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- EMDB-21980: Bridging of double-strand DNA break activates PARP2/HPF1 to modif... -

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Basic information

Entry
Database: EMDB / ID: EMD-21980
TitleBridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin
Map dataPARP2/HPF1_Nucleosome complex
Sample
  • Complex: Histone H3.2, Histone H4, Histone H2A type 1, Histone H2B 1.1, Histone PARylation factor 1, Poly [ADP-ribose] polymerase 2/DNA Complex
    • Complex: Histone H3.2, Histone H4, Histone H2A type 1, Histone H2B 1.1
      • Protein or peptide: Histone H3.2
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B 1.1
    • Complex: DNA
      • DNA: DNA (167-MER)
      • DNA: DNA (167-MER)
    • Complex: Histone PARylation factor 1, Poly [ADP-ribose] polymerase 2
      • Protein or peptide: Histone PARylation factor 1
      • Protein or peptide: Poly [ADP-ribose] polymerase 2
KeywordsDNA repair / PARP1 / PARP2 / HPF1 / ADP-ribosylation / chromatin / histone modifications / GENE REGULATION
Function / homology
Function and homology information


protein ADP-ribosyltransferase-substrate adaptor activity / regulation of protein ADP-ribosylation / hippocampal neuron apoptotic process / response to oxygen-glucose deprivation / poly-ADP-D-ribose binding / positive regulation of cell growth involved in cardiac muscle cell development / poly-ADP-D-ribose modification-dependent protein binding / NAD+-protein-serine ADP-ribosyltransferase activity / NAD DNA ADP-ribosyltransferase activity / NAD+-protein-aspartate ADP-ribosyltransferase activity ...protein ADP-ribosyltransferase-substrate adaptor activity / regulation of protein ADP-ribosylation / hippocampal neuron apoptotic process / response to oxygen-glucose deprivation / poly-ADP-D-ribose binding / positive regulation of cell growth involved in cardiac muscle cell development / poly-ADP-D-ribose modification-dependent protein binding / NAD+-protein-serine ADP-ribosyltransferase activity / NAD DNA ADP-ribosyltransferase activity / NAD+-protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / DNA ADP-ribosylation / HDR through MMEJ (alt-NHEJ) / NAD+ ADP-ribosyltransferase / protein auto-ADP-ribosylation / DNA repair-dependent chromatin remodeling / protein poly-ADP-ribosylation / NAD+-protein ADP-ribosyltransferase activity / site of DNA damage / decidualization / NAD+-protein poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / nucleosome binding / POLB-Dependent Long Patch Base Excision Repair / extrinsic apoptotic signaling pathway / nucleotidyltransferase activity / DNA Damage Recognition in GG-NER / base-excision repair / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / structural constituent of chromatin / nucleosome / double-strand break repair / nucleosome assembly / histone binding / damaged DNA binding / protein heterodimerization activity / DNA repair / DNA damage response / chromatin binding / chromatin / nucleolus / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Histone PARylation factor 1 / Histone PARylation factor 1 / : / Poly(ADP-ribose) polymerase, regulatory domain / WGR domain / WGR domain superfamily / WGR domain / WGR domain profile. / Proposed nucleic acid binding domain / Poly(ADP-ribose) polymerase, regulatory domain superfamily ...Histone PARylation factor 1 / Histone PARylation factor 1 / : / Poly(ADP-ribose) polymerase, regulatory domain / WGR domain / WGR domain superfamily / WGR domain / WGR domain profile. / Proposed nucleic acid binding domain / Poly(ADP-ribose) polymerase, regulatory domain superfamily / Poly(ADP-ribose) polymerase, regulatory domain / PARP alpha-helical domain profile. / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / Histone H2A / Histone 2A / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
Histone H2B 1.1 / Histone H2A type 1 / Histone H4 / Histone H3.2 / Histone H2A / Histone PARylation factor 1 / Poly [ADP-ribose] polymerase 2
Similarity search - Component
Biological speciesAfrican clawed frog (African clawed frog) / synthetic construct (others) / Homo sapiens (human) / Xenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.0 Å
AuthorsHalic M / Bilokapic S
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM135599-01 United States
CitationJournal: Nature / Year: 2020
Title: Bridging of DNA breaks activates PARP2-HPF1 to modify chromatin.
Authors: Silvija Bilokapic / Marcin J Suskiewicz / Ivan Ahel / Mario Halic /
Abstract: Breaks in DNA strands recruit the protein PARP1 and its paralogue PARP2 to modify histones and other substrates through the addition of mono- and poly(ADP-ribose) (PAR). In the DNA damage responses, ...Breaks in DNA strands recruit the protein PARP1 and its paralogue PARP2 to modify histones and other substrates through the addition of mono- and poly(ADP-ribose) (PAR). In the DNA damage responses, this post-translational modification occurs predominantly on serine residues and requires HPF1, an accessory factor that switches the amino acid specificity of PARP1 and PARP2 from aspartate or glutamate to serine. Poly(ADP) ribosylation (PARylation) is important for subsequent chromatin decompaction and provides an anchor for the recruitment of downstream signalling and repair factors to the sites of DNA breaks. Here, to understand the molecular mechanism by which PARP enzymes recognize DNA breaks within chromatin, we determined the cryo-electron-microscopic structure of human PARP2-HPF1 bound to a nucleosome. This showed that PARP2-HPF1 bridges two nucleosomes, with the broken DNA aligned in a position suitable for ligation, revealing the initial step in the repair of double-strand DNA breaks. The bridging induces structural changes in PARP2 that signal the recognition of a DNA break to the catalytic domain, which licenses HPF1 binding and PARP2 activation. Our data suggest that active PARP2 cycles through different conformational states to exchange NAD and substrate, which may enable PARP enzymes to act processively while bound to chromatin. The processes of PARP activation and the PARP catalytic cycle we describe can explain mechanisms of resistance to PARP inhibitors and will aid the development of better inhibitors as cancer treatments.
History
DepositionMay 16, 2020-
Header (metadata) releaseSep 16, 2020-
Map releaseSep 16, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
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  • Surface level: 0.01
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  • Surface view with fitted model
  • Atomic models: PDB-6x0n
  • Surface level: 0.01
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6x0n
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21980.png

Downloads & links

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Map

FileDownload / File: emd_21980.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPARP2/HPF1_Nucleosome complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 480 pix.
= 508.8 Å		1.06 Å/pix.
x 480 pix.
= 508.8 Å		1.06 Å/pix.
x 480 pix.
= 508.8 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: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.0070163524 - 0.036107153
Average (Standard dev.)0.00014669662 (±0.0016195979)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 508.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z508.800508.800508.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.0070.0360.000

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Supplemental data

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Sample components

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Entire : Histone H3.2, Histone H4, Histone H2A type 1, Histone H2B 1.1, Hi...

EntireName: Histone H3.2, Histone H4, Histone H2A type 1, Histone H2B 1.1, Histone PARylation factor 1, Poly [ADP-ribose] polymerase 2/DNA Complex
Components
  • Complex: Histone H3.2, Histone H4, Histone H2A type 1, Histone H2B 1.1, Histone PARylation factor 1, Poly [ADP-ribose] polymerase 2/DNA Complex
    • Complex: Histone H3.2, Histone H4, Histone H2A type 1, Histone H2B 1.1
      • Protein or peptide: Histone H3.2
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B 1.1
    • Complex: DNA
      • DNA: DNA (167-MER)
      • DNA: DNA (167-MER)
    • Complex: Histone PARylation factor 1, Poly [ADP-ribose] polymerase 2
      • Protein or peptide: Histone PARylation factor 1
      • Protein or peptide: Poly [ADP-ribose] polymerase 2

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Supramolecule #1: Histone H3.2, Histone H4, Histone H2A type 1, Histone H2B 1.1, Hi...

SupramoleculeName: Histone H3.2, Histone H4, Histone H2A type 1, Histone H2B 1.1, Histone PARylation factor 1, Poly [ADP-ribose] polymerase 2/DNA Complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8 / Details: PARP2/HPF1 from PARP2/HPF1_Nucleosome complex
Molecular weightTheoretical: 100 KDa

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Supramolecule #2: Histone H3.2, Histone H4, Histone H2A type 1, Histone H2B 1.1

SupramoleculeName: Histone H3.2, Histone H4, Histone H2A type 1, Histone H2B 1.1
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: African clawed frog (African clawed frog)

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Supramolecule #3: DNA

SupramoleculeName: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: synthetic construct (others)

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Supramolecule #4: Histone PARylation factor 1, Poly [ADP-ribose] polymerase 2

SupramoleculeName: Histone PARylation factor 1, Poly [ADP-ribose] polymerase 2
type: complex / ID: 4 / Parent: 1 / Macromolecule list: #7-#8
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.30393 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEASEAY LVALFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3.2

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.263231 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.978241 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKQGGKT RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAVRN DEELNKLLGR VTIAQGGVLP NIQSVLLPKK TESSKSAKSK

UniProtKB: Histone H2A

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Macromolecule #4: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.524752 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AKSAPAPKKG SKKAVTKTQK KDGKKRRKTR KESYAIYVYK VLKQVHPDTG ISSKAMSIMN SFVNDVFERI AGEASRLAHY NKRSTITSR EIQTAVRLLL PGELAKHAVS EGTKAVTKYT SAK

UniProtKB: Histone H2B 1.1

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Macromolecule #7: Histone PARylation factor 1

MacromoleculeName: Histone PARylation factor 1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.598293 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGHHHHHHGG MVGGGGKRRP GGEGPQCEKT TDVKKSKFCE ADVSSDLRKE VENHYKLSLP EDFYHFWKFC EELDPEKPSD SLSASLGLQ LVGPYDILAG KHKTKKKSTG LNFNLHWRFY YDPPEFQTII IGDNKTQYHM GYFRDSPDEF PVYVGINEAK K NCIIVPNG ...String:
MGHHHHHHGG MVGGGGKRRP GGEGPQCEKT TDVKKSKFCE ADVSSDLRKE VENHYKLSLP EDFYHFWKFC EELDPEKPSD SLSASLGLQ LVGPYDILAG KHKTKKKSTG LNFNLHWRFY YDPPEFQTII IGDNKTQYHM GYFRDSPDEF PVYVGINEAK K NCIIVPNG DNVFAAVKLF LTKKLKEITD KKKINLLKNI DEKLTEAARE LGYSLEQRTV KMKQRDKKVV TKTFHGAGLV VP VDKNDVG YRELPETDAD LKRICKTIVE AASDEERLKA FAPIQEMMTF VQFANDECDY GMGLELGMDL FCYGSHYFHK VAG QLLPLA YNLLKRNLFA EIIEEHLANR SQENIDQLAA

UniProtKB: Histone PARylation factor 1

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Macromolecule #8: Poly [ADP-ribose] polymerase 2

MacromoleculeName: Poly [ADP-ribose] polymerase 2 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO / EC number: NAD+ ADP-ribosyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 67.0725 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MAARRRRSTG GGRARALNES KRVNNGNTAP EDSSPAKKTR RCQRQESKKM PVAGGKANKD RTEDKQDES VKALLLKGKA PVDPECTAKV GKAHVYCEGN DVYDVMLNQT NLQFNNNKYY LIQLLEDDAQ RNFSVWMRWG R VGKMGQHS ...String:
MGSSHHHHHH SSGLVPRGSH MAARRRRSTG GGRARALNES KRVNNGNTAP EDSSPAKKTR RCQRQESKKM PVAGGKANKD RTEDKQDES VKALLLKGKA PVDPECTAKV GKAHVYCEGN DVYDVMLNQT NLQFNNNKYY LIQLLEDDAQ RNFSVWMRWG R VGKMGQHS LVACSGNLNK AKEIFQKKFL DKTKNNWEDR EKFEKVPGKY DMLQMDYATN TQDEEETKKE ESLKSPLKPE SQ LDLRVQE LIKLICNVQA MEEMMMEMKY NTKKAPLGKL TVAQIKAGYQ SLKKIEDCIR AGQHGRALME ACNEFYTRIP HDF GLRTPP LIRTQKELSE KIQLLEALGD IEIAIKLVKT ELQSPEHPLD QHYRNLHCAL RPLDHESYEF KVISQYLQST HAPT HSDYT MTLLDLFEVE KDGEKEAFRE DLHNRMLLWH GSRMSNWVGI LSHGLRIAPP EAPITGYMFG KGIYFADMSS KSANY CFAS RLKNTGLLLL SEVALGQCNE LLEANPKAEG LLQGKHSTKG LGKMAPSSAH FVTLNGSTVP LGPASDTGIL NPDGYT LNY NEYIVYNPNQ VRMRYLLKVQ FNFLQLW

UniProtKB: Poly [ADP-ribose] polymerase 2

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Macromolecule #5: DNA (167-MER)

MacromoleculeName: DNA (167-MER) / type: dna / ID: 5 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 51.776004 KDa
SequenceString: (DC)(DA)(DA)(DT)(DA)(DC)(DA)(DT)(DG)(DC) (DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA) (DC)(DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG) (DG) (DA)(DG)(DA)(DC)(DT)(DA) ...String:
(DC)(DA)(DA)(DT)(DA)(DC)(DA)(DT)(DG)(DC) (DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA) (DC)(DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG) (DG) (DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG) (DG)(DA)(DG)(DT)(DA)(DA)(DT)(DC)(DC)(DC) (DC)(DT) (DT)(DG)(DG)(DC)(DG)(DG)(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)(DG)(DG)(DG)(DA)(DT)(DT)(DC)(DT) (DC)(DC)(DA)(DG)(DG)(DG)(DC) (DA)(DT) (DC)(DA)(DT)(DA)(DG)

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Macromolecule #6: DNA (167-MER)

MacromoleculeName: DNA (167-MER) / type: dna / ID: 6 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 51.330684 KDa
SequenceString: (DC)(DT)(DA)(DT)(DG)(DA)(DT)(DG)(DC)(DC) (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG) (DA)(DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA) (DT)(DT)(DG)(DG)(DT)(DC) ...String:
(DC)(DT)(DA)(DT)(DG)(DA)(DT)(DG)(DC)(DC) (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(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)(DC)(DC)(DG)(DC) (DC)(DA)(DA)(DG)(DG)(DG)(DG)(DA)(DT)(DT) (DA)(DC)(DT)(DC)(DC) (DC)(DT)(DA)(DG) (DT)(DC)(DT)(DC)(DC)(DA)(DG)(DG)(DC)(DA) (DC)(DG)(DT)(DG)(DT)(DC) (DA)(DG)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DC)(DA)(DT)(DC) (DC)(DT)(DG)(DT)(DG)(DC)(DA) (DT)(DG) (DT)(DA)(DT)(DT)(DG)

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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

Concentration0.1 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 934000
Startup modelType of model: EMDB MAP
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 17000
Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD

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