[English] 日本語
Yorodumi
- EMDB-17226: Cryo-EM structure of CBF1-CCAN bound topologically to a centromer... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-17226
TitleCryo-EM structure of CBF1-CCAN bound topologically to a centromeric CENP-A nucleosome
Map data
Sample
  • Complex: A complex of CBF1-CCAN bound to centromeric C0N3 DNA
    • DNA: x 2 types
    • Protein or peptide: x 18 types
Keywordskinetochore / point centromere / CENP-A nucleosome / topological entrapment / centromeric DNA / CELL CYCLE
Function / homology
Function and homology information


Cbf1-Met4-Met28 complex / positive regulation of sulfate assimilation / regulation of sulfur metabolic process / negative regulation of kinetochore assembly / positive regulation of inositol biosynthetic process / 2-micrometer circle DNA / 2-micrometer plasmid partitioning / negative regulation of meiotic DNA double-strand break formation involved in reciprocal meiotic recombination / COMA complex / maintenance of meiotic sister chromatid cohesion ...Cbf1-Met4-Met28 complex / positive regulation of sulfate assimilation / regulation of sulfur metabolic process / negative regulation of kinetochore assembly / positive regulation of inositol biosynthetic process / 2-micrometer circle DNA / 2-micrometer plasmid partitioning / negative regulation of meiotic DNA double-strand break formation involved in reciprocal meiotic recombination / COMA complex / maintenance of meiotic sister chromatid cohesion / PKMTs methylate histone lysines / HDMs demethylate histones / Mis6-Sim4 complex / : / meiotic sister chromatid segregation / negative regulation of ceramide biosynthetic process / establishment of meiotic sister chromatid cohesion / ascospore formation / HATs acetylate histones / RNA polymerase I upstream activating factor complex / attachment of spindle microtubules to kinetochore / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / CENP-A containing chromatin assembly / centromeric DNA binding / Assembly of the ORC complex at the origin of replication / HDACs deacetylate histones / kinetochore assembly / protein localization to chromosome, centromeric region / outer kinetochore / condensed chromosome, centromeric region / establishment of mitotic sister chromatid cohesion / protein localization to kinetochore / cellular response to methionine / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Oxidative Stress Induced Senescence / spindle pole body / RMTs methylate histone arginines / DNA damage tolerance / SUMOylation of chromatin organization proteins / mitotic spindle assembly checkpoint signaling / RNA Polymerase I Promoter Escape / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / Estrogen-dependent gene expression / rRNA transcription / mitotic sister chromatid segregation / chromosome, centromeric region / DNA replication initiation / Ub-specific processing proteases / protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / meiotic cell cycle / chromosome segregation / kinetochore / DNA-binding transcription repressor activity, RNA polymerase II-specific / structural constituent of chromatin / peroxisome / nucleosome / heterochromatin formation / mitotic cell cycle / nucleosome assembly / chromatin organization / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / DNA-binding transcription factor activity / protein heterodimerization activity / cell division / DNA repair / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein-containing complex binding / structural molecule activity / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
: / Kinetochore subunit Nkp2/Cnl2 / Cnl2/NKP2 family protein / : / : / CENPH protein / CENPU protein / Centromere protein O / Cenp-O kinetochore centromere component / Centromere protein Chl4/mis15/CENP-N ...: / Kinetochore subunit Nkp2/Cnl2 / Cnl2/NKP2 family protein / : / : / CENPH protein / CENPU protein / Centromere protein O / Cenp-O kinetochore centromere component / Centromere protein Chl4/mis15/CENP-N / Kinetochore protein CHL4 like / Helix-loop-helix DNA-binding domain / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold
Similarity search - Domain/homology
Histone H2B.1 / Histone H4 / Histone H2A.1 / Centromere-binding protein 1 / Histone H3-like centromeric protein CSE4 / Inner kinetochore subunit IML3 / Inner kinetochore subunit AME1 / Inner kinetochore subunit CHL4 / Inner kinetochore subunit CNN1 / Inner kinetochore subunit MCM22 ...Histone H2B.1 / Histone H4 / Histone H2A.1 / Centromere-binding protein 1 / Histone H3-like centromeric protein CSE4 / Inner kinetochore subunit IML3 / Inner kinetochore subunit AME1 / Inner kinetochore subunit CHL4 / Inner kinetochore subunit CNN1 / Inner kinetochore subunit MCM22 / Inner kinetochore subunit OKP1 / Inner kinetochore subunit CTF19 / Inner kinetochore subunit NKP2 / Inner kinetochore subunit MCM21 / Inner kinetochore subunit MCM16 / Inner kinetochore subunit NKP1 / Inner kinetochore subunit CTF3 / Inner kinetochore subunit WIP1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsDendooven TD / Zhang Z / Yang J / McLaughlin S / Schwabb J / Scheres S / Yatskevich S / Barford D
Funding support United Kingdom, Germany, 4 items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)MC_UP_1201/6 United Kingdom
Cancer Research UKC576/A14109 United Kingdom
UK Research and Innovation (UKRI)MC_UP_ A025_1013 United Kingdom
Boehringer Ingelheim Fonds (BIF) Germany
CitationJournal: Sci Adv / Year: 2023
Title: Cryo-EM structure of the complete inner kinetochore of the budding yeast point centromere.
Authors: Tom Dendooven / Ziguo Zhang / Jing Yang / Stephen H McLaughlin / Johannes Schwab / Sjors H W Scheres / Stanislau Yatskevich / David Barford /
Abstract: The point centromere of budding yeast specifies assembly of the large kinetochore complex to mediate chromatid segregation. Kinetochores comprise the centromere-associated inner kinetochore (CCAN) ...The point centromere of budding yeast specifies assembly of the large kinetochore complex to mediate chromatid segregation. Kinetochores comprise the centromere-associated inner kinetochore (CCAN) complex and the microtubule-binding outer kinetochore KNL1-MIS12-NDC80 (KMN) network. The budding yeast inner kinetochore also contains the DNA binding centromere-binding factor 1 (CBF1) and CBF3 complexes. We determined the cryo-electron microscopy structure of the yeast inner kinetochore assembled onto the centromere-specific centromere protein A nucleosomes (CENP-A). This revealed a central CENP-A with extensively unwrapped DNA ends. These free DNA duplexes bind two CCAN protomers, one of which entraps DNA topologically, positioned on the centromere DNA element I (CDEI) motif by CBF1. The two CCAN protomers are linked through CBF3 forming an arch-like configuration. With a structural mechanism for how CENP-A can also be linked to KMN involving only CENP-QU, we present a model for inner kinetochore assembly onto a point centromere and how it organizes the outer kinetochore for chromosome attachment to the mitotic spindle.
History
DepositionApr 26, 2023-
Header (metadata) releaseAug 9, 2023-
Map releaseAug 9, 2023-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_17226.png

Downloads & links

-
Map

FileDownload / File: emd_17226.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 360 pix.
= 307.08 Å		0.85 Å/pix.
x 360 pix.
= 307.08 Å		0.85 Å/pix.
x 360 pix.
= 307.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.853 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.149
Minimum - Maximum-0.63788563 - 0.97546124
Average (Standard dev.)0.0008011289 (±0.0661623)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 307.08 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: #1

Fileemd_17226_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_17226_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_17226_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : A complex of CBF1-CCAN bound to centromeric C0N3 DNA

EntireName: A complex of CBF1-CCAN bound to centromeric C0N3 DNA
Components
  • Complex: A complex of CBF1-CCAN bound to centromeric C0N3 DNA
    • DNA: C0N3 DNA
    • DNA: C0N3 DNA
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2B.1
    • Protein or peptide: Histone H3-like centromeric protein CSE4
    • Protein or peptide: Histone H2A.1
    • Protein or peptide: Centromere-binding protein 1
    • Protein or peptide: Inner kinetochore subunit MCM16
    • Protein or peptide: Inner kinetochore subunit CTF3
    • Protein or peptide: Inner kinetochore subunit MCM22
    • Protein or peptide: Inner kinetochore subunit IML3
    • Protein or peptide: Inner kinetochore subunit CHL4
    • Protein or peptide: Inner kinetochore subunit MCM21
    • Protein or peptide: Inner kinetochore subunit CTF19
    • Protein or peptide: Inner kinetochore subunit OKP1
    • Protein or peptide: Inner kinetochore subunit CNN1
    • Protein or peptide: Inner kinetochore subunit AME1
    • Protein or peptide: Inner kinetochore subunit WIP1
    • Protein or peptide: Inner kinetochore subunit NKP1
    • Protein or peptide: Inner kinetochore subunit NKP2

+
Supramolecule #1: A complex of CBF1-CCAN bound to centromeric C0N3 DNA

SupramoleculeName: A complex of CBF1-CCAN bound to centromeric C0N3 DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

+
Macromolecule #1: C0N3 DNA

MacromoleculeName: C0N3 DNA / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 47.239277 KDa
SequenceString: (DA)(DT)(DA)(DA)(DG)(DT)(DC)(DA)(DC)(DA) (DT)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DA) (DC)(DA)(DG)(DC)(DT)(DC) ...String:
(DA)(DT)(DA)(DA)(DG)(DT)(DC)(DA)(DC)(DA) (DT)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DA) (DC)(DA)(DG)(DC)(DT)(DC)(DT)(DA) (DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT)(DA) (DA)(DA) (DC)(DG)(DC)(DA)(DC)(DG)(DT) (DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT)(DC) (DC)(DC)(DC) (DC)(DG)(DC)(DG)(DT)(DT) (DT)(DT)(DA)(DA)(DT)(DA)(DT)(DT)(DA)(DG) (DT)(DG)(DT)(DA) (DT)(DT)(DT)(DG)(DA) (DT)(DT)(DT)(DC)(DC)(DG)(DA)(DA)(DA)(DG) (DT)(DT)(DA)(DA)(DA) (DA)(DA)(DA)(DG) (DA)(DA)(DA)(DT)(DA)(DG)(DT)(DA)(DA)(DG) (DA)(DA)(DA)(DT)(DA)(DT) (DA)(DT)(DA) (DT)(DT)(DT)(DC)(DA)(DT)(DT)(DG)(DA)(DA)

+
Macromolecule #2: C0N3 DNA

MacromoleculeName: C0N3 DNA / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 47.194199 KDa
SequenceString: (DT)(DT)(DC)(DA)(DA)(DT)(DG)(DA)(DA)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DT)(DT)(DC) (DT)(DT)(DA)(DC)(DT)(DA)(DT)(DT)(DT) (DC)(DT)(DT)(DT)(DT)(DT)(DT)(DA)(DA)(DC) (DT) (DT)(DT)(DC)(DG)(DG)(DA) ...String:
(DT)(DT)(DC)(DA)(DA)(DT)(DG)(DA)(DA)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DT)(DT)(DC) (DT)(DT)(DA)(DC)(DT)(DA)(DT)(DT)(DT) (DC)(DT)(DT)(DT)(DT)(DT)(DT)(DA)(DA)(DC) (DT) (DT)(DT)(DC)(DG)(DG)(DA)(DA)(DA) (DT)(DC)(DA)(DA)(DA)(DT)(DA)(DC)(DA)(DC) (DT)(DA) (DA)(DT)(DA)(DT)(DT)(DA)(DA) (DA)(DA)(DC)(DG)(DC)(DG)(DG)(DG)(DG)(DG) (DA)(DC)(DA) (DG)(DC)(DG)(DC)(DG)(DT) (DA)(DC)(DG)(DT)(DG)(DC)(DG)(DT)(DT)(DT) (DA)(DA)(DG)(DC) (DG)(DG)(DT)(DG)(DC) (DT)(DA)(DG)(DA)(DG)(DC)(DT)(DG)(DT)(DC) (DT)(DA)(DC)(DG)(DA) (DC)(DC)(DA)(DA) (DT)(DT)(DG)(DA)(DG)(DC)(DG)(DG)(DC)(DC) (DT)(DC)(DG)(DG)(DC)(DA) (DC)(DC)(DA) (DT)(DG)(DT)(DG)(DA)(DC)(DT)(DT)(DA)(DT)

+
Macromolecule #3: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 11.39539 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KILRDNIQGI TKPAIRRLAR RGGVKRISGL IYEEVRAVLK SFLESVIRDS VTYTEHAKRK TVTSLDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

+
Macromolecule #4: Histone H2B.1

MacromoleculeName: Histone H2B.1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 14.280362 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSAKAEKKPA SKAPAEKKPA AKKTSTSTDG KKRSKARKET YSSYIYKVLK QTHPDTGISQ KSMSILNSFV NDIFERIATE ASKLAAYNK KSTISAREIQ TAVRLILPGE LAKHAVSEGT RAVTKYSSST QA

UniProtKB: Histone H2B.1

+
Macromolecule #5: Histone H3-like centromeric protein CSE4

MacromoleculeName: Histone H3-like centromeric protein CSE4 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 26.885434 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSSKQQWVSS AIQSDSSGRS LSNVNRLAGD QQSINDRALS LLQRTRATKN LFPRREERRR YESSKSDLDI ETDYEDQAGN LEIETENEE EAEMETEVPA PVRTHSYALD RYVRQKRREK QRKQSLKRVE KKYTPSELAL YEIRKYQRST DLLISKIPFA R LVKEVTDE ...String:
MSSKQQWVSS AIQSDSSGRS LSNVNRLAGD QQSINDRALS LLQRTRATKN LFPRREERRR YESSKSDLDI ETDYEDQAGN LEIETENEE EAEMETEVPA PVRTHSYALD RYVRQKRREK QRKQSLKRVE KKYTPSELAL YEIRKYQRST DLLISKIPFA R LVKEVTDE FTTKDQDLRW QSMAIMALQE ASEAYLVGLL EHTNLLALHA KRITIMKKDM QLARRIRGQF I

UniProtKB: Histone H3-like centromeric protein CSE4

+
Macromolecule #6: Histone H2A.1

MacromoleculeName: Histone H2A.1 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 14.013177 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGGKGGKAG SAAKASQSRS AKAGLTFPVG RVHRLLRRGN YAQRIGSGAP VYLTAVLEYL AAEILELAGN AARDNKKTRI IPRHLQLAI RNDDELNKLL GNVTIAQGGV LPNIHQNLLP KKSAKATKAS QEL

UniProtKB: Histone H2A.1

+
Macromolecule #7: Centromere-binding protein 1

MacromoleculeName: Centromere-binding protein 1 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 39.444715 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MNSLANNNKL STEDEEIHSA RKRGYNEEQN YSEARKKQRD QGLLSQESND GNIDSALLSE GATLKGTQSQ YESGLTSNKD EKGSDDEDA SVAEAAVAAT VNYTDLIQGQ EDSSDAHTSN QTNANGEHKD SLNGERAITP SNEGVKPNTS LEGMTSSPME S TQQSKNDM ...String:
MNSLANNNKL STEDEEIHSA RKRGYNEEQN YSEARKKQRD QGLLSQESND GNIDSALLSE GATLKGTQSQ YESGLTSNKD EKGSDDEDA SVAEAAVAAT VNYTDLIQGQ EDSSDAHTSN QTNANGEHKD SLNGERAITP SNEGVKPNTS LEGMTSSPME S TQQSKNDM LIPLAEHDRG PEHQQDDEDN DDADIDLKKD ISMQPGRRGR KPTTLATTDE WKKQRKDSHK EVERRRRENI NT AINVLSD LLPVRESSKA AILACAAEYI QKLKETDEAN IEKWTLQKLL SEQNASQLAS ANEKLQEELG NAYKEIEYMK RVL RKEGIE YEDMHTHKKQ ENERKSTRSD NPHEA

UniProtKB: Centromere-binding protein 1

+
Macromolecule #8: Inner kinetochore subunit MCM16

MacromoleculeName: Inner kinetochore subunit MCM16 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 21.1661 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MTNSSEKQWE RIQQLEKEHV EVYRELLITL DRLYLIRKHN HAVILSHTQQ RLLEIRHQLQ INLEKTALLI RLLEKPDNTN VLFTKLQNL LEESNSLDYE LLQSLGAQSS LHKQLIESRA ERDELMSKLI ELSSKFPKPT IPPDDSDTAG KQVEVEKENE T IQELMIAL QIHSGYTNIS YTI

UniProtKB: Inner kinetochore subunit MCM16

+
Macromolecule #9: Inner kinetochore subunit CTF3

MacromoleculeName: Inner kinetochore subunit CTF3 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 84.345633 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSLILDDIIL SLTNANERTP PQALKTTLSL LYEKSKQYGL SSPQLQALVR LLCETSIIDT VTKVYIVENC FLPDGYLTKE LLLEIINHL GTPTVFSRYR IQTPPVLQSA LCKWLVHVYF LFPVHSEREH NISSSIWLHL WQFSFLQKWI TPLVIWQATT P VDVKPWKL ...String:
MSLILDDIIL SLTNANERTP PQALKTTLSL LYEKSKQYGL SSPQLQALVR LLCETSIIDT VTKVYIVENC FLPDGYLTKE LLLEIINHL GTPTVFSRYR IQTPPVLQSA LCKWLVHVYF LFPVHSEREH NISSSIWLHL WQFSFLQKWI TPLVIWQATT P VDVKPWKL SIIKRCAMHP GYRDAPGSAT LILQRFQCLV GASSQITESI ITINCNRKTL KSHRNLKLDA HFLSILKRIL SR AHPANFP ADTVQNTIDM YLSEIHQLGA DSIYPLRLQS LPEYVPSDST VSLWDVTSLE QLAQNWPQLH IPNDVDYMMK PSL NSNVLL PRKVMSRDSL KHLYSSIILI KNSRDESSSP YEWCIWQLKR CFAHQIETPQ EVIPIIISVS SMDNKLSSRI IQTF CNLKY LKLDELTLKK VCGGILPLWK PELISGTREF FVKFMASIFM WSTRDGHDNN CTFSETCFYV LQMITNWVLD DKLIA LGLT LLHDMQSLLT LDKIFNNATS NRFSTMAFIS SLDILTQLSK QTKSDYAIQY LIVGPDIMNK VFSSDDPLLL SAACRY LVA TKNKLMQYPS TNKFVRMQNQ YIMDLTNYLY RNKVLSSKSL FGVSPDFFKQ ILENLYIPTA DFKNAKFFTI TGIPALS YI CIIILRRLET AENTKIKFTS GIINEETFNN FFRVHHDEIG QHGWIKGVNN IHDLRVKILM HLSNTANPYR DIAAFLFT Y LKSLSKYSVQ NS

UniProtKB: Inner kinetochore subunit CTF3

+
Macromolecule #10: Inner kinetochore subunit MCM22

MacromoleculeName: Inner kinetochore subunit MCM22 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 27.602541 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDVEKDVLDV YIKNLENQIG NKRYFLKQAQ GAIDEITKRS LDTEGKPVNS EVFTELLRKP MFFSERADPI GFSLTSNFLS LRAQSSSEW LSLMNDQSVD QKAMLLLQNN INSDLKELLR KLQHQMTIMD SKKQDHAHIR TRKARNKELW DSLADFLKGY L VPNLDDND ...String:
MDVEKDVLDV YIKNLENQIG NKRYFLKQAQ GAIDEITKRS LDTEGKPVNS EVFTELLRKP MFFSERADPI GFSLTSNFLS LRAQSSSEW LSLMNDQSVD QKAMLLLQNN INSDLKELLR KLQHQMTIMD SKKQDHAHIR TRKARNKELW DSLADFLKGY L VPNLDDND ESIDSLTNEV MLLMKRLIEH DLNLTLNDFS SKTIPIYRLL LRANIITVIE GSTNPGTKYI KLIDFNETSL T

UniProtKB: Inner kinetochore subunit MCM22

+
Macromolecule #11: Inner kinetochore subunit IML3

MacromoleculeName: Inner kinetochore subunit IML3 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 28.093223 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MPYTWKFLGI SKQLSLENGI AKLNQLLNLE VDLDIQTIRV PSDPDGGTAA DEYIRYEMRL DISNLDEGTY SKFIFLGNSK MEVPMFLCY CGTDNRNEVV LQWLKAEYGV IMWPIKFEQK TMIKLADASI VHVTKENIEQ ITWFSSKLYF EPETQDKNLR Q FSIEIPRE ...String:
MPYTWKFLGI SKQLSLENGI AKLNQLLNLE VDLDIQTIRV PSDPDGGTAA DEYIRYEMRL DISNLDEGTY SKFIFLGNSK MEVPMFLCY CGTDNRNEVV LQWLKAEYGV IMWPIKFEQK TMIKLADASI VHVTKENIEQ ITWFSSKLYF EPETQDKNLR Q FSIEIPRE SCEGLALGYG NTMHPYNDAI VPYIYNETGM AVERLPLTSV ILAGHTKIMR ESIVTSTRSL RNRVLAVVLQ SI QFTSE

UniProtKB: Inner kinetochore subunit IML3

+
Macromolecule #12: Inner kinetochore subunit CHL4

MacromoleculeName: Inner kinetochore subunit CHL4 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 52.743723 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSNELRLEDN YVPTSDTLVV FKQLMKLPVT VLYDLTLSWF AKFGGSFDGD IYLLTETLDL LIEKGVRRNV IVNRILYVYW PDGLNVFQL AEIDCHLMIS KPEKFKWLPS KALRGDGKPY VVKLQPAKFI ENLQTDLAKI YHCHVYMFKH PSLPVLITRI Q LFDSNNLF ...String:
MSNELRLEDN YVPTSDTLVV FKQLMKLPVT VLYDLTLSWF AKFGGSFDGD IYLLTETLDL LIEKGVRRNV IVNRILYVYW PDGLNVFQL AEIDCHLMIS KPEKFKWLPS KALRGDGKPY VVKLQPAKFI ENLQTDLAKI YHCHVYMFKH PSLPVLITRI Q LFDSNNLF LSTPNIGSIN KESLYNKLDK FQGKPLISRR PYYVAFPLNS PIIFHSVDKD IYARLVLQSI SRTISERETI IF KPVQKIP VKSIHNIMTL LGPSRFAESM GPWECYASAN FERSPLHDYK KHQGLTGKKV MVREFDDSFL NDDENFYGKE EPE IRRLRL EKNMIKFKGS ANGVMDQKYN DLKEFNEHVH NIRNGKKNED SGEPVYISRY SSLVPIEKVG FTLKNEINSR IITI KLKFN GNDIFGGLHE LCDKNLINID KVPGWLAGEN GSFSGTIMNG DFQREQVAKG GLL

UniProtKB: Inner kinetochore subunit CHL4

+
Macromolecule #13: Inner kinetochore subunit MCM21

MacromoleculeName: Inner kinetochore subunit MCM21 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 43.028879 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSRIDDLQQD IESLLSEINS LEESREKLKA KIKDKRKNEE SANPIVQEFE DLFDQFPQLN NFLFNEHPEL EETDDKDISR AQADIPATP IPYEPKKRAK LENEEILPEQ EWVLKTQPMV QHQMFDPGVA DLLDTDILTS PSKRKRKLKI DDISTSDRSE L EDYIVLEN ...String:
MSRIDDLQQD IESLLSEINS LEESREKLKA KIKDKRKNEE SANPIVQEFE DLFDQFPQLN NFLFNEHPEL EETDDKDISR AQADIPATP IPYEPKKRAK LENEEILPEQ EWVLKTQPMV QHQMFDPGVA DLLDTDILTS PSKRKRKLKI DDISTSDRSE L EDYIVLEN VYRMFGITFF PLVDPIDLKI KDASGEIFVD REMLGIRLEV FSERTSQFEK PHYVLLKKRI KSNSWFLFKH TI PSFIDVQ GIFDDTNGGL VISHDDAYLF AKRVFLQLVE VQKRRQIFKD LEAKKIIHDL DLDLESSMVS FFVKDIKVEL FVK QNEIVS CSILDDIHDF SQNNKSKWEI ALLGSLDDLE LKLNHSFATI FK

UniProtKB: Inner kinetochore subunit MCM21

+
Macromolecule #14: Inner kinetochore subunit CTF19

MacromoleculeName: Inner kinetochore subunit CTF19 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 42.841113 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDFTSDTTNS HDTSNSHLSL EDAVGTHHAG EADVNIDGDE KQQLSLLDDD QVRALKLQEE KDALLTRRNT LLQEIQTYQN ILMKENNSK TKNGDILQND ITQDFLNLIS ISSSNPNSAI SDRKRVERIN GLTNLQKELV TKYDTLPLLN MNLRLSYLRD H TYPHLQVS ...String:
MDFTSDTTNS HDTSNSHLSL EDAVGTHHAG EADVNIDGDE KQQLSLLDDD QVRALKLQEE KDALLTRRNT LLQEIQTYQN ILMKENNSK TKNGDILQND ITQDFLNLIS ISSSNPNSAI SDRKRVERIN GLTNLQKELV TKYDTLPLLN MNLRLSYLRD H TYPHLQVS VQSRDRVHND GIEVLVVNYK FCRNTMNPFE IQFKMFYKFE DSTLLKWEIL RISTNVRLKA KQLLATRNFQ KC LLSLYEF DKIKSKKTGI FQNLINLLKR KTRCYLMNNS DSLIVERVIR EGRLTTIKLQ INFIITMPGE RGKPRNCFLP MSK ISIALW KGGERFNQID LDEICYGLIK EYGVKTGLKE ICNVCLFPDM YAR

UniProtKB: Inner kinetochore subunit CTF19

+
Macromolecule #15: Inner kinetochore subunit OKP1

MacromoleculeName: Inner kinetochore subunit OKP1 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 47.427246 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MAADRDNFLQ NIENDSINNG QAMDLSPNRS SSESDSSILM NVNDIKTLRL DVAPEAKSTQ SKKSLFYENS DDAEEGEIEE RTNKEEGQY HHKGSKQLRF EVGKESTGKL QSHLSDGSAT SGEGNVRPWE FRKVIQAEYR ERLPRNYELK HWKKPSKIMI G SILRLLET ...String:
MAADRDNFLQ NIENDSINNG QAMDLSPNRS SSESDSSILM NVNDIKTLRL DVAPEAKSTQ SKKSLFYENS DDAEEGEIEE RTNKEEGQY HHKGSKQLRF EVGKESTGKL QSHLSDGSAT SGEGNVRPWE FRKVIQAEYR ERLPRNYELK HWKKPSKIMI G SILRLLET NTVSALDSVF EKYEKEMNQM THGDNNEVKR IYSKKERLLE IILTKIKKKL RQAKFPSRIS ERDLDIEYIY SK RQFIQNR YSQELQNNER LEAILSREQN LLEETRKLCM NLKTNNKKRL TEKLIQKDLH PVLNKAMEYT YGLESTNGFM HPD GPVTFR NDSHELNLML NDPIKSTADV RLDKEEVLSL LPSLKEYTKK SKELKETMGQ MISDSHEEEI KEVFVPHHES HQDK TEEDI H

UniProtKB: Inner kinetochore subunit OKP1

+
Macromolecule #16: Inner kinetochore subunit CNN1

MacromoleculeName: Inner kinetochore subunit CNN1 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 41.359785 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSTPRKAAGN NENTEVSEIR TPFRERALEE QRLKDEVLIR NTPGYRKLLS ASTKSHDILN KDPNEVRSFL QDLSQVLARK SQGNDTTTN KTQARNLIDE LAYEESQPEE NELLRSRSEK LTDNNIGNET QPDYTSLSQT VFAKLQERDK GLKSRKIDPI I IQDVPTTG ...String:
MSTPRKAAGN NENTEVSEIR TPFRERALEE QRLKDEVLIR NTPGYRKLLS ASTKSHDILN KDPNEVRSFL QDLSQVLARK SQGNDTTTN KTQARNLIDE LAYEESQPEE NELLRSRSEK LTDNNIGNET QPDYTSLSQT VFAKLQERDK GLKSRKIDPI I IQDVPTTG HEDELTVHSP DKANSISMEV LRTSPSIGMD QVDEPPVRDP VPISITQQEE PLSEDLPSDD KEETEEAENE DY SFENTSD ENLDDIGNDP IRLNVPAVRR SSIKPLQIMD LKHLTRQFLN ENRIILPKQT WSTIQEESLN IMDFLKQKIG TLQ KQELVD SFIDMGIINN VDDMFELAHE LLPLELQSRI ESYLF

UniProtKB: Inner kinetochore subunit CNN1

+
Macromolecule #17: Inner kinetochore subunit AME1

MacromoleculeName: Inner kinetochore subunit AME1 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 37.506723 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDRDTKLAFR LRGSHSRRTD DIDDDVIVFK TPNAVYREEN SPIQSPVQPI LSSPKLANSF EFPITTNNVN AQDRHEHGYQ PLDAEDYPM IDSENKSLIS ESPQNVRNDE DLTTRYNFDD IPIRQLSSSI TSVTTIDVLS SLFINLFEND LIPQALKDFN K SDDDQFRK ...String:
MDRDTKLAFR LRGSHSRRTD DIDDDVIVFK TPNAVYREEN SPIQSPVQPI LSSPKLANSF EFPITTNNVN AQDRHEHGYQ PLDAEDYPM IDSENKSLIS ESPQNVRNDE DLTTRYNFDD IPIRQLSSSI TSVTTIDVLS SLFINLFEND LIPQALKDFN K SDDDQFRK LLYKLDLRLF QTISDQMTRD LKDILDINVS NNELCYQLKQ VLARKEDLNQ QIISVRNEIQ ELKAGKDWHD LQ NEQAKLN DKVKLNKRLN DLTSTLLGKY EGDRKIMSQD SEDDSIRDDS NILDIAHFVD LMDPYNGLLK KINKINENLS NEL QPSL

UniProtKB: Inner kinetochore subunit AME1

+
Macromolecule #18: Inner kinetochore subunit WIP1

MacromoleculeName: Inner kinetochore subunit WIP1 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 10.255458 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MDTEALANYL LRQLSLDAEE NKLEDLLQRQ NEDQESSQEY NKKLLLACGF QAILRKILLD ARTRATAEGL REVYPYHIEA ATQAFLDSQ

UniProtKB: Inner kinetochore subunit WIP1

+
Macromolecule #19: Inner kinetochore subunit NKP1

MacromoleculeName: Inner kinetochore subunit NKP1 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 27.006451 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MTDTYNSISN FIENELTALL SSDDYLMDDL AGELPNEVCR LLKAQVIEKR KDAMSRGKQD LLSKEIYDNE SELRASQSQQ IMELVGDIP KYSLGSELRN RVEGEPQSTS IERLIEDVLK LPQMEVADEE EVEVENDLKV LSEYSNLRKD LILKCQALQI G ESKLSDIL ...String:
MTDTYNSISN FIENELTALL SSDDYLMDDL AGELPNEVCR LLKAQVIEKR KDAMSRGKQD LLSKEIYDNE SELRASQSQQ IMELVGDIP KYSLGSELRN RVEGEPQSTS IERLIEDVLK LPQMEVADEE EVEVENDLKV LSEYSNLRKD LILKCQALQI G ESKLSDIL SQTNSINSLT TSIKEASEDD DISEYFATYN GKLVVALEEM KLLLEEAVKT FGNSPEKREK IKKILSELKK

UniProtKB: Inner kinetochore subunit NKP1

+
Macromolecule #20: Inner kinetochore subunit NKP2

MacromoleculeName: Inner kinetochore subunit NKP2 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 17.877033 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MNSEQLLHNY VSDSLLTTLI SFQEFKQQLQ SYTSDEQQLQ HWYELLQARD ARVTSELEAR IKQFFITLRS RLLRFLESEQ LSHSLSLET LIDALYKIND LLQQRLQILD DAIQEKTSEL AEFENMVRSP SAGDNAIPGL LQIIQSYINL LEEN

UniProtKB: Inner kinetochore subunit NKP2

-
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: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 100311
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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