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- PDB-8q5h: Human KMN network (outer kinetochore) -

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Basic information

Entry
Database: PDB / ID: 8q5h
TitleHuman KMN network (outer kinetochore)
Components
  • (Kinetochore protein ...) x 2
  • (Kinetochore-associated protein ...) x 2
  • Kinetochore scaffold 1
  • Polyamine-modulated factor 1
  • Protein MIS12 homolog
KeywordsCELL CYCLE / OUTER KINETOCHORE / KMN / COMPLEX
Function / homology
Function and homology information


Knl1/Spc105 complex / positive regulation of meiosis I spindle assembly checkpoint / homologous chromosome orientation in meiotic metaphase I / MIS12/MIND type complex / skeletal muscle satellite cell proliferation / Ndc80 complex / leucine zipper domain binding / acrosome assembly / regulation of mitotic cell cycle spindle assembly checkpoint / attachment of spindle microtubules to kinetochore ...Knl1/Spc105 complex / positive regulation of meiosis I spindle assembly checkpoint / homologous chromosome orientation in meiotic metaphase I / MIS12/MIND type complex / skeletal muscle satellite cell proliferation / Ndc80 complex / leucine zipper domain binding / acrosome assembly / regulation of mitotic cell cycle spindle assembly checkpoint / attachment of spindle microtubules to kinetochore / kinetochore assembly / attachment of mitotic spindle microtubules to kinetochore / protein localization to kinetochore / mitotic spindle assembly checkpoint signaling / 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 / mitotic spindle organization / acrosomal vesicle / chromosome segregation / RHO GTPases Activate Formins / kinetochore / fibrillar center / spindle pole / Separation of Sister Chromatids / azurophil granule lumen / transcription regulator complex / transcription by RNA polymerase II / transcription coactivator activity / nuclear body / nuclear speck / cell division / intracellular membrane-bounded organelle / Neutrophil degranulation / nucleolus / Golgi apparatus / extracellular region / nucleoplasm / nucleus / cytosol
Similarity search - Function
Knl1, C-terminal RWD domain / Knl1 RWD C-terminal domain / Chromosome segregation protein Spc25, C-terminal / Kinetochore Mis14/Nsl1 / Kinetochore scaffold 1 / KNL1 MELT repeat / Kinetochore protein Spc25 / Chromosome segregation protein Spc25 / Kinetochore protein Mis14 like / MELT motif ...Knl1, C-terminal RWD domain / Knl1 RWD C-terminal domain / Chromosome segregation protein Spc25, C-terminal / Kinetochore Mis14/Nsl1 / Kinetochore scaffold 1 / KNL1 MELT repeat / Kinetochore protein Spc25 / Chromosome segregation protein Spc25 / Kinetochore protein Mis14 like / MELT motif / Nuclear MIS12/MIND complex subunit PMF1/Nnf1 / Centromere protein Mis12 / Nnf1 / Mis12 protein / Kinetochore-associated protein Dsn1/Mis13 / Mis12-Mtw1 protein family / Kinetochore-Ndc80 subunit Spc24 / Spc24 subunit of Ndc80
Similarity search - Domain/homology
Polyamine-modulated factor 1 / Kinetochore protein Spc24 / Kinetochore scaffold 1 / Kinetochore-associated protein NSL1 homolog / Protein MIS12 homolog / Kinetochore-associated protein DSN1 homolog / Kinetochore protein Spc25
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsRaisch, T. / Polley, S. / Vetter, I. / Musacchio, A. / Raunser, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: To Be Published
Title: Insights into human outer kinetochore assembly and force transmission from a structure-function analysis of the KMN network
Authors: Polley, S. / Raisch, T. / Aponte, C. / Koerner, M. / Terbeck, M. / Raunser, S. / Graeter, F. / Vetter, I. / Musacchio, A.
History
DepositionAug 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
4: Kinetochore protein Spc24
5: Kinetochore protein Spc25
A: Protein MIS12 homolog
B: Polyamine-modulated factor 1
D: Kinetochore-associated protein DSN1 homolog
K: Kinetochore scaffold 1
N: Kinetochore-associated protein NSL1 homolog


Theoretical massNumber of molelcules
Total (without water)185,9747
Polymers185,9747
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Kinetochore protein ... , 2 types, 2 molecules 45

#1: Protein Kinetochore protein Spc24 / / hSpc24


Mass: 10344.515 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPC24, SPBC24 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NBT2
#2: Protein Kinetochore protein Spc25 / / hSpc25


Mass: 16285.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPC25, SPBC25, AD024 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HBM1

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Protein , 3 types, 3 molecules ABK

#3: Protein Protein MIS12 homolog


Mass: 24170.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MIS12 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9H081
#4: Protein Polyamine-modulated factor 1 / PMF-1


Mass: 23368.311 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PMF1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6P1K2
#6: Protein Kinetochore scaffold 1 / 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 CASC5 / Protein D40/AF15q14


Mass: 38644.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KNL1, CASC5, KIAA1570 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NG31

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Kinetochore-associated protein ... , 2 types, 2 molecules DN

#5: Protein Kinetochore-associated protein DSN1 homolog


Mass: 40951.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DSN1, C20orf172, MIS13 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9H410
#7: Protein Kinetochore-associated protein NSL1 homolog


Mass: 32208.951 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NSL1, C1orf48, DC31, DC8, MIS14 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96IY1

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: KMN network / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 63.9 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 230597 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039763
ELECTRON MICROSCOPYf_angle_d0.70713173
ELECTRON MICROSCOPYf_dihedral_angle_d4.9481259
ELECTRON MICROSCOPYf_chiral_restr0.0431452
ELECTRON MICROSCOPYf_plane_restr0.0061710

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