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- PDB-8t0p: Structure of Cse4 bound to Ame1 and Okp1 -

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Basic information

Entry
Database: PDB / ID: 8t0p
TitleStructure of Cse4 bound to Ame1 and Okp1
Components
  • Histone H3-like centromeric protein CSE4
  • Inner kinetochore subunit AME1
  • Inner kinetochore subunit OKP1
KeywordsCELL CYCLE / Okp1 / Cse4 / Ame1 / Kinetochore
Function / homology
Function and homology information


2-micrometer circle DNA / 2-micrometer plasmid partitioning / COMA complex / attachment of spindle microtubules to kinetochore / centromeric DNA binding / kinetochore assembly / condensed chromosome, centromeric region / spindle pole body / protein localization to kinetochore / mitotic sister chromatid segregation ...2-micrometer circle DNA / 2-micrometer plasmid partitioning / COMA complex / attachment of spindle microtubules to kinetochore / centromeric DNA binding / kinetochore assembly / condensed chromosome, centromeric region / spindle pole body / protein localization to kinetochore / mitotic sister chromatid segregation / rRNA transcription / protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / meiotic cell cycle / kinetochore / structural constituent of chromatin / sequence-specific DNA binding / protein heterodimerization activity / cell division / nucleus / cytoplasm
Similarity search - Function
: / CENPU protein / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
Histone H3-like centromeric protein CSE4 / Inner kinetochore subunit AME1 / Inner kinetochore subunit OKP1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsDeng, S. / Harrison, S.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Embo Rep. / Year: 2023
Title: Recognition of centromere-specific histone Cse4 by the inner kinetochore Okp1-Ame1 complex.
Authors: Deng, S. / Cai, J. / Harrison, S.C. / Zhou, H. / Hinshaw, S.M.
History
DepositionJun 1, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 20, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Dec 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Inner kinetochore subunit AME1
A: Inner kinetochore subunit OKP1
C: Histone H3-like centromeric protein CSE4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7669
Polymers33,1903
Non-polymers5766
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8440 Å2
ΔGint-144 kcal/mol
Surface area15950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.305, 154.305, 37.114
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11B-408-

HOH

21A-426-

HOH

31C-207-

HOH

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Components

#1: Protein Inner kinetochore subunit AME1


Mass: 12506.218 Da / Num. of mol.: 1 / Fragment: residues 125-231
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288C / Gene: AME1 / Production host: Escherichia coli (E. coli) / References: UniProt: P38313
#2: Protein Inner kinetochore subunit OKP1 / CENP-Q homolog / Constitutive centromere-associated network protein OKP1 / Outer kinetochore protein 1


Mass: 18608.498 Da / Num. of mol.: 1 / Fragment: residues 125-275
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288C / Gene: OKP1, YGR179C / Production host: Escherichia coli (E. coli) / References: UniProt: P53298
#3: Protein/peptide Histone H3-like centromeric protein CSE4 / CENP-A homolog / CENPA homolog / Chromosome segregation protein 4


Mass: 2075.375 Da / Num. of mol.: 1 / Fragment: residues 32-49 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36012
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.33 Å3/Da / Density % sol: 63.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 19% PEG 8000, 0.55 M Lithium sulfate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.73→109.11 Å / Num. obs: 47590 / % possible obs: 100 % / Redundancy: 14.2 % / CC1/2: 1 / Rmerge(I) obs: 0.1254 / Rpim(I) all: 0.025 / Rrim(I) all: 0.128 / Net I/σ(I): 16.93
Reflection shellResolution: 1.73→1.76 Å / Mean I/σ(I) obs: 0.95 / Num. unique obs: 2301 / CC1/2: 0.3553 / % possible all: 97.75

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→69.01 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2364 2441 5.14 %
Rwork0.2067 --
obs0.2082 47499 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.73→69.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2272 0 30 185 2487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172376
X-RAY DIFFRACTIONf_angle_d1.5543200
X-RAY DIFFRACTIONf_dihedral_angle_d4.769311
X-RAY DIFFRACTIONf_chiral_restr0.1363
X-RAY DIFFRACTIONf_plane_restr0.012405
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.760.31751480.29762576X-RAY DIFFRACTION98
1.76-1.80.32951170.28612589X-RAY DIFFRACTION100
1.8-1.840.28771330.27492631X-RAY DIFFRACTION100
1.84-1.890.31071510.28422578X-RAY DIFFRACTION100
1.89-1.940.35141380.29642634X-RAY DIFFRACTION100
1.94-20.28521380.24792585X-RAY DIFFRACTION100
2-2.060.24791550.2022658X-RAY DIFFRACTION100
2.06-2.140.21561390.18362588X-RAY DIFFRACTION100
2.14-2.220.24051300.19172639X-RAY DIFFRACTION100
2.22-2.320.19221510.18482648X-RAY DIFFRACTION100
2.32-2.450.18741460.1952639X-RAY DIFFRACTION100
2.45-2.60.30141270.20332652X-RAY DIFFRACTION100
2.6-2.80.2181450.20022655X-RAY DIFFRACTION100
2.8-3.080.21211640.19852670X-RAY DIFFRACTION100
3.08-3.530.2271390.19942698X-RAY DIFFRACTION100
3.53-4.450.20971640.17752715X-RAY DIFFRACTION100
4.45-69.010.25921560.2242903X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 37.0604 Å / Origin y: -22.958 Å / Origin z: 13.227 Å
111213212223313233
T0.214 Å20.0047 Å20.0091 Å2-0.1778 Å20.0217 Å2--0.1388 Å2
L1.5667 °21.2101 °20.5038 °2-3.6123 °20.7522 °2--0.8983 °2
S-0.0596 Å °-0.0258 Å °0.2497 Å °-0.106 Å °-0.0579 Å °0.0884 Å °-0.1827 Å °0.0193 Å °0.0096 Å °
Refinement TLS groupSelection details: all

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