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- PDB-4nfa: Structure of the C-terminal doamin of Knl1 -

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Basic information

Entry
Database: PDB / ID: 4nfa
TitleStructure of the C-terminal doamin of Knl1
ComponentsProtein CASC5
KeywordsCELL CYCLE / RWD domain
Function / homology
Function and homology information


Knl1/Spc105 complex / positive regulation of meiosis I spindle assembly checkpoint / homologous chromosome orientation in meiotic metaphase I / acrosome assembly / regulation of mitotic cell cycle spindle assembly checkpoint / attachment of spindle microtubules to kinetochore / protein localization to kinetochore / mitotic sister chromatid segregation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase ...Knl1/Spc105 complex / positive regulation of meiosis I spindle assembly checkpoint / homologous chromosome orientation in meiotic metaphase I / acrosome assembly / regulation of mitotic cell cycle spindle assembly checkpoint / attachment of spindle microtubules to kinetochore / protein localization to kinetochore / mitotic sister chromatid segregation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Deposition of new CENPA-containing nucleosomes at the centromere / Resolution of Sister Chromatid Cohesion / acrosomal vesicle / RHO GTPases Activate Formins / kinetochore / Separation of Sister Chromatids / nuclear body / cell division / nucleoplasm / nucleus / cytosol
Similarity search - Function
Knl1, C-terminal RWD domain / Knl1 RWD C-terminal domain / Kinetochore scaffold 1 / KNL1 MELT repeat / MELT motif
Similarity search - Domain/homology
Kinetochore scaffold 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.497 Å
AuthorsPetrovic, A. / Mosalaganti, S. / Keller, J. / Mattiuzzo, M. / Overlack, K. / Wohlgemuth, S. / Pasqualato, S. / Raunser, S. / Musacchio, A.
CitationJournal: Mol Cell / Year: 2014
Title: Modular assembly of RWD domains on the Mis12 complex underlies outer kinetochore organization.
Authors: Arsen Petrovic / Shyamal Mosalaganti / Jenny Keller / Marta Mattiuzzo / Katharina Overlack / Veronica Krenn / Anna De Antoni / Sabine Wohlgemuth / Valentina Cecatiello / Sebastiano ...Authors: Arsen Petrovic / Shyamal Mosalaganti / Jenny Keller / Marta Mattiuzzo / Katharina Overlack / Veronica Krenn / Anna De Antoni / Sabine Wohlgemuth / Valentina Cecatiello / Sebastiano Pasqualato / Stefan Raunser / Andrea Musacchio /
Abstract: Faithful chromosome segregation is mandatory for cell and organismal viability. Kinetochores, large protein assemblies embedded in centromeric chromatin, establish a mechanical link between ...Faithful chromosome segregation is mandatory for cell and organismal viability. Kinetochores, large protein assemblies embedded in centromeric chromatin, establish a mechanical link between chromosomes and spindle microtubules. The KMN network, a conserved 10-subunit kinetochore complex, harbors the microtubule-binding interface. RWD domains in the KMN subunits Spc24 and Spc25 mediate kinetochore targeting of the microtubule-binding subunits by interacting with the Mis12 complex, a KMN subcomplex that tethers directly onto the underlying chromatin layer. Here, we show that Knl1, a KMN subunit involved in mitotic checkpoint signaling, also contains RWD domains that bind the Mis12 complex and that mediate kinetochore targeting of Knl1. By reporting the first 3D electron microscopy structure of the KMN network, we provide a comprehensive framework to interpret how interactions of RWD-containing proteins with the Mis12 complex shape KMN network topology. Our observations unveil a regular pattern in the construction of the outer kinetochore.
History
DepositionOct 31, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein CASC5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4855
Polymers24,1731
Non-polymers3124
Water1,820101
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.855, 74.855, 88.756
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2401-

CL

21A-2519-

HOH

31A-2568-

HOH

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Components

#1: Protein Protein CASC5 / ALL1-fused gene from chromosome 15q14 protein / AF15q14 / Bub-linking kinetochore protein / Blinkin ...ALL1-fused gene from chromosome 15q14 protein / AF15q14 / Bub-linking kinetochore protein / Blinkin / Cancer susceptibility candidate gene 5 protein / Cancer/testis antigen 29 / CT29 / Kinetochore-null protein 1 / Protein D40/AF15q14


Mass: 24173.303 Da / Num. of mol.: 1 / Fragment: Knl1 C-terminal domain, UNP residues 2131-2337
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASC5, KIAA1570, KNL1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NG31
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.77 Å3/Da / Density % sol: 55.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 120-300 KSCN, 100 mM BisTris Propane (pH 8.6-9.2), 17 % (v/v) PEG 3350 and 1 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.497→32.413 Å / Num. obs: 10352 / % possible obs: 99.8 % / Observed criterion σ(F): 1.35 / Observed criterion σ(I): 1.35
Reflection shellResolution: 2.5→2.59 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
Auto-Rickshawphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.497→32.413 Å / SU ML: 0.74 / σ(F): 1.35 / Phase error: 24.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2416 498 4.82 %RANDOM
Rwork0.1905 ---
obs0.193 10328 99.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 79.29 Å2 / ksol: 0.372 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.0627 Å2-0 Å20 Å2
2---2.0627 Å2-0 Å2
3---4.1253 Å2
Refinement stepCycle: LAST / Resolution: 2.497→32.413 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1684 0 19 101 1804
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071741
X-RAY DIFFRACTIONf_angle_d1.0262364
X-RAY DIFFRACTIONf_dihedral_angle_d17.87624
X-RAY DIFFRACTIONf_chiral_restr0.062263
X-RAY DIFFRACTIONf_plane_restr0.005301
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4974-2.74860.2891300.22442405X-RAY DIFFRACTION100
2.7486-3.1460.26821210.19172433X-RAY DIFFRACTION100
3.146-3.96250.22891160.1652447X-RAY DIFFRACTION100
3.9625-32.41590.22321310.19212545X-RAY DIFFRACTION99

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