+Open data
-Basic information
Entry | Database: PDB / ID: 4z2n | ||||||
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Title | Crystal structure of human FACT SPT16 middle domain | ||||||
Components | FACT complex subunit SPT16 | ||||||
Keywords | TRANSCRIPTION | ||||||
Function / homology | Function and homology information FACT complex / positive regulation of DNA-templated transcription, elongation / nucleosome disassembly / 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 / nucleosome binding ...FACT complex / positive regulation of DNA-templated transcription, elongation / nucleosome disassembly / 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 / nucleosome binding / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / transcription elongation by RNA polymerase II / nucleosome assembly / DNA replication / Regulation of TP53 Activity through Phosphorylation / transcription by RNA polymerase II / DNA repair / RNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.923 Å | ||||||
Authors | Tsunaka, Y. / Fujiwara, Y. / Oyama, T. / Hirose, S. / Morikawa, K. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4z2n.cif.gz | 75.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4z2n.ent.gz | 53.9 KB | Display | PDB format |
PDBx/mmJSON format | 4z2n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4z2n_validation.pdf.gz | 422.7 KB | Display | wwPDB validaton report |
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Full document | 4z2n_full_validation.pdf.gz | 424.9 KB | Display | |
Data in XML | 4z2n_validation.xml.gz | 14 KB | Display | |
Data in CIF | 4z2n_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z2/4z2n ftp://data.pdbj.org/pub/pdb/validation_reports/z2/4z2n | HTTPS FTP |
-Related structure data
Related structure data | 4z2mC 4ioyS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.57 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.4 / Details: 5% PEG1000, 100mM citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jul 18, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→50 Å / Num. obs: 23921 / % possible obs: 99.9 % / Redundancy: 3.7 % / Net I/σ(I): 33.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.923→34.485 Å
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Refine LS restraints |
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LS refinement shell |
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