[English] 日本語
Yorodumi
- EMDB-0523: Yeast Ctf19 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0523
TitleYeast Ctf19 complex
Map dataBiological protomer from reconstruction of real space-subtracted images
Sample
  • Complex: Ctf19 complex
    • Protein or peptide: x 12 types
KeywordsKinetochore / CELL CYCLE
Function / homology
Function and homology information


negative regulation of meiotic DNA double-strand break formation involved in reciprocal meiotic recombination / COMA complex / maintenance of meiotic sister chromatid cohesion / Mis6-Sim4 complex / meiotic sister chromatid segregation / establishment of meiotic sister chromatid cohesion / ascospore formation / attachment of spindle microtubules to kinetochore / CENP-A containing chromatin assembly / protein localization to chromosome, centromeric region ...negative regulation of meiotic DNA double-strand break formation involved in reciprocal meiotic recombination / COMA complex / maintenance of meiotic sister chromatid cohesion / Mis6-Sim4 complex / meiotic sister chromatid segregation / establishment of meiotic sister chromatid cohesion / ascospore formation / attachment of spindle microtubules to kinetochore / CENP-A containing chromatin assembly / protein localization to chromosome, centromeric region / kinetochore assembly / outer kinetochore / establishment of mitotic sister chromatid cohesion / protein localization to kinetochore / spindle pole body / mitotic spindle assembly checkpoint signaling / DNA replication initiation / meiotic cell cycle / chromosome segregation / kinetochore / cell division / structural molecule activity / nucleus / cytoplasm
Similarity search - Function
Kinetochore subunit Nkp2/Cnl2 / Cnl2/NKP2 family protein / : / CENPU protein / Centromere protein O / Cenp-O kinetochore centromere component / Centromere protein Chl4/mis15/CENP-N / Kinetochore protein CHL4 like
Similarity search - Domain/homology
Inner kinetochore subunit IML3 / Inner kinetochore subunit AME1 / Inner kinetochore subunit CHL4 / Inner kinetochore subunit OKP1 / Inner kinetochore subunit CTF19 / Inner kinetochore subunit NKP2 / Inner kinetochore subunit MCM21 / Inner kinetochore subunit NKP1 / Inner kinetochore subunit CTF3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Saccharomyces cerevisiae S288c (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.25 Å
AuthorsHinshaw SM / Harrison SC
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Elife / Year: 2019
Title: The structure of the Ctf19c/CCAN from budding yeast.
Authors: Stephen M Hinshaw / Stephen C Harrison /
Abstract: Eukaryotic kinetochores connect spindlemicrotubules to chromosomal centromeres. A group of proteins called the Ctf19 complex (Ctf19c) in yeast and the constitutive centromere associated network (CCAN) ...Eukaryotic kinetochores connect spindlemicrotubules to chromosomal centromeres. A group of proteins called the Ctf19 complex (Ctf19c) in yeast and the constitutive centromere associated network (CCAN) in other organisms creates the foundation of a kinetochore. The Ctf19c/CCAN influences the timing of kinetochore assembly, sets its location by associating with a specialized nucleosome containing the histone H3 variant Cse4/CENP-A, and determines the organization of the microtubule attachment apparatus. We present here the structure of a reconstituted 13-subunit Ctf19c determined by cryo-electron microscopy at ~4 Å resolution. The structure accounts for known and inferred contacts with the Cse4 nucleosome and for an observed assembly hierarchy. We describe its implications for establishment of kinetochores and for their regulation by kinases throughout the cell cycle.
History
DepositionFeb 3, 2019-
Header (metadata) releaseMar 27, 2019-
Map releaseApr 3, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6nuw
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0523.png

Downloads & links

-
Map

FileDownload / File: emd_0523.map.gz / Format: CCP4 / Size: 107.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBiological protomer from reconstruction of real space-subtracted images
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.23 Å/pix.
x 304 pix.
= 373.92 Å		1.23 Å/pix.
x 304 pix.
= 373.92 Å		1.23 Å/pix.
x 304 pix.
= 373.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.23 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.095592484 - 0.17549318
Average (Standard dev.)0.00033433523 (±0.0035447697)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions304304304
Spacing304304304
CellA=B=C: 373.92 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.231.231.23
M x/y/z304304304
origin x/y/z0.0000.0000.000
length x/y/z373.920373.920373.920
α/β/γ90.00090.00090.000
start NX/NY/NZ-383-383-383
NX/NY/NZ768768768
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS304304304
D min/max/mean-0.0960.1750.000

-
Supplemental data

-
Additional map: Dimeric assembly. Twofold symmetry enforced during reconstruction.

Fileemd_0523_additional.map
AnnotationDimeric assembly. Twofold symmetry enforced during reconstruction.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Ctf19 complex

EntireName: Ctf19 complex
Components
  • Complex: Ctf19 complex
    • Protein or peptide: Inner kinetochore subunit IML3
    • Protein or peptide: Inner kinetochore subunit MCM21
    • Protein or peptide: Inner kinetochore subunit CTF19
    • Protein or peptide: Inner kinetochore subunit CHL4
    • Protein or peptide: Inner kinetochore subunit OKP1
    • Protein or peptide: Inner kinetochore subunit NKP1
    • Protein or peptide: Inner kinetochore subunit AME1
    • Protein or peptide: Inner kinetochore subunit CTF3,Inner kinetochore subunit CTF3
    • Protein or peptide: Inner kinetochore subunit NKP2
    • Protein or peptide: Inner kinetochore subunit Mcm22
    • Protein or peptide: Inner kinetochore subunit Mcm16
    • Protein or peptide: Unknown (unassigned)

+
Supramolecule #1: Ctf19 complex

SupramoleculeName: Ctf19 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

+
Macromolecule #1: Inner kinetochore subunit IML3

MacromoleculeName: Inner kinetochore subunit IML3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 28.365484 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SNAMPYTWKF LGISKQLSLE NGIAKLNQLL NLEVDLDIQT IRVPSDPDGG TAADEYIRYE MRLDISNLDE GTYSKFIFLG NSKMEVPMF LCYCGTDNRN EVVLQWLKAE YGVIMWPIKF EQKTMIKLAD ASIVHVTKEN IEQITWFSSK LYFEPETQDK N LRQFSIEI ...String:
SNAMPYTWKF LGISKQLSLE NGIAKLNQLL NLEVDLDIQT IRVPSDPDGG TAADEYIRYE MRLDISNLDE GTYSKFIFLG NSKMEVPMF LCYCGTDNRN EVVLQWLKAE YGVIMWPIKF EQKTMIKLAD ASIVHVTKEN IEQITWFSSK LYFEPETQDK N LRQFSIEI PRESCEGLAL GYGNTMHPYN DAIVPYIYNE TGMAVERLPL TSVILAGHTK IMRESIVTST RSLRNRVLAV VL QSIQFTS E

UniProtKB: Inner kinetochore subunit IML3

+
Macromolecule #2: Inner kinetochore subunit MCM21

MacromoleculeName: Inner kinetochore subunit MCM21 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 43.301133 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SNAMSRIDDL QQDIESLLSE INSLEESREK LKAKIKDKRK NEESANPIVQ EFEDLFDQFP QLNNFLFNEH PELEETDDKD ISRAQADIP ATPIPYEPKK RAKLENEEIL PEQEWVLKTQ PMVQHQMFDP GVADLLDTDI LTSPSKRKRK LKIDDISTSD R SELEDYIV ...String:
SNAMSRIDDL QQDIESLLSE INSLEESREK LKAKIKDKRK NEESANPIVQ EFEDLFDQFP QLNNFLFNEH PELEETDDKD ISRAQADIP ATPIPYEPKK RAKLENEEIL PEQEWVLKTQ PMVQHQMFDP GVADLLDTDI LTSPSKRKRK LKIDDISTSD R SELEDYIV LENVYRMFGI TFFPLVDPID LKIKDASGEI FVDREMLGIR LEVFSERTSQ FEKPHYVLLK KRIKSNSWFL FK HTIPSFI DVQGIFDDTN GGLVISHDDA YLFAKRVFLQ LVEVQKRRQI FKDLEAKKII HDLDLDLESS MVSFFVKDIK VEL FVKQNE IVSCSILDDI HDFSQNNKSK WEIALLGSLD DLELKLNHSF ATIFK

UniProtKB: Inner kinetochore subunit MCM21

+
Macromolecule #3: Inner kinetochore subunit CTF19

MacromoleculeName: Inner kinetochore subunit CTF19 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 42.841113 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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 #4: Inner kinetochore subunit CHL4

MacromoleculeName: Inner kinetochore subunit CHL4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 53.015977 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SNAMSNELRL EDNYVPTSDT LVVFKQLMKL PVTVLYDLTL SWFAKFGGSF DGDIYLLTET LDLLIEKGVR RNVIVNRILY VYWPDGLNV FQLAEIDCHL MISKPEKFKW LPSKALRGDG KPYVVKLQPA KFIENLQTDL AKIYHCHVYM FKHPSLPVLI T RIQLFDSN ...String:
SNAMSNELRL EDNYVPTSDT LVVFKQLMKL PVTVLYDLTL SWFAKFGGSF DGDIYLLTET LDLLIEKGVR RNVIVNRILY VYWPDGLNV FQLAEIDCHL MISKPEKFKW LPSKALRGDG KPYVVKLQPA KFIENLQTDL AKIYHCHVYM FKHPSLPVLI T RIQLFDSN NLFLSTPNIG SINKESLYNK LDKFQGKPLI SRRPYYVAFP LNSPIIFHSV DKDIYARLVL QSISRTISER ET IIFKPVQ KIPVKSIHNI MTLLGPSRFA ESMGPWECYA SANFERSPLH DYKKHQGLTG KKVMVREFDD SFLNDDENFY GKE EPEIRR LRLEKNMIKF KGSANGVMDQ KYNDLKEFNE HVHNIRNGKK NEDSGEPVYI SRYSSLVPIE KVGFTLKNEI NSRI ITIKL KFNGNDIFGG LHELCDKNLI NIDKVPGWLA GENGSFSGTI MNGDFQREQV AKGGLL

UniProtKB: Inner kinetochore subunit CHL4

+
Macromolecule #5: Inner kinetochore subunit OKP1

MacromoleculeName: Inner kinetochore subunit OKP1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 47.427246 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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 #6: Inner kinetochore subunit NKP1

MacromoleculeName: Inner kinetochore subunit NKP1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 27.278709 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SNAMTDTYNS ISNFIENELT ALLSSDDYLM DDLAGELPNE VCRLLKAQVI EKRKDAMSRG KQDLLSKEIY DNESELRASQ SQQIMELVG DIPKYSLGSE LRNRVEGEPQ STSIERLIED VLKLPQMEVA DEEEVEVEND LKVLSEYSNL RKDLILKCQA L QIGESKLS ...String:
SNAMTDTYNS ISNFIENELT ALLSSDDYLM DDLAGELPNE VCRLLKAQVI EKRKDAMSRG KQDLLSKEIY DNESELRASQ SQQIMELVG DIPKYSLGSE LRNRVEGEPQ STSIERLIED VLKLPQMEVA DEEEVEVEND LKVLSEYSNL RKDLILKCQA L QIGESKLS DILSQTNSIN SLTTSIKEAS EDDDISEYFA TYNGKLVVAL EEMKLLLEEA VKTFGNSPEK REKIKKILSE LK K

UniProtKB: Inner kinetochore subunit NKP1

+
Macromolecule #7: Inner kinetochore subunit AME1

MacromoleculeName: Inner kinetochore subunit AME1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 38.335594 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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 QPSLHH HHHH

UniProtKB: Inner kinetochore subunit AME1

+
Macromolecule #8: Inner kinetochore subunit CTF3,Inner kinetochore subunit CTF3

MacromoleculeName: Inner kinetochore subunit CTF3,Inner kinetochore subunit CTF3
type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 87.766664 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SNAMSLILDD IILSLTNANE RTPPQALKTT LSLLYEKSKQ YGLSSPQLQA LVRLLCETSI IDTVTKVYIV ENCFLPDGYL TKELLLEII NHLGTPTVFS RYRIQTPPVL QSALCKWLVH VYFLFPVHSE REHNISSSIW LHLWQFSFLQ KWITPLVIWQ A TTPVDVKP ...String:
SNAMSLILDD IILSLTNANE RTPPQALKTT LSLLYEKSKQ YGLSSPQLQA LVRLLCETSI IDTVTKVYIV ENCFLPDGYL TKELLLEII NHLGTPTVFS RYRIQTPPVL QSALCKWLVH VYFLFPVHSE REHNISSSIW LHLWQFSFLQ KWITPLVIWQ A TTPVDVKP WKLSIIKRCA MHPGYRDAPG SATLILQRFQ CLVGASSQIT ESIITINCNR KTLKSHRNLK LDAHFLSILK RI LSRAHPA NFPADTVQNT IDMYLSEIHQ LGADSIYPLR LQSLPEYVPS DSTVSLWDVT SLEQLAQNWP QLHIPNDVDY MMK PSLNSN VLLPRKVMSR DSLKHLYSSI ILIKNSRDES SSPYEWCIWQ LKRCFAHQIE TPQEVIPIII SVSSMDNKLS SRII QTFCN LKYLKLDELT LKKVCGGILP LWKPELISGT REFFVKFMAS IFMWSTRDGH DNNCTFSETC FYVLQMITNW VLDDK LIAL GLTLLHDMQS LLTLDKIFNN ATSNRFSTMA FISSLDILTQ LSKQTKSDYA IQYLIVGPDI MNKVFSSDDP LLLSAA CRY LVATKNKLMQ YPSTNKFVRM QNQYIMDLTN YLYRNKVLSS KSLFGVSPDF FKQILENLYI PTADFKNAKF FTITGIP AL SYICIIILRR LETAENTKIK FTSGIINEET FNNFFRVHHD EIGQHGWIKG VNNIHDLRVK ILMHLSNTAN PYRDIAAF L FTYLKSLSKY SVQNS(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)

UniProtKB: Inner kinetochore subunit CTF3

+
Macromolecule #9: Inner kinetochore subunit NKP2

MacromoleculeName: Inner kinetochore subunit NKP2 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 17.877033 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MNSEQLLHNY VSDSLLTTLI SFQEFKQQLQ SYTSDEQQLQ HWYELLQARD ARVTSELEAR IKQFFITLRS RLLRFLESEQ LSHSLSLET LIDALYKIND LLQQRLQILD DAIQEKTSEL AEFENMVRSP SAGDNAIPGL LQIIQSYINL LEEN

UniProtKB: Inner kinetochore subunit NKP2

+
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 S288c (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 10.741231 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)

+
Macromolecule #11: Inner kinetochore subunit Mcm16

MacromoleculeName: Inner kinetochore subunit Mcm16 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 6.400881 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

+
Macromolecule #12: Unknown (unassigned)

MacromoleculeName: Unknown (unassigned) / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 1.975426 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8.5
GridDetails: unspecified
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 47.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: OTHER
Details: Starting model from low resolution reconstruction from F20 data (described in accompanying manuscript).
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.25 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 119469
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD
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