[English] 日本語
Yorodumi
- EMDB-18179: Human KMN network (outer kinetochore) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-18179
TitleHuman KMN network (outer kinetochore)
Map dataSharpened map
Sample
  • Complex: KMN network
    • Protein or peptide: Kinetochore protein Spc24
    • Protein or peptide: Kinetochore protein Spc25
    • Protein or peptide: Protein MIS12 homolog
    • Protein or peptide: Polyamine-modulated factor 1
    • Protein or peptide: Kinetochore-associated protein DSN1 homolog
    • Protein or peptide: Kinetochore scaffold 1
    • Protein or peptide: Kinetochore-associated protein NSL1 homolog
KeywordsOUTER 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 / 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 / outer kinetochore / 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 / Deposition of new CENPA-containing nucleosomes at the centromere / acrosomal vesicle / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / mitotic spindle organization / chromosome segregation / RHO GTPases Activate Formins / kinetochore / fibrillar center / spindle pole / azurophil granule lumen / Separation of Sister Chromatids / transcription regulator complex / microtubule binding / transcription by RNA polymerase II / transcription coactivator activity / nuclear speck / nuclear body / cell division / intracellular membrane-bounded organelle / Neutrophil degranulation / nucleolus / Golgi apparatus / extracellular region / nucleoplasm / nucleus / cytosol
Similarity search - Function
Chromosome segregation protein Spc25, C-terminal / Kinetochore Mis14/Nsl1 / Kinetochore scaffold 1 / Knl1, C-terminal RWD domain / KNL1 MELT repeat / Kinetochore protein Spc25 / Chromosome segregation protein Spc25 / Kinetochore protein Mis14 like / Knl1 RWD C-terminal domain / MELT motif ...Chromosome segregation protein Spc25, C-terminal / Kinetochore Mis14/Nsl1 / Kinetochore scaffold 1 / Knl1, C-terminal RWD domain / KNL1 MELT repeat / Kinetochore protein Spc25 / Chromosome segregation protein Spc25 / Kinetochore protein Mis14 like / Knl1 RWD C-terminal domain / 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 / Outer kinetochore KNL1 complex subunit KNL1 / Kinetochore-associated protein NSL1 homolog / Protein MIS12 homolog / Kinetochore-associated protein DSN1 homolog / Kinetochore protein Spc25
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsRaisch T / Polley S / Vetter I / Musacchio A / Raunser S
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Structure of the human KMN complex and implications for regulation of its assembly.
Authors: Soumitra Polley / Tobias Raisch / Sabrina Ghetti / Marie Körner / Melina Terbeck / Frauke Gräter / Stefan Raunser / Camilo Aponte-Santamaría / Ingrid R Vetter / Andrea Musacchio /
Abstract: Biorientation of chromosomes during cell division is necessary for precise dispatching of a mother cell's chromosomes into its two daughters. Kinetochores, large layered structures built on ...Biorientation of chromosomes during cell division is necessary for precise dispatching of a mother cell's chromosomes into its two daughters. Kinetochores, large layered structures built on specialized chromosome loci named centromeres, promote biorientation by binding and sensing spindle microtubules. One of the outer layer main components is a ten-subunit assembly comprising Knl1C, Mis12C and Ndc80C (KMN) subcomplexes. The KMN is highly elongated and docks on kinetochores and microtubules through interfaces at its opposite extremes. Here, we combine cryogenic electron microscopy reconstructions and AlphaFold2 predictions to generate a model of the human KMN that reveals all intra-KMN interfaces. We identify and functionally validate two interaction interfaces that link Mis12C to Ndc80C and Knl1C. Through targeted interference experiments, we demonstrate that this mutual organization strongly stabilizes the KMN assembly. Our work thus reports a comprehensive structural and functional analysis of this part of the kinetochore microtubule-binding machinery and elucidates the path of connections from the chromatin-bound components to the force-generating components.
History
DepositionAug 9, 2023-
Header (metadata) releaseFeb 14, 2024-
Map releaseFeb 14, 2024-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_18179.png

Downloads & links

-
Map

FileDownload / File: emd_18179.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 256 pix.
= 348.16 Å		1.36 Å/pix.
x 256 pix.
= 348.16 Å		1.36 Å/pix.
x 256 pix.
= 348.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.49
Minimum - Maximum-1.0764635 - 2.0538406
Average (Standard dev.)0.0013203623 (±0.049932174)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 348.16 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_18179_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Non-sharpened map

Fileemd_18179_additional_1.map
AnnotationNon-sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Map sharpened by DeepEMhancer

Fileemd_18179_additional_2.map
AnnotationMap sharpened by DeepEMhancer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map B

Fileemd_18179_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map A

Fileemd_18179_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : KMN network

EntireName: KMN network
Components
  • Complex: KMN network
    • Protein or peptide: Kinetochore protein Spc24
    • Protein or peptide: Kinetochore protein Spc25
    • Protein or peptide: Protein MIS12 homolog
    • Protein or peptide: Polyamine-modulated factor 1
    • Protein or peptide: Kinetochore-associated protein DSN1 homolog
    • Protein or peptide: Kinetochore scaffold 1
    • Protein or peptide: Kinetochore-associated protein NSL1 homolog

-
Supramolecule #1: KMN network

SupramoleculeName: KMN network / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Kinetochore protein Spc24

MacromoleculeName: Kinetochore protein Spc24 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.344515 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MELKEIEADL ERQEKEVDED TTVTIPSAVY VAQLYHQVSK IEWDYECEPG MVKGIHHGPS VAQPIHLDST QLSRKFISDY LWSLVDTEW

UniProtKB: Kinetochore protein Spc24

-
Macromolecule #2: Kinetochore protein Spc25

MacromoleculeName: Kinetochore protein Spc25 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.285332 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKQELEVLTA NIQDLKEEYS RKKETISTAN KANAERLKRL QKSADLYKDR LGLEIRKIYG EKLQFIFTNI DPKNPESPFM FSLHLNEAR DYEVSDSAPH LEGLAEFQEN VRKTNNFSAF LANVRKAFTA TVYNHHHHHH

UniProtKB: Kinetochore protein Spc25

-
Macromolecule #3: Protein MIS12 homolog

MacromoleculeName: Protein MIS12 homolog / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.170922 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: 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

MacromoleculeName: Polyamine-modulated factor 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.368311 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: 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

MacromoleculeName: Kinetochore-associated protein DSN1 homolog / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.951062 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: 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

MacromoleculeName: Kinetochore scaffold 1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.644453 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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: Outer kinetochore KNL1 complex subunit KNL1

-
Macromolecule #7: Kinetochore-associated protein NSL1 homolog

MacromoleculeName: Kinetochore-associated protein NSL1 homolog / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.208951 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: 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

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 63.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 230597
Initial angle assignmentType: OTHER
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more