.923→34.485 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2206 0 0 240 2446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072258
X-RAY DIFFRACTIONf_angle_d1.0533049
X-RAY DIFFRACTIONf_dihedral_angle_d14.042845
X-RAY DIFFRACTIONf_chiral_restr0.045332
X-RAY DIFFRACTIONf_plane_restr0.005391
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.923-1.97110.26611380.17881507X-RAY DIFFRACTION97
1.9711-2.02440.23191420.16751563X-RAY DIFFRACTION100
2.0244-2.08390.21461420.16611561X-RAY DIFFRACTION100
2.0839-2.15120.241460.16451590X-RAY DIFFRACTION100
2.1512-2.22810.21451430.16231581X-RAY DIFFRACTION100
2.2281-2.31730.21441420.1681552X-RAY DIFFRACTION100
2.3173-2.42270.2591450.18631585X-RAY DIFFRACTION100
2.4227-2.55040.21261440.18131583X-RAY DIFFRACTION100
2.5504-2.71010.22451440.18281571X-RAY DIFFRACTION100
2.7101-2.91930.23631450.18451593X-RAY DIFFRACTION100
2.9193-3.21280.21641430.17531569X-RAY DIFFRACTION100
3.2128-3.67730.1931470.1691597X-RAY DIFFRACTION100
3.6773-4.63120.18641400.15991551X-RAY DIFFRACTION97
4.6312-34.49080.21981380.18941515X-RAY DIFFRACTION92

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