[English] 日本語
Yorodumi
- EMDB-18304: Outer kinetochore Ndc80-Dam1 alpha/beta-tubulin complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-18304
TitleOuter kinetochore Ndc80-Dam1 alpha/beta-tubulin complex
Map data3D flex reconstruction
Sample
  • Complex: Outer kinetochore Ndc80-Nuf2 CH domains bound to Dam1 in complex with alpha-beta tubulin
    • Protein or peptide: Tubulin alpha-1A chain
    • Protein or peptide: Tubulin beta chain
    • Protein or peptide: Kinetochore protein NDC80
    • Protein or peptide: Kinetochore protein NUF2
    • Protein or peptide: DASH complex subunit DAM1
  • Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: TAXOLPaclitaxel
KeywordsKinetochore / microtubule / error correction / chromosome segregation / CELL CYCLE
Function / homology
Function and homology information


mitotic spindle polar microtubule / Ndc80 complex / DASH complex / protein transport along microtubule to mitotic spindle pole body / mitotic sister chromatid biorientation / kinetochore organization / positive regulation of attachment of spindle microtubules to kinetochore / mitotic spindle pole body / meiotic chromosome segregation / attachment of spindle microtubules to kinetochore ...mitotic spindle polar microtubule / Ndc80 complex / DASH complex / protein transport along microtubule to mitotic spindle pole body / mitotic sister chromatid biorientation / kinetochore organization / positive regulation of attachment of spindle microtubules to kinetochore / mitotic spindle pole body / meiotic chromosome segregation / attachment of spindle microtubules to kinetochore / attachment of mitotic spindle microtubules to kinetochore / condensed chromosome, centromeric region / spindle pole body / protein localization to kinetochore / positive regulation of microtubule polymerization / mitotic spindle organization / chromosome segregation / spindle microtubule / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / mitotic spindle / kinetochore / microtubule cytoskeleton organization / mitotic cell cycle / microtubule / hydrolase activity / cell division / GTPase activity / protein-containing complex binding / GTP binding / identical protein binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
DASH complex subunit Dam1 / DASH complex subunit Dam1 / Kinetochore protein Nuf2, N-terminal / Nuf2, N-terminal domain superfamily / Nuf2 family / Kinetochore protein Ndc80 / Ndc80 domain superfamily / Domain of unknown function DUF5595 / HEC/Ndc80p family / Domain of unknown function (DUF5595) ...DASH complex subunit Dam1 / DASH complex subunit Dam1 / Kinetochore protein Nuf2, N-terminal / Nuf2, N-terminal domain superfamily / Nuf2 family / Kinetochore protein Ndc80 / Ndc80 domain superfamily / Domain of unknown function DUF5595 / HEC/Ndc80p family / Domain of unknown function (DUF5595) / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
Tubulin alpha-1A chain / Tubulin beta chain / Kinetochore protein NUF2 / Kinetochore protein NDC80 / DASH complex subunit DAM1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Sus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.54 Å
AuthorsMuir KW / Barford D
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)MC_UP_1201/6 United Kingdom
Cancer Research UKC576/A14109 United Kingdom
CitationJournal: Biorxiv / Year: 2023
Title: Mechanism of outer kinetochore assembly on microtubules and its regulation by mitotic error correction
Authors: Muir KW / Batters C / Dendooven T / Yang J / Zhang Z / Burt A / Barford D
History
DepositionAug 23, 2023-
Header (metadata) releaseApr 3, 2024-
Map releaseApr 3, 2024-
UpdateApr 3, 2024-
Current statusApr 3, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_18304.png

Downloads & links

-
Map

FileDownload / File: emd_18304.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D flex reconstruction
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 300 pix.
= 318. Å		1.06 Å/pix.
x 300 pix.
= 318. Å		1.06 Å/pix.
x 300 pix.
= 318. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.004
Minimum - Maximum-0.022294858 - 0.042420395
Average (Standard dev.)0.000082289516 (±0.0015254626)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 317.99997 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: 3D flex halfmap A

Fileemd_18304_additional_1.map
Annotation3D flex halfmap A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: 3D flex halfmap B

Fileemd_18304_additional_2.map
Annotation3D flex halfmap B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Local resolution filtered 3D flex map

Fileemd_18304_additional_3.map
AnnotationLocal resolution filtered 3D flex map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Local refinement reconstruction

Fileemd_18304_additional_4.map
AnnotationLocal refinement reconstruction
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Local refinement half map B

Fileemd_18304_half_map_1.map
AnnotationLocal refinement half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Local refinement half map A

Fileemd_18304_half_map_2.map
AnnotationLocal refinement half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Outer kinetochore Ndc80-Nuf2 CH domains bound to Dam1 in complex ...

EntireName: Outer kinetochore Ndc80-Nuf2 CH domains bound to Dam1 in complex with alpha-beta tubulin
Components
  • Complex: Outer kinetochore Ndc80-Nuf2 CH domains bound to Dam1 in complex with alpha-beta tubulin
    • Protein or peptide: Tubulin alpha-1A chain
    • Protein or peptide: Tubulin beta chain
    • Protein or peptide: Kinetochore protein NDC80
    • Protein or peptide: Kinetochore protein NUF2
    • Protein or peptide: DASH complex subunit DAM1
  • Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: TAXOLPaclitaxel

+
Supramolecule #1: Outer kinetochore Ndc80-Nuf2 CH domains bound to Dam1 in complex ...

SupramoleculeName: Outer kinetochore Ndc80-Nuf2 CH domains bound to Dam1 in complex with alpha-beta tubulin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

+
Macromolecule #1: Tubulin alpha-1A chain

MacromoleculeName: Tubulin alpha-1A chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 50.121266 KDa
SequenceString: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFSVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE ...String:
MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFSVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE FSIYPAPQVS TAVVEPYNSI LTTHTTLEHS DCAFMVDNEA IYDICRRNLD IERPTYTNLN RLIGQIVSSI TA SLRFDGA LNVDLTEFQT NLVPYPRAHF PLATYAPVIS AEKAYHEQLS VAEITNACFE PANQMVKCDP RHGKYMACCL LYR GDVVPK DVNAAIATIK TKRTIQFVDW CPTGFKVGIN YEPPTVVPGG DLAKVQRAVC MLSNTTAIAE AWARLDHKFD LMYA KRAFV HWYVGEGMEE GEFSEAREDM AALEKDYEEV GVDSVEGEGE EEGEEY

UniProtKB: Tubulin alpha-1A chain

+
Macromolecule #2: Tubulin beta chain

MacromoleculeName: Tubulin beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 49.90777 KDa
SequenceString: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEAAGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKESESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS ...String:
MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEAAGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKESESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS VVPSPKVSDT VVEPYNATLS VHQLVENTDE TYCIDNEALY DICFRTLKLT TPTYGDLNHL VSATMSGVTT CL RFPGQLN ADLRKLAVNM VPFPRLHFFM PGFAPLTSRG SQQYRALTVP ELTQQMFDAK NMMAACDPRH GRYLTVAAVF RGR MSMKEV DEQMLNVQNK NSSYFVEWIP NNVKTAVCDI PPRGLKMSAT FIGNSTAIQE LFKRISEQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QDATADEQGE FEEEGEEDEA

UniProtKB: Tubulin beta chain

+
Macromolecule #3: Kinetochore protein NDC80

MacromoleculeName: Kinetochore protein NDC80 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 80.609375 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MQSSTSTDQH VLHHMDPHRF TSQIPTATSS QLRRRNSTNQ GLTDMINKSI ARNTISGTGI PTGGINKNKR TRSTVAGGTN GTALALNDK SNSRNSVSRL SINQLGSLQQ HLSNRDPRPL RDKNFQSAIQ EEIYDYLKKN KFDIETNHPI SIKFLKQPTQ K GFIIIFKW ...String:
MQSSTSTDQH VLHHMDPHRF TSQIPTATSS QLRRRNSTNQ GLTDMINKSI ARNTISGTGI PTGGINKNKR TRSTVAGGTN GTALALNDK SNSRNSVSRL SINQLGSLQQ HLSNRDPRPL RDKNFQSAIQ EEIYDYLKKN KFDIETNHPI SIKFLKQPTQ K GFIIIFKW LYLRLDPGYG FTKSIENEIY QILKNLRYPF LESINKSQIS AVGGSNWHKF LGMLHWMVRT NIKLDMCLNK VD RSLINQN TQEITILSQP LKTLDEQDQR QERYELMVEK LLIDYFTESY KSFLKLEDNY EPSMQELKLG FEKFVHIINT DIA NLQTQN DNLYEKYQEV MKISQKIKTT REKWKALKSD SNKYENYVNA MKQKSQEWPG KLEKMKSECE LKEEEIKALQ SNIS ELHKI LRKKGISTEQ FELQNQEREK LTRELDKINI QSDKLTSSIK SRKLEAEGIF KSLLDTLRQY DSSIQNLTRS RSQLG HNVN DSSLKINISE NLLDRDFHEG ISYEQLFPKG SGINESIKKS ILKLNDEIQE RIKTIEKDNI TLEKDIKNLK HDINEK TQI NEKLELELSE ANSKFELSKQ ENERLLVAQR IEIEKMEKKI NDSNLLMKTK ISDAEELVTS TELKLEELKV DLNRKRY KL HQQVIHVIDI TSKFKINIQS SLENSENELG NVIEELRNLE FETEHNVTN

UniProtKB: Kinetochore protein NDC80

+
Macromolecule #4: Kinetochore protein NUF2

MacromoleculeName: Kinetochore protein NUF2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 53.025949 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSRNQDVFPI LDLQELVICL QSCDFALATQ ENISRPTSDY MVTLYKQIIE NFMGISVESL LNSSNQETGD GHLQEENENI YLDTLNVLV LNKICFKFFE NIGVQDFNMT DLYKPEAQRT QRLLSAVVNY ARFREERMFD CNSFILQMES LLGQLRSKFD D YNLIQQQL ...String:
MSRNQDVFPI LDLQELVICL QSCDFALATQ ENISRPTSDY MVTLYKQIIE NFMGISVESL LNSSNQETGD GHLQEENENI YLDTLNVLV LNKICFKFFE NIGVQDFNMT DLYKPEAQRT QRLLSAVVNY ARFREERMFD CNSFILQMES LLGQLRSKFD D YNLIQQQL KQYEDVDGDN IPDEQELQKL EEQNKELEIQ LKKLTKIQET LSIDYNDYKI SKQSIFKDLE ALSFQIVELE SN RDKLIKI SNTDMEELSE GIKELNDLLI QRKKTLDDLT AQQKNLQDTV TTFETIISEL YDVLRIISSE VQESNRTETE LVG LKQNLI NNKLKLMNVL ETGIMYKLEI LQEQLDLQLK NLEKLSQDTK EESRLNDTKL MDLQIKYENE IKPKIDKTDI FIQE ELISG KINKLNDEIK QLQKDFEVEV KEIEIEYSLL SGHINKYMNE MLEYMQ

UniProtKB: Kinetochore protein NUF2

+
Macromolecule #5: DASH complex subunit DAM1

MacromoleculeName: DASH complex subunit DAM1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 38.477871 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSEDKAKLGT TRSATEYRLS IGSAPTSRRS SMGESSSLMK FADQEGLTSS VGEYNENTIQ QLLLPKIREL SDSIITLDSN FTRLNFIHE SLADLNESLG SLLYGIMSNS WCVEFSQAPH DIQDDLIAIK QLKSLEDEKN NLVMELSNME RGIKRKKDEQ G ENDLAKAS ...String:
MSEDKAKLGT TRSATEYRLS IGSAPTSRRS SMGESSSLMK FADQEGLTSS VGEYNENTIQ QLLLPKIREL SDSIITLDSN FTRLNFIHE SLADLNESLG SLLYGIMSNS WCVEFSQAPH DIQDDLIAIK QLKSLEDEKN NLVMELSNME RGIKRKKDEQ G ENDLAKAS QNKQFNQPLF PSSQVRKYRS YDNRDKRKPS KIGNNLQVEN EEDYEDDTSS EASFVLNPTN IGMSKSSQGH VT KTTRLNN NTNSKLRRKS ILHTIRNSIA SGADLPIEND NVVNLGDLHP NNRISLGSGA ARVVNGPVTK NRNSMFSGRA ERK PTESRH SVAKKTEKKI NTRPPFR

UniProtKB: DASH complex subunit DAM1

+
Macromolecule #6: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM / Guanosine triphosphate

+
Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #8: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 8 / Number of copies: 1 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM / Guanosine diphosphate

+
Macromolecule #9: TAXOL

MacromoleculeName: TAXOL / type: ligand / ID: 9 / Number of copies: 1 / Formula: TA1
Molecular weightTheoretical: 853.906 Da
Chemical component information

ChemComp-TA1:
TAXOL / medication, chemotherapy*YM / Paclitaxel

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 6.8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: INSILICO MODEL
In silico model: Sub-volume extracted from larger outer kinetochore microtubule consensus volume
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 95730

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
DetailsInitial rigid body fitting was performed in chimera, with manual correction in coot and real-space refinement in PHENIX
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 540.98
Output model

PDB-8qau:
Outer kinetochore Ndc80-Dam1 alpha/beta-tubulin complex

+
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