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- PDB-4z2m: Crystal structure of human SPT16 Mid-AID/H3-H4 tetramer FACT Hist... -

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Basic information

Entry
Database: PDB / ID: 4z2m
TitleCrystal structure of human SPT16 Mid-AID/H3-H4 tetramer FACT Histone complex
Components
  • FACT complex subunit SPT16
  • Histone H3.1
  • Histone H4
KeywordsTranscription/DNA binding protein / Transcription / Transcription-DNA binding protein complex
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 / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / nucleosome binding / Chromatin modifying enzymes / RNA Polymerase II Transcription Elongation / Replacement of protamines by nucleosomes in the male pronucleus / Formation of RNA Pol II elongation complex / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / RNA Polymerase II Pre-transcription Events / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / telomere organization / Interleukin-7 signaling / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / epigenetic regulation of gene expression / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / TP53 Regulates Transcription of DNA Repair Genes / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / transcription elongation by RNA polymerase II / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Regulation of TP53 Activity through Phosphorylation / gene expression / Estrogen-dependent gene expression / transcription by RNA polymerase II / chromosome, telomeric region / DNA replication / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / DNA repair / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane
Similarity search - Function
PH-domain like - #150 / FACT complex subunit Spt16, peptidase M24-like domain / : / FACT complex subunit SPT16, C-terminal domain / : / FACT complex subunit SPT16 PH-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 ...PH-domain like - #150 / FACT complex subunit Spt16, peptidase M24-like domain / : / FACT complex subunit SPT16, C-terminal domain / : / FACT complex subunit SPT16 PH-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 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / 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 / PH-like domain superfamily / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Histone H4 / Histone H3.1 / FACT complex subunit SPT16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.981 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

Downloads & links

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Assembly

Deposited unit
B: FACT complex subunit SPT16
G: Histone H3.1
H: Histone H4
I: Histone H3.1
J: Histone H4


Theoretical massNumber of molelcules
Total (without water)79,9995
Polymers79,9995
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11910 Å2
ΔGint-94 kcal/mol
Surface area29490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.442, 69.784, 187.853
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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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: Protein Histone H3.1


Mass: 11919.018 Da / Num. of mol.: 2 / Fragment: UNP residues 35-136
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H3A / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: P68431
#3: Protein Histone H4


Mass: 11394.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H4A / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: P62805

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% PEG400, 0.9-1.1 M Imidazole, 100-150 mM L-histidine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX-300 / 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: 2.98→50 Å / Num. obs: 17819 / % possible obs: 97.7 % / Redundancy: 6.8 % / Rsym value: 0.078 / Net I/σ(I): 17.4

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CV5

2cv5


Resolution: 2.981→46.963 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2465 1797 10.09 %
Rwork0.1904 --
obs0.196 17812 97.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.981→46.963 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4594 0 0 0 4594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094669
X-RAY DIFFRACTIONf_angle_d1.2526283
X-RAY DIFFRACTIONf_dihedral_angle_d15.4941791
X-RAY DIFFRACTIONf_chiral_restr0.048714
X-RAY DIFFRACTIONf_plane_restr0.006801
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9812-3.06180.3571300.28081152X-RAY DIFFRACTION95
3.0618-3.15180.321400.24521215X-RAY DIFFRACTION97
3.1518-3.25360.31321240.23931201X-RAY DIFFRACTION97
3.2536-3.36980.33021400.24391185X-RAY DIFFRACTION96
3.3698-3.50470.30171390.21891216X-RAY DIFFRACTION97
3.5047-3.66410.27371370.21231229X-RAY DIFFRACTION98
3.6641-3.85720.25791400.19971221X-RAY DIFFRACTION98
3.8572-4.09880.27031290.19011219X-RAY DIFFRACTION98
4.0988-4.4150.22621420.17541221X-RAY DIFFRACTION98
4.415-4.85890.18961390.15871231X-RAY DIFFRACTION98
4.8589-5.5610.24731410.17581260X-RAY DIFFRACTION98
5.561-7.00260.25891490.20671293X-RAY DIFFRACTION100
7.0026-46.96910.19311470.15981372X-RAY DIFFRACTION99

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