[English] 日本語
Yorodumi
- EMDB-54586: Multibody refinement cryo-EM density map of the base of the Sacch... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-54586
TitleMultibody refinement cryo-EM density map of the base of the Saccharomyces cerevisiae KMN junction complex with Mis12c(Mtw1c) head 2 domain resolved
Map dataNote not resampled to the consensus map to preserve higher resolution information.
Sample
  • Complex: Saccharomyces cerevisiae outer kinetochore KMN junction complex
    • Complex: Saccharomyces cerevisiae outer kinetochore Mis12c(Mtw1c) subcomplex
      • Protein or peptide: Kinetochore-associated protein DSN1
      • Protein or peptide: Kinetochore-associated protein MTW1
      • Protein or peptide: Kinetochore-associated protein NNF1
      • Protein or peptide: Kinetochore-associated protein NSL1
    • Complex: Saccharomyces cerevisiae outer kinetochore Knl1c subcomplex
    • Complex: Saccharomyces cerevisiae outer kinetochore Ndc80c
KeywordsKinetochore / chromosome segregation / mitosis / cell cycle
Function / homology
Function and homology information


MIS12/MIND type complex / spindle attachment to meiosis I kinetochore / attachment of spindle microtubules to kinetochore / meiotic sister chromatid cohesion, centromeric / kinetochore assembly / outer kinetochore / protein localization to kinetochore / mitotic sister chromatid segregation / Neutrophil degranulation / chromosome segregation ...MIS12/MIND type complex / spindle attachment to meiosis I kinetochore / attachment of spindle microtubules to kinetochore / meiotic sister chromatid cohesion, centromeric / kinetochore assembly / outer kinetochore / protein localization to kinetochore / mitotic sister chromatid segregation / Neutrophil degranulation / chromosome segregation / kinetochore / spindle pole / cell division / nucleus
Similarity search - Function
Kinetochore-associated protein Nnf1 / Kinetochore Mis14/Nsl1 / Kinetochore protein Mis14 like / Nuclear MIS12/MIND complex subunit PMF1/Nnf1 / Centromere protein Mis12 / Nnf1 / Mis12 protein / Kinetochore-associated protein Dsn1/Mis13 / Mis12-Mtw1 protein family / EF-Hand 1, calcium-binding site
Similarity search - Domain/homology
Kinetochore-associated protein MTW1 / Kinetochore-associated protein DSN1 / Kinetochore-associated protein NNF1 / Kinetochore-associated protein NSL1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.5 Å
AuthorsTurner NN / Barford D
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Cancer Research UKC576/A25675 United Kingdom
Cancer Research UKC576/A14109 United Kingdom
UK Research and Innovation (UKRI)MC_UP_1201/6 United Kingdom
CitationJournal: To Be Published
Title: Assembly and phospho-regulatory mechanisms of the budding yeast outer kinetochore KMN complex
Authors: Turner NN / Zhang Z / Yang J / Muir KW / McLaughlin SH / Morgan T / Barford D
History
DepositionJul 29, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_54586.png

Downloads & links

-
Map

FileDownload / File: emd_54586.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNote not resampled to the consensus map to preserve higher resolution information.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.65 Å/pix.
x 192 pix.
= 316.8 Å		1.65 Å/pix.
x 192 pix.
= 316.8 Å		1.65 Å/pix.
x 192 pix.
= 316.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.035442203 - 0.14359112
Average (Standard dev.)0.00016740304 (±0.0026028291)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 316.8 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Local resolution file for the deposited map.

Fileemd_54586_additional_1.map
AnnotationLocal resolution file for the deposited map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Masked, post-processed and filtered map used for molecular...

Fileemd_54586_additional_2.map
AnnotationMasked, post-processed and filtered map used for molecular model building. Note resampled to the consensus map for molecular model building.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Note not resampled to the consensus map to...

Fileemd_54586_half_map_1.map
AnnotationNote not resampled to the consensus map to preserve higher resolution information.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Note not resampled to the consensus map to...

Fileemd_54586_half_map_2.map
AnnotationNote not resampled to the consensus map to preserve higher resolution information.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Saccharomyces cerevisiae outer kinetochore KMN junction complex

EntireName: Saccharomyces cerevisiae outer kinetochore KMN junction complex
Components
  • Complex: Saccharomyces cerevisiae outer kinetochore KMN junction complex
    • Complex: Saccharomyces cerevisiae outer kinetochore Mis12c(Mtw1c) subcomplex
      • Protein or peptide: Kinetochore-associated protein DSN1
      • Protein or peptide: Kinetochore-associated protein MTW1
      • Protein or peptide: Kinetochore-associated protein NNF1
      • Protein or peptide: Kinetochore-associated protein NSL1
    • Complex: Saccharomyces cerevisiae outer kinetochore Knl1c subcomplex
    • Complex: Saccharomyces cerevisiae outer kinetochore Ndc80c

-
Supramolecule #1: Saccharomyces cerevisiae outer kinetochore KMN junction complex

SupramoleculeName: Saccharomyces cerevisiae outer kinetochore KMN junction complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Imaged sample also contained Saccharomyces cerevisiae kinetochore protein NDC80 (UniProtKB accession P40460); Saccharomyces cerevisiae kinetochore protein NUF2 (UniProtKB accession P33895) ...Details: Imaged sample also contained Saccharomyces cerevisiae kinetochore protein NDC80 (UniProtKB accession P40460); Saccharomyces cerevisiae kinetochore protein NUF2 (UniProtKB accession P33895) with a C-terminal HRV-3C protease cleavage site and twin-strep-tag II affinity tag; Saccharomyces cerevisiae kinetochore protein SPC24 (UniProtKB accession code Q04477); Saccharomyces cerevisiae Kinetochore protein SPC25 (UniProtKB accession code P40014); Saccharomyces cerevisiae outer kinetochore KNL1 complex subunit SPC105 (UniProtKB accession code P53148); and Saccharomyces cerevisiae outer kinetochore KNL1 complex subunit KRE28 (UniProtKB accession code Q04431) with a C-terminal TEV protease cleavage site and twin-strep-tag II affinity tag
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: 288c
Molecular weightTheoretical: 187.080 kDa/nm

-
Supramolecule #2: Saccharomyces cerevisiae outer kinetochore Mis12c(Mtw1c) subcomplex

SupramoleculeName: Saccharomyces cerevisiae outer kinetochore Mis12c(Mtw1c) subcomplex
type: complex / ID: 2 / Parent: 1 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: 288c

-
Supramolecule #3: Saccharomyces cerevisiae outer kinetochore Knl1c subcomplex

SupramoleculeName: Saccharomyces cerevisiae outer kinetochore Knl1c subcomplex
type: complex / ID: 3 / Parent: 1
Details: N-terminal truncation of Knl1(Spc105) residues 1-444
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: 288c

-
Supramolecule #4: Saccharomyces cerevisiae outer kinetochore Ndc80c

SupramoleculeName: Saccharomyces cerevisiae outer kinetochore Ndc80c / type: complex / ID: 4 / Parent: 1 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: 288c

-
Macromolecule #1: Kinetochore-associated protein DSN1

MacromoleculeName: Kinetochore-associated protein DSN1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 65.777023 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSLEPTQTVS GTPPMLHQRT HKQVYPLRME TIPILESDSK ATLQSNEPTQ KDEEETEYFE NKQSVSNLSP DLKFKRHKNK HIQGFPTLG ERLDNLQDIK KAKRVENFNS SAPIADDNHS GDATANATAN ATANATANVN ASAMPAPYMP YYYYYHPMNA P TPAMIPYP ...String:
MSLEPTQTVS GTPPMLHQRT HKQVYPLRME TIPILESDSK ATLQSNEPTQ KDEEETEYFE NKQSVSNLSP DLKFKRHKNK HIQGFPTLG ERLDNLQDIK KAKRVENFNS SAPIADDNHS GDATANATAN ATANATANVN ASAMPAPYMP YYYYYHPMNA P TPAMIPYP GSPMHSIMPN SSLQPFYSQP TAAGGPDMTT PQNISSSQQL LPAPQLFPYG SFHQQQLQQP HYIQRTRERK KS IGSQRGR RLSMLASQAN GGSTIISPHK DIPEEDFYTV VGNASFGKNL QIRQLFNWCL MRSLHKLELK AKNQEEEGEL EHL TKKSKL ESTKAETDYV DPKRLAMVII KEFVDDLKKD HIAIDWEDEE KYEDEDEEKI LDNTENYDDT ELRQLFQEND DDDD DDDEV DYSEIQRSRR KFSERRKALP KEPKKLLPNS KNVENTKNLS ILTSKVNAIK NEVKEWAVTL DTSRPDLEWQ ELTSF SSQP LEPLSDTEEP DLAIADVETK LETKVDELRY QSHILNSHSL ALNEITNSKV NKLNIETMRK ISSETDDDHS QVINPQ QLL KGLSLSFSKK LDL

UniProtKB: Kinetochore-associated protein DSN1

-
Macromolecule #2: Kinetochore-associated protein MTW1

MacromoleculeName: Kinetochore-associated protein MTW1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 33.29118 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSAPTMRSTS ILTEHLGYPP ISLVDDIINA VNEIMYKCTA AMEKYLLSKS KIGEEDYGEE IKSGVAKLES LLENSVDKNF DKLELYVLR NVLRIPEEYL DANVFRLENQ KDLVIVDENE LKKSEEKLRE KVNDVELAFK KNEMLLKRVT KVKRLLFTIR G FKQKLNEL ...String:
MSAPTMRSTS ILTEHLGYPP ISLVDDIINA VNEIMYKCTA AMEKYLLSKS KIGEEDYGEE IKSGVAKLES LLENSVDKNF DKLELYVLR NVLRIPEEYL DANVFRLENQ KDLVIVDENE LKKSEEKLRE KVNDVELAFK KNEMLLKRVT KVKRLLFTIR G FKQKLNEL LKCKDDVQLQ KILESLKPID DTMTLLTDSL RKLYVDSEST SSTEEVEALL QRLKTNGKQN NKDFRTRYID IR TNNVLRK LGLLGDKEDE KQSAKPDART QAGDIVSIDI EEPQLDLLDD VL

UniProtKB: Kinetochore-associated protein MTW1

-
Macromolecule #3: Kinetochore-associated protein NNF1

MacromoleculeName: Kinetochore-associated protein NNF1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 23.668541 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MVNSHGIRYI RLKQVFNRAL DQSISKLQSW DKVSSCFPQY VNSKQGAINV ANCQRQLTEF WTELCQREFK EIMEERNVEQ KLNELDELI LEAKERYTDR DQDEVNKGPA IDELSSKELV ECHLYSQRMH AIHEIDERLA KVNEMNDQLA QELKDLETQV E VEKNEIGK ...String:
MVNSHGIRYI RLKQVFNRAL DQSISKLQSW DKVSSCFPQY VNSKQGAINV ANCQRQLTEF WTELCQREFK EIMEERNVEQ KLNELDELI LEAKERYTDR DQDEVNKGPA IDELSSKELV ECHLYSQRMH AIHEIDERLA KVNEMNDQLA QELKDLETQV E VEKNEIGK MYDEYLGSHT DQPANVLLVQ SLNDMVLELK ENY

UniProtKB: Kinetochore-associated protein NNF1

-
Macromolecule #4: Kinetochore-associated protein NSL1

MacromoleculeName: Kinetochore-associated protein NSL1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 25.448398 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSQGQSKKLD VTVEQLRSIY HQFHDILEEK TDLHLPKKEY DDDAVRREVQ IQLQEFLLSA MTMASKSLEV VNADTVGKTV KQLIMESQE KYMEPFDLDL NEQVRKMYQE WEDETVKVAQ LRQTGPAKIN EVYNNSKDEY LAQLDGRIGV LQARMMQQQS A DHDDSTDD ...String:
MSQGQSKKLD VTVEQLRSIY HQFHDILEEK TDLHLPKKEY DDDAVRREVQ IQLQEFLLSA MTMASKSLEV VNADTVGKTV KQLIMESQE KYMEPFDLDL NEQVRKMYQE WEDETVKVAQ LRQTGPAKIN EVYNNSKDEY LAQLDGRIGV LQARMMQQQS A DHDDSTDD ADDHINWEHI KQDYVASLNE LYQTQQDLPK VRYNVEKVKR LMDFLEED

UniProtKB: Kinetochore-associated protein NSL1

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
Component:
ConcentrationNameFormula
20.0 mMHEPES
150.0 mMSodium chlorideNaCl
1.0 mMTCEP
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK III

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 26390 / Average exposure time: 1.75 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 2592458
Details: Selected using Topaz particle picker trained on manually picked micrographs
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Details: CTFFIND 4.1 used as implemented in Relion 4.0 / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0)
Details: Multibody refinement in RELION 5.0 using Blush regularization
Number images used: 18160
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 4 / Avg.num./class: 80269 / Software - Name: RELION (ver. 5.0)
Details: Focussed classification using Blush regularization.
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
ChainPDB ID
chain_id: Dsn1, residue_range: 229-365, source_name: AlphaFold, initial_model_type: in silico model
chain_id: Nsl1, residue_range: 2-96, source_name: AlphaFold, initial_model_type: in silico model
chain_id: Mtw1, residue_range: 1-151, source_name: PDB, initial_model_type: experimental model

9s4q

chain_id: Nnf1, residue_range: 1-153, source_name: PDB, initial_model_type: experimental model

9s4q

chain_id: Dsn1, residue_range: 435-483, source_name: PDB, initial_model_type: experimental model

9s4q

chain_id: Nsl1, residue_range: 97-159, source_name: PDB, initial_model_type: experimental model

9s4q

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9s53:
Cryo-EM structure of the base of the Saccharomyces cerevisiae KMN junction complex containing the Mis12c(Mtw1c) head 2 domain

+
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