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- PDB-5wjc: Crystal structure of Schizosaccharomyces pombe Mis16 in complex w... -

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Basic information

Entry
Database: PDB / ID: 5wjc
TitleCrystal structure of Schizosaccharomyces pombe Mis16 in complex with Eic1
Components
  • Eic1 protein
  • Kinetochore protein Mis16
KeywordsPROTEIN BINDING / Fission yeast chaperone for histone H4 / Subcomponent of Mis18 complex / Eic1 binding / WD-40 repeats domain
Function / homology
Function and homology information


HATs acetylate histones / RMTs methylate histone arginines / Neddylation / HDACs deacetylate histones / CENP-A recruiting complex / chromosome, centromeric core domain / H3-H4 histone complex chaperone activity / CENP-A containing chromatin assembly / protein localization to chromosome, centromeric region / attachment of mitotic spindle microtubules to kinetochore ...HATs acetylate histones / RMTs methylate histone arginines / Neddylation / HDACs deacetylate histones / CENP-A recruiting complex / chromosome, centromeric core domain / H3-H4 histone complex chaperone activity / CENP-A containing chromatin assembly / protein localization to chromosome, centromeric region / attachment of mitotic spindle microtubules to kinetochore / mitotic sister chromatid segregation / chromosome, centromeric region / kinetochore / histone binding / chromatin remodeling / cell division / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
EIPR1 beta-propeller / Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / : / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site ...EIPR1 beta-propeller / Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / : / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
CENP-A recruiting complex protein mis19 / Histone acetyltransferase type B subunit 2
Similarity search - Component
Biological speciesSchizosaccharomyces pombe 972h- (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.298 Å
AuthorsAn, S. / Cho, U.-S. / Koldewey, P. / Chik, J. / Subramanian, L.
Funding support United States, 4items
OrganizationGrant numberCountry
American Diabetes Association1-16-JDF-017 United States
March of dimesN019154-00 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)AG050903 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK111465 United States
CitationJournal: Structure / Year: 2018
Title: Mis16 Switches Function from a Histone H4 Chaperone to a CENP-ACnp1-Specific Assembly Factor through Eic1 Interaction.
Authors: An, S. / Koldewey, P. / Chik, J. / Subramanian, L. / Cho, U.S.
History
DepositionJul 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 16, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kinetochore protein Mis16
B: Eic1 protein


Theoretical massNumber of molelcules
Total (without water)61,9352
Polymers61,9352
Non-polymers00
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-8 kcal/mol
Surface area17130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.591, 154.591, 52.744
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Kinetochore protein Mis16


Mass: 48481.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe 972h- (yeast)
Strain: 972 / ATCC 24843 / Gene: mis16, hat2, SPCC1672.10 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: O94244
#2: Protein Eic1 protein


Mass: 13453.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe 972h- (yeast)
Strain: 972 / ATCC 24843 / Gene: SPBC27B12.02, SPBC30B4.10 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: O42995
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O

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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: 2.58 Å3/Da / Density % sol: 52.24 % / Description: Thick needle
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 100 mM Tris-HCl pH 8.5, 25% PEG 2000MME

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 26459 / % possible obs: 90.8 % / Redundancy: 8 % / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.035 / Net I/σ(I): 22.4
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1698 / Rpim(I) all: 0.39 / % possible all: 59.7

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data processing
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XYH

4xyh


Resolution: 2.298→48.886 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2198 1999 7.57 %
Rwork0.1723 --
obs0.1758 26414 90.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.298→48.886 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3172 0 0 168 3340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083252
X-RAY DIFFRACTIONf_angle_d0.9314439
X-RAY DIFFRACTIONf_dihedral_angle_d6.7161934
X-RAY DIFFRACTIONf_chiral_restr0.06492
X-RAY DIFFRACTIONf_plane_restr0.005580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2983-2.35570.3134900.24441097X-RAY DIFFRACTION59
2.3557-2.41940.30991000.22051219X-RAY DIFFRACTION65
2.4194-2.49060.25331130.22351375X-RAY DIFFRACTION73
2.4906-2.5710.26071230.21651512X-RAY DIFFRACTION81
2.571-2.66290.29851450.20721773X-RAY DIFFRACTION93
2.6629-2.76950.23081560.20921906X-RAY DIFFRACTION100
2.7695-2.89550.26461540.19671875X-RAY DIFFRACTION100
2.8955-3.04820.23771560.19261900X-RAY DIFFRACTION100
3.0482-3.23910.23611570.19231915X-RAY DIFFRACTION100
3.2391-3.48910.23061570.16971921X-RAY DIFFRACTION100
3.4891-3.84010.19771580.1481932X-RAY DIFFRACTION100
3.8401-4.39550.19271590.14391951X-RAY DIFFRACTION100
4.3955-5.53670.18181610.13241962X-RAY DIFFRACTION100
5.5367-48.8970.2011700.18382077X-RAY DIFFRACTION99

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