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- EMDB-18247: Outer kinetochore Dam1 protomer monomer Ndc80-Nuf2 coiled-coil complex -

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Basic information

Entry
Database: EMDB / ID: EMD-18247
TitleOuter kinetochore Dam1 protomer monomer Ndc80-Nuf2 coiled-coil complex
Map dataLocal resolution filtered map
Sample
  • Complex: Outer kinetochore Dam1 protomer monomer with staple and Ndc80-Nuf2 coiled-coils
    • Protein or peptide: x 12 types
KeywordsKinetochore / microtubule / error correction / chromosome segregation / CELL CYCLE
Function / homology
Function and homology information


mitotic spindle polar microtubule / centromere clustering / Ndc80 complex / DASH complex / protein transport along microtubule to mitotic spindle pole body / mitotic sister chromatid biorientation / kinetochore organization / meiotic chromosome segregation / positive regulation of attachment of spindle microtubules to kinetochore / mitotic spindle midzone ...mitotic spindle polar microtubule / centromere clustering / Ndc80 complex / DASH complex / protein transport along microtubule to mitotic spindle pole body / mitotic sister chromatid biorientation / kinetochore organization / meiotic chromosome segregation / positive regulation of attachment of spindle microtubules to kinetochore / mitotic spindle midzone / mitotic spindle pole body / attachment of spindle microtubules to kinetochore / protein localization to chromosome, centromeric region / attachment of mitotic spindle microtubules to kinetochore / condensed chromosome, centromeric region / protein localization to kinetochore / spindle pole body / positive regulation of microtubule polymerization / mitotic spindle organization / spindle microtubule / chromosome segregation / mitotic spindle / kinetochore / spindle pole / microtubule binding / microtubule / cell division / protein-containing complex binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
DASH complex subunit Duo1 / DASH complex subunit Spc34 / DASH complex subunit Hsk3 / DASH complex subunit Duo1 / DASH complex subunit Spc34 / DASH complex subunit Hsk3-like / DASH complex subunit Hsk3 like / DASH complex subunit Spc19 / DASH complex subunit Dad1 / DASH complex subunit Dad2 ...DASH complex subunit Duo1 / DASH complex subunit Spc34 / DASH complex subunit Hsk3 / DASH complex subunit Duo1 / DASH complex subunit Spc34 / DASH complex subunit Hsk3-like / DASH complex subunit Hsk3 like / DASH complex subunit Spc19 / DASH complex subunit Dad1 / DASH complex subunit Dad2 / DASH complex subunit Ask1 / DASH complex subunit Dad3 / Spc19 / DASH complex subunit Dad1 / DASH complex subunit Dad2 / DASH complex subunit Ask1 / DASH complex subunit Dad3 / 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 Dad4 / DASH complex subunit Dad4
Similarity search - Domain/homology
Kinetochore protein NUF2 / DASH complex subunit ASK1 / DASH complex subunit SPC34 / DASH complex subunit DAD2 / Kinetochore protein NDC80 / DASH complex subunit DUO1 / DASH complex subunit DAM1 / DASH complex subunit DAD3 / DASH complex subunit DAD4 / DASH complex subunit HSK3 ...Kinetochore protein NUF2 / DASH complex subunit ASK1 / DASH complex subunit SPC34 / DASH complex subunit DAD2 / Kinetochore protein NDC80 / DASH complex subunit DUO1 / DASH complex subunit DAM1 / DASH complex subunit DAD3 / DASH complex subunit DAD4 / DASH complex subunit HSK3 / DASH complex subunit SPC19 / DASH complex subunit DAD1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.97 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: Science / Year: 2023
Title: Structural mechanism of outer kinetochore Dam1-Ndc80 complex assembly on microtubules.
Authors: Kyle W Muir / Christopher Batters / Tom Dendooven / Jing Yang / Ziguo Zhang / Alister Burt / David Barford /
Abstract: Kinetochores couple chromosomes to the mitotic spindle to segregate the genome during cell division. An error correction mechanism drives the turnover of kinetochore-microtubule attachments until ...Kinetochores couple chromosomes to the mitotic spindle to segregate the genome during cell division. An error correction mechanism drives the turnover of kinetochore-microtubule attachments until biorientation is achieved. The structural basis for how kinetochore-mediated chromosome segregation is accomplished and regulated remains an outstanding question. In this work, we describe the cryo-electron microscopy structure of the budding yeast outer kinetochore Ndc80 and Dam1 ring complexes assembled onto microtubules. Complex assembly occurs through multiple interfaces, and a staple within Dam1 aids ring assembly. Perturbation of key interfaces suppresses yeast viability. Force-rupture assays indicated that this is a consequence of impaired kinetochore-microtubule attachment. The presence of error correction phosphorylation sites at Ndc80-Dam1 ring complex interfaces and the Dam1 staple explains how kinetochore-microtubule attachments are destabilized and reset.
History
DepositionAug 17, 2023-
Header (metadata) releaseDec 6, 2023-
Map releaseDec 6, 2023-
UpdateDec 20, 2023-
Current statusDec 20, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18247.png

Downloads & links

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Map

FileDownload / File: emd_18247.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal resolution filtered map
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: 0.006
Minimum - Maximum-0.0470734 - 0.07658132
Average (Standard dev.)0.00012976732 (±0.0017874141)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Additional map: Homogeneous refinement map

Fileemd_18247_additional_1.map
AnnotationHomogeneous refinement map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: 3D Flex EM map

Fileemd_18247_additional_2.map
Annotation3D Flex EM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: 3D Flex EM half map B

Fileemd_18247_additional_3.map
Annotation3D Flex EM half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: 3D Flex EM half map A

Fileemd_18247_additional_4.map
Annotation3D Flex EM half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Homogeneous refinement half map B

Fileemd_18247_half_map_1.map
AnnotationHomogeneous refinement half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Homogeneous refinement half map A

Fileemd_18247_half_map_2.map
AnnotationHomogeneous refinement half map A
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Outer kinetochore Dam1 protomer monomer with staple and Ndc80-Nuf...

EntireName: Outer kinetochore Dam1 protomer monomer with staple and Ndc80-Nuf2 coiled-coils
Components
  • Complex: Outer kinetochore Dam1 protomer monomer with staple and Ndc80-Nuf2 coiled-coils
    • Protein or peptide: Kinetochore protein NDC80
    • Protein or peptide: Kinetochore protein NUF2
    • Protein or peptide: DASH complex subunit DAM1
    • Protein or peptide: DASH complex subunit DUO1
    • Protein or peptide: DASH complex subunit DAD2
    • Protein or peptide: DASH complex subunit DAD1
    • Protein or peptide: DASH complex subunit DAD4
    • Protein or peptide: DASH complex subunit DAD3
    • Protein or peptide: DASH complex subunit SPC34
    • Protein or peptide: DASH complex subunit ASK1
    • Protein or peptide: DASH complex subunit HSK3
    • Protein or peptide: DASH complex subunit SPC19

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Supramolecule #1: Outer kinetochore Dam1 protomer monomer with staple and Ndc80-Nuf...

SupramoleculeName: Outer kinetochore Dam1 protomer monomer with staple and Ndc80-Nuf2 coiled-coils
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 673772.36 MDa

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Macromolecule #1: Kinetochore protein NDC80

MacromoleculeName: Kinetochore protein NDC80 / type: protein_or_peptide / ID: 1 / 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

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Macromolecule #2: Kinetochore protein NUF2

MacromoleculeName: Kinetochore protein NUF2 / type: protein_or_peptide / ID: 2 / 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

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Macromolecule #3: DASH complex subunit DAM1

MacromoleculeName: DASH complex subunit DAM1 / type: protein_or_peptide / ID: 3 / 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

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Macromolecule #4: DASH complex subunit DUO1

MacromoleculeName: DASH complex subunit DUO1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 27.515008 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSEQSQLDDS TIDKLIPQIF NEMRSNLNNT TNKFPKSTGG GASDNISANS NSIRSFNSIT TQSLLKESES LDKITAMIKN VTAALKNNL PVYVNQVHEV CKSTNSILDS WINIHSQAGY IHKLMSDQTY LKLINDRLHN ENVNTNDEDG STLHNVIALK K KEILDLRQ ...String:
MSEQSQLDDS TIDKLIPQIF NEMRSNLNNT TNKFPKSTGG GASDNISANS NSIRSFNSIT TQSLLKESES LDKITAMIKN VTAALKNNL PVYVNQVHEV CKSTNSILDS WINIHSQAGY IHKLMSDQTY LKLINDRLHN ENVNTNDEDG STLHNVIALK K KEILDLRQ KLENRKGEKD AAPAKPPNQG LNPRYGVQSG RRPVPSAGIS NNGRVRKTHV PASKRPSGIP RVTNRWTKPT AS SSRKMFR

UniProtKB: DASH complex subunit DUO1

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Macromolecule #5: DASH complex subunit DAD2

MacromoleculeName: DASH complex subunit DAD2 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 15.084501 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MDSIDEQIAI KRKELQSLQK ITSLTDGLKI QLTELNEQIK EMGMNADSVA QLMNNWDSII NNISQASLGL LQYAEGDYEI GPWKDSKKK ESEQSNETGL EAQENDKNDE DNDEDEDLVP LPETMVRIRV DGNE

UniProtKB: DASH complex subunit DAD2

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Macromolecule #6: DASH complex subunit DAD1

MacromoleculeName: DASH complex subunit DAD1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 10.522616 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MMASTSNDEE KLISTTDKYF IEQRNIVLQE INETMNSILN GLNGLNISLE SSIAVGREFQ SVSDLWKTLY DGLESLSDEA PIDEQPTLS QSKTK

UniProtKB: DASH complex subunit DAD1

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Macromolecule #7: DASH complex subunit DAD4

MacromoleculeName: DASH complex subunit DAD4 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 8.164255 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MENPHEQVQA NILSRIIGNV KRLNESVAIL NQELVTINNR NKNLEIMGAI CDNYHSSVQF NLEATNNKKP PL

UniProtKB: DASH complex subunit DAD4

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Macromolecule #8: DASH complex subunit DAD3

MacromoleculeName: DASH complex subunit DAD3 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 10.862234 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MEHNLSPLQQ EVLDKYKQLS LDLKALDETI KELNYSQHRQ QHSQQETVSP DEILQEMRDI EVKIGLVGTL LKGSVYSLIL QRKQEQESL GSNSK

UniProtKB: DASH complex subunit DAD3

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Macromolecule #9: DASH complex subunit SPC34

MacromoleculeName: DASH complex subunit SPC34 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 34.131812 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MGESLDRCID DINRAVDSMS TLYFKPPGIF HNAILQGASN KASIRKDITR LIKDCNHDEA YLLFKVNPEK QSVSRRDGKE GVFDYVIKR DTDMKRNRRL GRPGEKPIIH VPKEVYLNKD RLDLNNKRRR TATTSGGGLN GFIFDTDLIG SSVISNSSSG T FKALSAVF ...String:
MGESLDRCID DINRAVDSMS TLYFKPPGIF HNAILQGASN KASIRKDITR LIKDCNHDEA YLLFKVNPEK QSVSRRDGKE GVFDYVIKR DTDMKRNRRL GRPGEKPIIH VPKEVYLNKD RLDLNNKRRR TATTSGGGLN GFIFDTDLIG SSVISNSSSG T FKALSAVF KDDPQIQRLL YALENGSVLM EEESNNQRRK TIFVEDFPTD LILKVMAEVT DLWPLTEFKQ DYDQLYHNYE QL SSKLRFI KKEVLLQDDR LKTMSQYHPS SSHDVAKIIR KEKDEIRRLE MEIANLQE

UniProtKB: DASH complex subunit SPC34

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Macromolecule #10: DASH complex subunit ASK1

MacromoleculeName: DASH complex subunit ASK1 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 32.106631 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDSASKEETL EKLDQEITVN LQKIDSNLSF CFHKITQDII PHVATYSEIC ERIMDSTEWL GTMFQETGLV NLQANAAAPV GNAPVKSLV SNNVGIFPTS AEEASRQSQT DNGPNEADSA VHVNRDVHSM FNNDSIDDFH TANITSTGQI LKLPDSSDED T GSEAVPSR ...String:
MDSASKEETL EKLDQEITVN LQKIDSNLSF CFHKITQDII PHVATYSEIC ERIMDSTEWL GTMFQETGLV NLQANAAAPV GNAPVKSLV SNNVGIFPTS AEEASRQSQT DNGPNEADSA VHVNRDVHSM FNNDSIDDFH TANITSTGQI LKLPDSSDED T GSEAVPSR EQTDLTGEGH GGADDEQDES TIQRQSRKRK ISLLLQQQYG SSSSMVPSPI VPNKMRKQLA HEEHINNDGD ND DENSNNI ESSPLKQGHH HPKGQADDNN EGPDEEESTK EVPKPGTIIH FSTNR

UniProtKB: DASH complex subunit ASK1

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Macromolecule #11: DASH complex subunit HSK3

MacromoleculeName: DASH complex subunit HSK3 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 8.097205 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MNANKQRQYN QLAHELRELQ TNLQETTKQL DIMSKQCNEN LVGQLGKVHG SWLIGSYIYY MEQMLGKTQ

UniProtKB: DASH complex subunit HSK3

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Macromolecule #12: DASH complex subunit SPC19

MacromoleculeName: DASH complex subunit SPC19 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 18.935559 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MTDALEQSVL ALEGTVSVLK DSVESLKCAN EPSTNLASTM LQTKRVFRLV PEYDVERSKL DLIEEVEPLV RTLGDKLRKS MGRMQRELD TLQQTYELND LRLKKNISMD DDDALNSPDM GQEYEGRDAD DVVMMASSTN EELEELKKLK EKKKQLENKL E ILKQK

UniProtKB: DASH complex subunit SPC19

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 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: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

5254

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 77272
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Software: (Name: cryoSPARC (ver. 3.3.2), RELION (ver. 4.0-dev))
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2)

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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-8q85:
Outer kinetochore Dam1 protomer monomer Ndc80-Nuf2 coiled-coil complex

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