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- PDB-4zbj: UBN1 peptide bound to H3.3/H4/Asf1 -

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Basic information

Entry
Database: PDB / ID: 4zbj
TitleUBN1 peptide bound to H3.3/H4/Asf1
Components
  • Histone H3
  • Histone H4
  • Histone chaperone ASF1
  • Ubinuclein-1
KeywordsSTRUCTURAL PROTEIN / Histone Chaperone / Complex / Chromatin Assembly
Function / homology
Function and homology information


Factors involved in megakaryocyte development and platelet production / Oxidative Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / Transcriptional regulation by small RNAs / Assembly of the ORC complex at the origin of replication / RNA Polymerase I Promoter Escape / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Regulation of endogenous retroelements by KRAB-ZFP proteins / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / H3 histone acetyltransferase complex ...Factors involved in megakaryocyte development and platelet production / Oxidative Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / Transcriptional regulation by small RNAs / Assembly of the ORC complex at the origin of replication / RNA Polymerase I Promoter Escape / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Regulation of endogenous retroelements by KRAB-ZFP proteins / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / H3 histone acetyltransferase complex / DNA replication-dependent chromatin assembly / acetyltransferase activator activity / nucleosome disassembly / silent mating-type cassette heterochromatin formation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / cellular response to stress / negative regulation of DNA damage checkpoint / bicellular tight junction / subtelomeric heterochromatin formation / regulation of DNA repair / positive regulation of transcription elongation by RNA polymerase II / PML body / protein modification process / centriolar satellite / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / regulation of gene expression / histone binding / chromosome, telomeric region / nuclear body / protein heterodimerization activity / regulation of transcription by RNA polymerase II / chromatin / DNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Ubinuclein middle domain / Ubinuclein conserved middle domain / Hpc2-related domain / HPC2 and ubinuclein domain / Histone chaperone ASF1-like / Histone deposition protein Asf1 / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / Histone, subunit A ...Ubinuclein middle domain / Ubinuclein conserved middle domain / Hpc2-related domain / HPC2 and ubinuclein domain / Histone chaperone ASF1-like / Histone deposition protein Asf1 / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / 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 / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Histone chaperone ASF1 / Histone H4 / Histone H3.3 type 1 / Histone H3.3 / Ubinuclein-1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Xenopus laevis (African clawed frog)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.248 Å
AuthorsMarmorstein, R. / Ricketts, M.D. / Tang, Y.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)AG031862 United States
American Heart Association12PRE12030157 United States
CitationJournal: Nat Commun / Year: 2015
Title: Ubinuclein-1 confers histone H3.3-specific-binding by the HIRA histone chaperone complex.
Authors: Daniel Ricketts, M. / Frederick, B. / Hoff, H. / Tang, Y. / Schultz, D.C. / Singh Rai, T. / Grazia Vizioli, M. / Adams, P.D. / Marmorstein, R.
History
DepositionApr 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_entity_src_syn / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 18, 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
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone chaperone ASF1
B: Histone H3
C: Histone H4
D: Ubinuclein-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,56313
Polymers41,1614
Non-polymers4029
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9740 Å2
ΔGint-138 kcal/mol
Surface area16790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.024, 90.024, 120.734
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein Histone chaperone ASF1 / Anti-silencing function protein 1 / yASF1


Mass: 19663.973 Da / Num. of mol.: 1 / Fragment: UNP residues 2-169
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: ASF1, CIA1, YJL115W, J0755 / Plasmid: pST39 / Cell line (production host): Rosetta2(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P32447
#2: Protein Histone H3


Mass: 8812.344 Da / Num. of mol.: 1 / Fragment: UNP residues 62-136 / Mutation: G103A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pST39 / Cell line (production host): Rosetta2(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: Q10453, UniProt: Q6PI79*PLUS
#3: Protein Histone H4


Mass: 9540.251 Da / Num. of mol.: 1 / Fragment: UNP residues 21-103
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pST39 / Cell line (production host): Rosetta2(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799

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Protein/peptide , 1 types, 1 molecules D

#4: Protein/peptide Ubinuclein-1 / HIRA-binding protein / Protein VT4 / Ubiquitously expressed nuclear protein


Mass: 3144.248 Da / Num. of mol.: 1 / Fragment: UNP residues 122-148 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9NPG3

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Non-polymers , 3 types, 167 molecules

#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.43 Å3/Da / Density % sol: 64.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M Sodium Cacodylate pH 6.0, 8% PEG 8K, 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.248→25.406 Å / Num. obs: 26431 / % possible obs: 99.1 % / Redundancy: 6 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 26.4
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.7 / % possible all: 93.3

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIX1.8.4_1496phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HUE

2hue


Resolution: 2.248→25.406 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / Phase error: 26.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2348 1317 4.98 %
Rwork0.2082 --
obs0.2095 26431 96.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.248→25.406 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2681 0 16 158 2855
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032747
X-RAY DIFFRACTIONf_angle_d0.6373718
X-RAY DIFFRACTIONf_dihedral_angle_d11.7091035
X-RAY DIFFRACTIONf_chiral_restr0.023424
X-RAY DIFFRACTIONf_plane_restr0.003479
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.248-2.33790.29321320.27522629X-RAY DIFFRACTION93
2.3379-2.44430.31581490.29262824X-RAY DIFFRACTION98
2.4443-2.5730.32581480.30622730X-RAY DIFFRACTION95
2.573-2.7340.36571430.29472706X-RAY DIFFRACTION94
2.734-2.94480.2971330.2932677X-RAY DIFFRACTION93
2.9448-3.24070.28331510.24422735X-RAY DIFFRACTION95
3.2407-3.70830.24771470.19292891X-RAY DIFFRACTION99
3.7083-4.66740.1881550.16692890X-RAY DIFFRACTION99
4.6674-25.40740.1751590.16773032X-RAY DIFFRACTION99

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