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- PDB-6o2d: Schizosaccharomyces pombe Cnp3 Cupin Domain -

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Basic information

Entry
Database: PDB / ID: 6o2d
TitleSchizosaccharomyces pombe Cnp3 Cupin Domain
ComponentsInner kinetochore subunit cnp3
KeywordsCELL CYCLE / CENP-C / Kinetochore / Cupin / Dimer
Function / homology
Function and homology information


protein localization to kinetochore involved in kinetochore assembly / kinetochore => GO:0000776 / spindle attachment to meiosis I kinetochore / centromeric DNA binding / attachment of mitotic spindle microtubules to kinetochore / kinetochore assembly / condensed chromosome, centromeric region / mitotic sister chromatid segregation / chromosome, centromeric region / protein-containing complex binding ...protein localization to kinetochore involved in kinetochore assembly / kinetochore => GO:0000776 / spindle attachment to meiosis I kinetochore / centromeric DNA binding / attachment of mitotic spindle microtubules to kinetochore / kinetochore assembly / condensed chromosome, centromeric region / mitotic sister chromatid segregation / chromosome, centromeric region / protein-containing complex binding / nucleolus / nucleoplasm / nucleus
Similarity search - Function
Mif2, N-terminal / Kinetochore CENP-C fungal homologue, Mif2, N-terminal / Mif2/CENP-C cupin domain / Centromere protein C/Mif2/cnp3 / Mif2/CENP-C like / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold
Similarity search - Domain/homology
Inner kinetochore subunit cnp3
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.52 Å
AuthorsChik, J.K. / Cho, U.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01-DK111465 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32-GM007315 United States
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Structures of CENP-C cupin domains at regional centromeres reveal unique patterns of dimerization and recruitment functions for the inner pocket.
Authors: Chik, J.K. / Moiseeva, V. / Goel, P.K. / Meinen, B.A. / Koldewey, P. / An, S. / Mellone, B.G. / Subramanian, L. / Cho, U.S.
History
DepositionFeb 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inner kinetochore subunit cnp3
B: Inner kinetochore subunit cnp3


Theoretical massNumber of molelcules
Total (without water)36,0982
Polymers36,0982
Non-polymers00
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-35 kcal/mol
Surface area14460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.160, 55.160, 206.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Inner kinetochore subunit cnp3 / CENP-C homolog / Centromere protein 3 / Constitutive centromere-associated network protein cnp3


Mass: 18048.834 Da / Num. of mol.: 2 / Fragment: Cupin Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: cnp3, SPBC1861.01c, SPBC56F2.13 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9USR9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.18 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop
Details: Protein was mixed with 0.1 M HEPES (pH 7.0), 20% PEG 3350, and 6% w/v Trimethylamine N-oxide dihydrate in a 1:1 ratio (v/v). The reservoir solution was made up of 0.25 M potassium fluoride, ...Details: Protein was mixed with 0.1 M HEPES (pH 7.0), 20% PEG 3350, and 6% w/v Trimethylamine N-oxide dihydrate in a 1:1 ratio (v/v). The reservoir solution was made up of 0.25 M potassium fluoride, 0.125 M HEPES pH 7, and 25% PEG 3350

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Data collection

DiffractionMean temperature: 105 K / Serial crystal experiment: N
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: 2.52→34.44 Å / Num. obs: 11544 / % possible obs: 99.6 % / Redundancy: 13.2 % / Rpim(I) all: 0.016 / Net I/σ(I): 32.9
Reflection shellResolution: 2.52→2.59 Å / Num. unique obs: 804 / Rpim(I) all: 0.156

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
Cootmodel building
AutoSolphasing
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.52→33.074 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.2
RfactorNum. reflection% reflection
Rfree0.251 552 4.81 %
Rwork0.2171 --
obs0.2188 11475 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.52→33.074 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2246 0 0 5 2251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082293
X-RAY DIFFRACTIONf_angle_d1.2483089
X-RAY DIFFRACTIONf_dihedral_angle_d10.8111396
X-RAY DIFFRACTIONf_chiral_restr0.072332
X-RAY DIFFRACTIONf_plane_restr0.007400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5202-2.77370.40331300.29422642X-RAY DIFFRACTION100
2.7737-3.17480.31271340.26972659X-RAY DIFFRACTION100
3.1748-3.99880.28651410.22092727X-RAY DIFFRACTION100
3.9988-33.07730.19171470.192895X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -4.2362 Å / Origin y: 22.9454 Å / Origin z: -16.1351 Å
111213212223313233
T0.7092 Å20.1396 Å20.0534 Å2-0.3369 Å2-0.0002 Å2--0.3453 Å2
L2.8254 °20.7625 °2-0.0267 °2-2.5637 °2-0.0535 °2--4.0062 °2
S0.1922 Å °0.0507 Å °-0.0338 Å °-0.4155 Å °-0.0698 Å °-0.086 Å °-0.8164 Å °-0.0205 Å °-0.0865 Å °
Refinement TLS groupSelection details: all

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