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- EMDB-35416: Cryo-EM structure of the Clr6S (Clr6-HDAC) complex from S. pombe -

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Entry
Database: EMDB / ID: EMD-35416
TitleCryo-EM structure of the Clr6S (Clr6-HDAC) complex from S. pombe
Map dataCryo-EM map of Clr6-HDAC complex
Sample
  • Complex: Cryo-EM structure of the Clr6-HDAC (Clr6S) complex from S. pombe
    • Protein or peptide: RbAp48-related WD40 repeat-containing protein prw1
    • Protein or peptide: Paired amphipathic helix protein pst2
    • Protein or peptide: Histone deacetylase clr6
    • Protein or peptide: Chromatin modification-related protein eaf3
    • Protein or peptide: Cph1
    • Protein or peptide: Cph2
  • Ligand: ZINC ION
  • Ligand: water
KeywordsRpd3S / Histone deacetylase / HDAC / Clr6 / Rpd3 / Clr6S / Clr6 HDAC / TRANSCRIPTION
Function / homology
Function and homology information


histone H4K16 deacetylase activity, hydrolytic mechanism / histone H4K5 deacetylase activity, hydrolytic mechanism / histone H4K8 deacetylase activity, hydrolytic mechanism / histone H3K9 deacetylase activity, hydrolytic mechanism / histone H3K14 deacetylase activity, hydrolytic mechanism / HDACs deacetylate histones / histone H4K12 deacetylase activity, hydrolytic mechanism / SUMOylation of chromatin organization proteins / H3-H4 histone complex chaperone activity / Rpd3L complex ...histone H4K16 deacetylase activity, hydrolytic mechanism / histone H4K5 deacetylase activity, hydrolytic mechanism / histone H4K8 deacetylase activity, hydrolytic mechanism / histone H3K9 deacetylase activity, hydrolytic mechanism / histone H3K14 deacetylase activity, hydrolytic mechanism / HDACs deacetylate histones / histone H4K12 deacetylase activity, hydrolytic mechanism / SUMOylation of chromatin organization proteins / H3-H4 histone complex chaperone activity / Rpd3L complex / Rpd3L-Expanded complex / Rpd3S complex / histone deacetylase / protein lysine deacetylase activity / histone deacetylase activity / DNA repair-dependent chromatin remodeling / NuA4 histone acetyltransferase complex / Sin3-type complex / epigenetic regulation of gene expression / transcription initiation-coupled chromatin remodeling / heterochromatin formation / mitotic spindle / transcription corepressor activity / histone binding / molecular adaptor activity / chromatin remodeling / DNA repair / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
: / : / MSL3 chromodomain-like / Histone deacetylase interacting domain / Sin3, C-terminal / Transcriptional regulatory protein Sin3-like / Sin3 family co-repressor / C-terminal domain of Sin3a protein / Histone deacetylase (HDAC) interacting / Paired amphipathic helix ...: / : / MSL3 chromodomain-like / Histone deacetylase interacting domain / Sin3, C-terminal / Transcriptional regulatory protein Sin3-like / Sin3 family co-repressor / C-terminal domain of Sin3a protein / Histone deacetylase (HDAC) interacting / Paired amphipathic helix / Paired amphipathic helix superfamily / Paired amphipathic helix repeat / PAH domain profile. / MRG / MRG domain / MRG, C-terminal domain superfamily / MRG / MRG domain profile. / Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / : / Histone deacetylase / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Paired amphipathic helix protein pst2 / Chromatin modification-related protein eaf3 / RbAp48-related WD40 repeat-containing protein prw1 / Histone deacetylase clr6 / Uncharacterized protein C2F7.07c / Uncharacterized protein C16C9.05
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast) / Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsZhang HQ / Wang X / Wang YN / Liu SM / Zhang Y / Xu K / Ji LT / Kornberg RD
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: Class I histone deacetylase complex: Structure and functional correlates.
Authors: Xiao Wang / Yannan Wang / Simiao Liu / Yi Zhang / Ke Xu / Liting Ji / Roger D Kornberg / Heqiao Zhang /
Abstract: The Clr6S complex, a class I histone deacetylase complex, functions as a zinc-dependent enzyme to remove acetyl groups from lysine residues in histone tails. We report here the cryo-EM structure of ...The Clr6S complex, a class I histone deacetylase complex, functions as a zinc-dependent enzyme to remove acetyl groups from lysine residues in histone tails. We report here the cryo-EM structure of Clr6S alone and a cryo-EM map of Clr6S in complex with a nucleosome. The active center, revealed at near-atomic resolution, includes features important for catalysis-A water molecule coordinated by zinc, the likely nucleophile for attack on the acetyl-lysine bond, and a loop that may position the substrate for catalysis. The cryo-EM map in the presence of a nucleosome reveals multiple Clr6S-nucleosome contacts and a high degree of relative motion of Clr6S and the nucleosome. Such flexibility may be attributed to interaction at a site in the flexible histone tail and is likely important for the function of the deacetylase, which acts at multiple sites in other histone tails.
History
DepositionFeb 17, 2023-
Header (metadata) releaseJan 3, 2024-
Map releaseJan 3, 2024-
UpdateJan 3, 2024-
Current statusJan 3, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_35416.png

Downloads & links

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Map

FileDownload / File: emd_35416.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of Clr6-HDAC complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 250 pix.
= 265. Å		1.06 Å/pix.
x 250 pix.
= 265. Å		1.06 Å/pix.
x 250 pix.
= 265. 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: 0.0378
Minimum - Maximum-0.95258015 - 1.4380814
Average (Standard dev.)0.000020033383 (±0.033607423)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 265.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map

Fileemd_35416_half_map_1.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map

Fileemd_35416_half_map_2.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of the Clr6-HDAC (Clr6S) complex from S. pombe

EntireName: Cryo-EM structure of the Clr6-HDAC (Clr6S) complex from S. pombe
Components
  • Complex: Cryo-EM structure of the Clr6-HDAC (Clr6S) complex from S. pombe
    • Protein or peptide: RbAp48-related WD40 repeat-containing protein prw1
    • Protein or peptide: Paired amphipathic helix protein pst2
    • Protein or peptide: Histone deacetylase clr6
    • Protein or peptide: Chromatin modification-related protein eaf3
    • Protein or peptide: Cph1
    • Protein or peptide: Cph2
  • Ligand: ZINC ION
  • Ligand: water

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Supramolecule #1: Cryo-EM structure of the Clr6-HDAC (Clr6S) complex from S. pombe

SupramoleculeName: Cryo-EM structure of the Clr6-HDAC (Clr6S) complex from S. pombe
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 600 KDa

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Macromolecule #1: RbAp48-related WD40 repeat-containing protein prw1

MacromoleculeName: RbAp48-related WD40 repeat-containing protein prw1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Molecular weightTheoretical: 48.528926 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MAVSAVPHPS KQAQASEEGI NQEKCINEEY KIWKKNSPFL YDLIITRALE WPCMSLQWYP EQQIFAEHGY TEQKMFLGVR ADVGKYLLA VASIQLPYLN QTVPPTTMEG ASAGDESSLR VNISNLYSHP ESVCSAKLMP QDDSCVATVG NYHNDVLVFD K ESFESYSS ...String:
MAVSAVPHPS KQAQASEEGI NQEKCINEEY KIWKKNSPFL YDLIITRALE WPCMSLQWYP EQQIFAEHGY TEQKMFLGVR ADVGKYLLA VASIQLPYLN QTVPPTTMEG ASAGDESSLR VNISNLYSHP ESVCSAKLMP QDDSCVATVG NYHNDVLVFD K ESFESYSS ASESPLKPKY RLTKHTQPCT SVCWNFLSKG TLVSGSQDAT LSCWDLNAYN ESDSASVLKV HISSHEKQVS DV RFHYKHQ DLLASVSYDQ YLHVHDIRRP DASTKPARSV HAHSGPIHSV AFNPHNDFIL ATCSTDKTIA LWDLRNLNQR LHT LEGHED IVTKISFSPH EEPILASTSA DRRTLVWDLS RIGEDQPAEE AQDGPPELLF MHGGHTSCTI DMDWCPNYNW TMAT AAEDN ILQIWTPSRS IWGNEQLEED ATAYLS

UniProtKB: RbAp48-related WD40 repeat-containing protein prw1

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Macromolecule #2: Paired amphipathic helix protein pst2

MacromoleculeName: Paired amphipathic helix protein pst2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Molecular weightTheoretical: 125.011609 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MEQTLAILKN DNSTLVAEMQ NQLVHDFSPN GTALPELDIK AFVQKLGQRL CHRPYVYSAF MDVVKALHNE IVDFPGFIER ISVILRDYP DLLEYLNIFL PSSYKYLLSN SGANFTLQFT TPSGPVSTPS TYVATYNDLP CTYHRAIGFV SRVRRALLSN P EQFFKLQD ...String:
MEQTLAILKN DNSTLVAEMQ NQLVHDFSPN GTALPELDIK AFVQKLGQRL CHRPYVYSAF MDVVKALHNE IVDFPGFIER ISVILRDYP DLLEYLNIFL PSSYKYLLSN SGANFTLQFT TPSGPVSTPS TYVATYNDLP CTYHRAIGFV SRVRRALLSN P EQFFKLQD SLRKFKNSEC SLSELQTIVT SLLAEHPSLA HEFHNFLPSS IFFGSKPPLG SFPLRGIQSS QFTLSNISDL LS QSRPDNL SPFSHLSNES SDFFKNVKNV LTDVETYHEF LKLLNLYVQG IIDRNILVSR GFGFLKSNSG LWRSFLSLTS LSP EEFLSV YNSACSDFPE CGPSYRLLPV EERNISCSGR DDFAWGILND DWVSHPTWAS EESGFIVQRK TPYEEAMTKL EEER YEFDR HIEATSWTIK SLKKIQNRIN ELPEEERETY TLEEGLGLPS KSIYKKTIKL VYTSEHAEEM FKALERMPCL TLPLV ISRL EEKNEEWKSV KRSLQPGWRS IEFKNYDKSL DSQCVYFKAR DKKNVSSKFL LAEADILRSQ AKLHFPLRSR SAFEFS FVY DNEIVLFDTC YMVCTYIVCN SPSGLKKVEH FFKNILPLHF GLEKDKFSIF LDQVFRGPDY DVNAPNIVGN KPVRRKR SN SITQLTEFVK QPKINGQRES RSAAAARKKE ESGNKSQSNS QNSLSDESGN VTPVSKKQLS QPAAAIKASL KYPSHPDS L LEHQDHAGDT ENEMHDDVDK EQFGYSSMYV FFRLFNLLYE RLYELQRLED QVSIIQQRII PNPVSQKQKI WRDRWNDLS DVPDEKTHYE NTYVMILRLI YGIVDQSAFE DYLRFYYGNK AYKIYTIDKL VWSAAKQVHH IVSDGKYKFV TSLVEQNSSA SPKKNYDDF LYRLEIEKLL NPDEILFRFC WINKFKSFGI KIMKRANLIV DQSLDTQRRV WKKYVQNYRI QKLTEEISYK N YRCPFLCR NIEKERTVEQ LVSRLQTKLL RSAELVSGLQ AKLCLDSFKL LYLPRTEDSY IDASYLRLRD TDFLDCQNKR KQ RWRNRWE SLLKSVRGTS DNTAEVNFDA DINALFIP

UniProtKB: Paired amphipathic helix protein pst2

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Macromolecule #3: Histone deacetylase clr6

MacromoleculeName: Histone deacetylase clr6 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: histone deacetylase
Source (natural)Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Molecular weightTheoretical: 45.773371 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: KKKVSYFYDE DVGNYHYGPQ HPMKPHRVRM VHNLVVNYNL YEKLNVITPV RATRNDMTRC HTDEYIEFLW RVTPDTMEKF QPHQLKFNV GDDCPVFDGL YEFCSISAGG SIGAAQELNS GNAEIAINWA GGLHHAKKRE ASGFCYVNDI ALAALELLKY H QRVLYIDI ...String:
KKKVSYFYDE DVGNYHYGPQ HPMKPHRVRM VHNLVVNYNL YEKLNVITPV RATRNDMTRC HTDEYIEFLW RVTPDTMEKF QPHQLKFNV GDDCPVFDGL YEFCSISAGG SIGAAQELNS GNAEIAINWA GGLHHAKKRE ASGFCYVNDI ALAALELLKY H QRVLYIDI DVHHGDGVEE FFYTTDRVMT CSFHKFGEYF PGTGHIKDTG IGTGKNYAVN VPLRDGIDDE SYESVFKPVI SH IMQWFRP EAVILQCGTD SLAGDRLGCF NLSMKGHSMC VDFVKSFNLP MICVGGGGYT VRNVARVWTY ETGLLAGEEL DEN LPYNDY LQYYGPDYKL NVLSNNMENH NTRQYLDSIT SEIIENLRNL SFAPSVQMHK TPGDFTFENA EKQNIAKEEI MDER V

UniProtKB: Histone deacetylase clr6

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Macromolecule #4: Chromatin modification-related protein eaf3

MacromoleculeName: Chromatin modification-related protein eaf3 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Molecular weightTheoretical: 39.191199 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MAVSYKVNER VLCFHGPLLY EAKIVDTEMK GDVTTYLIHY KGWKNSWDEW VEQDRILQWT EENLKTQKEL KNAAISTRQK PTSKKSASS TSKHDSTGVK TSGKRSRESS TVTVDGDSHE LPSRIKTQKS ESPIPQQVKR DGTTDAKNEE TTKPENNEKD D FEEEPPLP ...String:
MAVSYKVNER VLCFHGPLLY EAKIVDTEMK GDVTTYLIHY KGWKNSWDEW VEQDRILQWT EENLKTQKEL KNAAISTRQK PTSKKSASS TSKHDSTGVK TSGKRSRESS TVTVDGDSHE LPSRIKTQKS ESPIPQQVKR DGTTDAKNEE TTKPENNEKD D FEEEPPLP KHKISVPDVL KLWLVDDWEN ITKNQQLIAI PRNPTVRAAI AAFRESKISH LNNEIDVDVF EQAMAGLVIY FN KCLGNML LYRFERQQYL EIRQQYPDTE MCDLYGVEHL IRLFVSLPEL IDRTNMDSQS IECLLNYIEE FLKYLVLHKD EYF IKEYQN APPNYRSLVG V

UniProtKB: Chromatin modification-related protein eaf3

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Macromolecule #5: Cph1

MacromoleculeName: Cph1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Molecular weightTheoretical: 45.046082 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MASSINNSSQ PTVPSISNNS HGDSFVNEGP PSNFKNNSLT SSTHSSTDHV NVLPISQDKE MDISSPVKKQ KASYSNKSPN KAPIQKSRG SSLKSHLETE SQQTPVKRRR RKATIRNVDY CSACGGRGLF ICCEGCPCSF HLSCLEPPLT PENIPEGSWF C VTCSIKSH ...String:
MASSINNSSQ PTVPSISNNS HGDSFVNEGP PSNFKNNSLT SSTHSSTDHV NVLPISQDKE MDISSPVKKQ KASYSNKSPN KAPIQKSRG SSLKSHLETE SQQTPVKRRR RKATIRNVDY CSACGGRGLF ICCEGCPCSF HLSCLEPPLT PENIPEGSWF C VTCSIKSH HPPKHPLSIW SQLYDWIDSQ NPSQYRLPDD LVHYFHGISR GDTGAYKETE GEMDTDEFSA LPTGSSITNL AY CGYCSKP SMGACWVYGC QLCDTFYHKN CKEHAKKCSH DSIGKKGMRV PKNAVVIRTP LVLDTTSNTL NPKVMISGWQ FLM GEFPSD ELLYFPRLPV SCLYKVSEDG LIKDFLYAIG IEAKKFNNER KKRELEVIPP DVKSALLPAR THPNLPIALR TLFN KART

UniProtKB: Uncharacterized protein C16C9.05

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Macromolecule #6: Cph2

MacromoleculeName: Cph2 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Molecular weightTheoretical: 68.871703 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDAKPWNHTS EAFQASILED LKIIQKAGAE RNAKSSHGSI NSRSASPNKA TSRRNRAQNG NSNGRASVDN SDDGSKDDLD YSPSVKRKH VNGEGAEKGD HDTSNNGPSI TKLRRKVRRT YDTKDGFVAW NTLDDDFRPI VPDQERSRKI NPQKGNNNNL L KENKSLKT ...String:
MDAKPWNHTS EAFQASILED LKIIQKAGAE RNAKSSHGSI NSRSASPNKA TSRRNRAQNG NSNGRASVDN SDDGSKDDLD YSPSVKRKH VNGEGAEKGD HDTSNNGPSI TKLRRKVRRT YDTKDGFVAW NTLDDDFRPI VPDQERSRKI NPQKGNNNNL L KENKSLKT TAKDLSDISS SSMKKANNSS KPLFSGKLTF KANIPVPTSE VVTENNVTRN VTVYSNQKHL GNESENFNDM EG RAEDISS NELLPTPEEY PYRYNNDYCS ACHGPGNFLC CETCPNSFHF TCIDPPIEEK NLPDDAWYCN ECKHHSLYNE LDE QEELES NVKEEGTMVD VWMQLCTYID SHNPIQFHLP HSISSFFRGV GSGVMGEYIE TDVLKHLKSS RRSNGEERDP LLLK SKSGT PILCFRCHKS ALVSQSILAC DYCNSYWHPD CLNPPLATLP SNLRKWKCPN HSDHVTPRYR LPEKAKVIRV GLPRG FKNK GNIVIDENED EPSVQTIQLQ GKIRVVPSKP FKLNFLEQIR DNVINLRKMV EQDEQLCIET FSKFDFYATR DCELPL RIL CDVANDNLEN DDYVLALRDL LRISKWDPNQ PVPAPFDLAN LLSY

UniProtKB: Uncharacterized protein C2F7.07c

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Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 1 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 721645
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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