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- PDB-5yje: Crystal structure of HIRA(644-1017) -

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Basic information

Entry
Database: PDB / ID: 5yje
TitleCrystal structure of HIRA(644-1017)
ComponentsProtein HIRA
KeywordsGENE REGULATION / Histone chaperone
Function / homology
Function and homology information


HIR complex / muscle cell differentiation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / anatomical structure morphogenesis / Replacement of protamines by nucleosomes in the male pronucleus / nucleosome binding / gastrulation / PML body / osteoblast differentiation / transcription corepressor activity ...HIR complex / muscle cell differentiation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / anatomical structure morphogenesis / Replacement of protamines by nucleosomes in the male pronucleus / nucleosome binding / gastrulation / PML body / osteoblast differentiation / transcription corepressor activity / nucleosome assembly / histone binding / RNA polymerase II-specific DNA-binding transcription factor binding / chromatin remodeling / DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / protein-containing complex / extracellular exosome / nucleoplasm / nucleus
Similarity search - Function
TUP1-like enhancer of split / WD repeat HIR1 / TUP1-like enhancer of split / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 Å
AuthorsSato, Y. / Senda, M. / Senda, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSPS16K14908 Japan
CitationJournal: Nat Commun / Year: 2018
Title: Functional activity of the H3.3 histone chaperone complex HIRA requires trimerization of the HIRA subunit
Authors: Ray-Gallet, D. / Ricketts, M.D. / Sato, Y. / Gupta, K. / Boyarchuk, E. / Senda, T. / Marmorstein, R. / Almouzni, G.
History
DepositionOct 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Experimental preparation / Refinement description
Category: exptl_crystal / refine / Item: _exptl_crystal.description / _refine.details
Revision 1.2Jul 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.year
Revision 1.3Aug 22, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.4Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Protein HIRA
B: Protein HIRA
C: Protein HIRA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,2416
Polymers125,9533
Non-polymers2883
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9110 Å2
ΔGint-79 kcal/mol
Surface area39780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.990, 86.800, 99.150
Angle α, β, γ (deg.)90.00, 102.49, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein HIRA / TUP1-like enhancer of split protein 1


Mass: 41984.348 Da / Num. of mol.: 3 / Fragment: UNP residues 644-1017
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIRA, DGCR1, HIR, TUPLE1 / Production host: Escherichia coli (E. coli) / References: UniProt: P54198
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsLeu1018 to Serine 1022 are derived from PTXB1 vector sequence.

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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: 2.5 Å3/Da / Density % sol: 50.83 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 0.12 M sodium citrate, 0.36-0.52 M ammonium sulfate, 0.02 M yttrium(III) chloride

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 20, 2015
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.45→74.9 Å / Num. obs: 89395 / % possible obs: 99.5 % / Redundancy: 3.48 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 19.4
Reflection shellResolution: 2.45→2.51 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.86 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.45→19.806 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.92 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER F_MINUS AND F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2562 3913 4.38 %
Rwork0.2017 --
obs0.2041 89387 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→19.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6804 0 15 16 6835
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086939
X-RAY DIFFRACTIONf_angle_d1.0269474
X-RAY DIFFRACTIONf_dihedral_angle_d20.0422369
X-RAY DIFFRACTIONf_chiral_restr0.1571166
X-RAY DIFFRACTIONf_plane_restr0.0061191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.47990.35151460.28493183X-RAY DIFFRACTION100
2.4799-2.51120.32111350.27892981X-RAY DIFFRACTION100
2.5112-2.54420.33721440.26643125X-RAY DIFFRACTION100
2.5442-2.57890.31091370.25832991X-RAY DIFFRACTION100
2.5789-2.61570.31481410.25593048X-RAY DIFFRACTION100
2.6157-2.65470.33381380.2313034X-RAY DIFFRACTION100
2.6547-2.6960.31271420.24543112X-RAY DIFFRACTION100
2.696-2.74010.25761380.23833007X-RAY DIFFRACTION100
2.7401-2.78730.30461400.23493052X-RAY DIFFRACTION100
2.7873-2.83780.29021430.24373089X-RAY DIFFRACTION100
2.8378-2.89220.36051400.24093082X-RAY DIFFRACTION100
2.8922-2.95110.30371360.24163008X-RAY DIFFRACTION100
2.9511-3.0150.28861390.2513022X-RAY DIFFRACTION100
3.015-3.08490.34941400.2393086X-RAY DIFFRACTION100
3.0849-3.16170.37461390.23813032X-RAY DIFFRACTION100
3.1617-3.24690.23321390.22043058X-RAY DIFFRACTION100
3.2469-3.3420.27931420.22833111X-RAY DIFFRACTION100
3.342-3.44930.27461390.22283015X-RAY DIFFRACTION100
3.4493-3.57190.28241420.21023075X-RAY DIFFRACTION100
3.5719-3.7140.31370.20133020X-RAY DIFFRACTION100
3.714-3.88180.26381400.20163047X-RAY DIFFRACTION99
3.8818-4.08480.22971410.1873063X-RAY DIFFRACTION100
4.0848-4.33820.23141420.16833086X-RAY DIFFRACTION100
4.3382-4.66910.19191370.14932997X-RAY DIFFRACTION100
4.6691-5.13160.19121430.1653067X-RAY DIFFRACTION100
5.1316-5.85730.22421370.19033012X-RAY DIFFRACTION99
5.8573-7.31720.23021400.2013035X-RAY DIFFRACTION99
7.3172-19.80660.21341360.16753036X-RAY DIFFRACTION99

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