+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18179 | |||||||||
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Title | Human KMN network (outer kinetochore) | |||||||||
Map data | Sharpened map | |||||||||
Sample |
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Keywords | OUTER KINETOCHORE / KMN / COMPLEX / CELL CYCLE | |||||||||
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 / regulation of mitotic cell cycle spindle assembly checkpoint / acrosome assembly / 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 / regulation of mitotic cell cycle spindle assembly checkpoint / acrosome assembly / 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 / microtubule binding / 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 | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||
Authors | Raisch T / Polley S / Vetter I / Musacchio A / Raunser S | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_18179.map.gz | 59.6 MB | EMDB map data format | |
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Header (meta data) | emd-18179-v30.xml emd-18179.xml | 24.6 KB 24.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_18179_fsc.xml | 8.5 KB | Display | FSC data file |
Images | emd_18179.png | 72.1 KB | ||
Masks | emd_18179_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-18179.cif.gz | 6.5 KB | ||
Others | emd_18179_additional_1.map.gz emd_18179_additional_2.map.gz emd_18179_half_map_1.map.gz emd_18179_half_map_2.map.gz | 32.1 MB 57.2 MB 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18179 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18179 | HTTPS FTP |
-Related structure data
Related structure data | 8q5hMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_18179.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Sharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.36 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_18179_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Non-sharpened map
File | emd_18179_additional_1.map | ||||||||||||
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Annotation | Non-sharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Map sharpened by DeepEMhancer
File | emd_18179_additional_2.map | ||||||||||||
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Annotation | Map sharpened by DeepEMhancer | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B
File | emd_18179_half_map_1.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A
File | emd_18179_half_map_2.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : KMN network
Entire | Name: KMN network |
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Components |
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-Supramolecule #1: KMN network
Supramolecule | Name: KMN network / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Kinetochore protein Spc24
Macromolecule | Name: Kinetochore protein Spc24 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 10.344515 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MELKEIEADL ERQEKEVDED TTVTIPSAVY VAQLYHQVSK IEWDYECEPG MVKGIHHGPS VAQPIHLDST QLSRKFISDY LWSLVDTEW UniProtKB: Kinetochore protein Spc24 |
-Macromolecule #2: Kinetochore protein Spc25
Macromolecule | Name: Kinetochore protein Spc25 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 16.285332 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKQELEVLTA NIQDLKEEYS RKKETISTAN KANAERLKRL QKSADLYKDR LGLEIRKIYG EKLQFIFTNI DPKNPESPFM FSLHLNEAR DYEVSDSAPH LEGLAEFQEN VRKTNNFSAF LANVRKAFTA TVYNHHHHHH UniProtKB: Kinetochore protein Spc25 |
-Macromolecule #3: Protein MIS12 homolog
Macromolecule | Name: Protein MIS12 homolog / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 24.170922 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MSVDPMTYEA QFFGFTPQTC MLRIYIAFQD YLFEVMQAVE QVILKKLDGI PDCDISPVQI RKCTEKFLCF MKGHFDNLFS KMEQLFLQL ILRIPSNILL PEDKCKETPY SEEDFQHLQK EIEQLQEKYK TELCTKQALL AELEEQKIVQ AKLKQTLTFF D ELHNVGRD ...String: MSVDPMTYEA QFFGFTPQTC MLRIYIAFQD YLFEVMQAVE QVILKKLDGI PDCDISPVQI RKCTEKFLCF MKGHFDNLFS KMEQLFLQL ILRIPSNILL PEDKCKETPY SEEDFQHLQK EIEQLQEKYK TELCTKQALL AELEEQKIVQ AKLKQTLTFF D ELHNVGRD HGTSDFRESL VSLVQNSRKL QNIRDNVEKE SKRLKIS UniProtKB: Protein MIS12 homolog |
-Macromolecule #4: Polyamine-modulated factor 1
Macromolecule | Name: Polyamine-modulated factor 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.368311 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MAEASSANLG SGCEEKRHEG SSSESVPPGT TISRVKLLDT MVDTFLQKLV AAGSYQRFTD CYKCFYQLQP AMTQQIYDKF IAQLQTSIR EEISDIKEEG NLEAVLNALD KIVEEGKVRK EPAWRPSGIP EKDLHSVMAP YFLQQRDTLR RHVQKQEAEN Q QLADAVLA ...String: MAEASSANLG SGCEEKRHEG SSSESVPPGT TISRVKLLDT MVDTFLQKLV AAGSYQRFTD CYKCFYQLQP AMTQQIYDKF IAQLQTSIR EEISDIKEEG NLEAVLNALD KIVEEGKVRK EPAWRPSGIP EKDLHSVMAP YFLQQRDTLR RHVQKQEAEN Q QLADAVLA GRRQVEELQL QVQAQQQAWQ ALHREQRELV AVLREPE UniProtKB: Polyamine-modulated factor 1 |
-Macromolecule #5: Kinetochore-associated protein DSN1 homolog
Macromolecule | Name: Kinetochore-associated protein DSN1 homolog / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 40.951062 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MTSVTRSEII DEKGPVMSKT HDHQLESSLS PVEVFAKTSA SLEMNQGVSE ERIHLGSSPK KGGNCDLSHQ ERLQSKSLHL SPQEQSASY QDRRQSWRRA SMKETNRRKS LHPIHQGITE LSRSISVDLA ESKRLGCLLL SSFQFSIQKL EPFLRDTKGF S LESFRAKA ...String: MTSVTRSEII DEKGPVMSKT HDHQLESSLS PVEVFAKTSA SLEMNQGVSE ERIHLGSSPK KGGNCDLSHQ ERLQSKSLHL SPQEQSASY QDRRQSWRRA SMKETNRRKS LHPIHQGITE LSRSISVDLA ESKRLGCLLL SSFQFSIQKL EPFLRDTKGF S LESFRAKA SSLSEELKHF ADGLETDGTL QKCFEDSNGK ASDFSLEASV AEMKEYITKF SLERQTWDQL LLHYQQEAKE IL SRGSTEA KITEVKVEPM TYLGSSQNEV LNTKPDYQKI LQNQSKVFDC MELVMDELQG SVKQLQAFMD ESTQCFQKVS VQL GKRSMQ QLDPSPARKL LKLQLQNPPA IHGSGSGSCQ HHHHHH UniProtKB: Kinetochore-associated protein DSN1 homolog |
-Macromolecule #6: Kinetochore scaffold 1
Macromolecule | Name: Kinetochore scaffold 1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 38.644453 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GAMGGSMGKL VQSAQNEREK LQIKIDEMDK ILKKIDNCLT EMETETKNLE DEEKNNPVEE WDSEMRAAEK ELEQLKTEEE ELQRNLLEL EVQKEQTLAQ IDFMQKQRNR TEELLDQLSL SEWDVVEWSD DQAVFTFVYD TIQLTITFEE SVVGFPFLDK R YRKIVDVN ...String: GAMGGSMGKL VQSAQNEREK LQIKIDEMDK ILKKIDNCLT EMETETKNLE DEEKNNPVEE WDSEMRAAEK ELEQLKTEEE ELQRNLLEL EVQKEQTLAQ IDFMQKQRNR TEELLDQLSL SEWDVVEWSD DQAVFTFVYD TIQLTITFEE SVVGFPFLDK R YRKIVDVN FQSLLDEDQA PPSSLLVHKL IFQYVEEKES WKKTCTTQHQ LPKMLEEFSL VVHHCRLLGE EIEYLKRWGP NY NLMNIDI NNNELRLLFS SSAAFAKFEI TLFLSAYYPS VPLPSTIQNH VGNTSQDDIA TILSKVPLEN NYLKNVVKQI YQD LFQDCH FYH UniProtKB: Kinetochore scaffold 1 |
-Macromolecule #7: Kinetochore-associated protein NSL1 homolog
Macromolecule | Name: Kinetochore-associated protein NSL1 homolog / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 32.208951 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MAGSPELVVL DPPWDKELAA GTESQALVSA TPREDFRVRC TSKRAVTEML QLCGRFVQKL GDALPEEIRE PALRDAQWTF ESAVQENIS INGQAWQEAS DNCFMDSDIK VLEDQFDEII VDIATKRKQY PRKILECVIK TIKAKQEILK QYHPVVHPLD L KYDPDPAP ...String: MAGSPELVVL DPPWDKELAA GTESQALVSA TPREDFRVRC TSKRAVTEML QLCGRFVQKL GDALPEEIRE PALRDAQWTF ESAVQENIS INGQAWQEAS DNCFMDSDIK VLEDQFDEII VDIATKRKQY PRKILECVIK TIKAKQEILK QYHPVVHPLD L KYDPDPAP HMENLKCRGE TVAKEISEAM KSLPALIEQG EGFSQVLRMQ PVIHLQRIHQ EVFSSCHRKP DAKPENFITQ IE TTPTETA SRKTSDMVLK RKQTKDCPQR KWYPLRPKKI NLDT UniProtKB: Kinetochore-associated protein NSL1 homolog |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 63.9 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |