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- EMDB-0559: Set2 bound to nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-0559
TitleSet2 bound to nucleosome
Map dataSet2 bound to the nucleosome
Sample
  • Complex: Set2 nucleosome complex
    • Complex: Histone-lysine N-methyltransferase
      • Protein or peptide: Histone-lysine N-methyltransferase
    • Complex: DNA
      • DNA: DNA (149-MER)
      • DNA: DNA (149-MER)
    • Complex: Histone H3, Histone H4, Ubiquitin-60S ribosomal protein L40,Histone H2A, Histone H2B 1.1
      • Protein or peptide: Histone H3
      • Protein or peptide: Histone H4
      • Protein or peptide: Ubiquitin-60S ribosomal protein L40,Histone H2A
      • Protein or peptide: Histone H2B 1.1
  • Ligand: ZINC ION
KeywordsSet2 / nucleosome / chromatin / KMT / GENE REGULATION
Function / homology
Function and homology information


[histone H3]-lysine36 N-trimethyltransferase / histone H3K36 trimethyltransferase activity / ribosomal large subunit export from nucleus / modification-dependent protein catabolic process / protein tag activity / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / ribosome biogenesis ...[histone H3]-lysine36 N-trimethyltransferase / histone H3K36 trimethyltransferase activity / ribosomal large subunit export from nucleus / modification-dependent protein catabolic process / protein tag activity / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / ribosome biogenesis / chromosome / ribosomal large subunit assembly / methylation / cytosolic large ribosomal subunit / cytoplasmic translation / protein ubiquitination / structural constituent of ribosome / protein heterodimerization activity / ubiquitin protein ligase binding / regulation of DNA-templated transcription / mitochondrion / DNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Histone-lysine N-methyltransferase, Set2, fungi / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / Set2 Rpb1 interacting domain superfamily / SETD2/Set2, SET domain / : / Set2 Rpb1 interacting domain / SRI (Set2 Rpb1 interacting) domain / AWS domain / AWS domain / AWS domain profile. ...Histone-lysine N-methyltransferase, Set2, fungi / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / Set2 Rpb1 interacting domain superfamily / SETD2/Set2, SET domain / : / Set2 Rpb1 interacting domain / SRI (Set2 Rpb1 interacting) domain / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / Transcription factor IIS, N-terminal / TFIIS helical bundle-like domain / Cysteine-rich motif following a subset of SET domains / TFIIS/LEDGF domain superfamily / Post-SET domain / Post-SET domain profile. / WW domain / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / WW domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / : / 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 H2A / Histone 2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / 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 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / : / Ubiquitin domain signature. / Histone H2A/H2B/H3 / Ubiquitin conserved site / Core histone H2A/H2B/H3/H4 / Ubiquitin domain / Histone-fold / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Histone H3 / Histone-lysine N-methyltransferase, H3 lysine-36 specific / Histone H2B 1.1 / Histone H3.3C / Ubiquitin-ribosomal protein eL40B fusion protein / Histone H4 / Histone H2A
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus) / synthetic construct (others) / Xenopus laevis (African clawed frog) / Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsHalic M / Bilokapic S
CitationJournal: Nat Commun / Year: 2019
Title: Nucleosome and ubiquitin position Set2 to methylate H3K36.
Authors: Silvija Bilokapic / Mario Halic /
Abstract: Histone H3 lysine 36 methylation (H3K36me) is a conserved histone modification deposited by the Set2 methyltransferases. Recent findings show that over-expression or mutation of Set2 enzymes promotes ...Histone H3 lysine 36 methylation (H3K36me) is a conserved histone modification deposited by the Set2 methyltransferases. Recent findings show that over-expression or mutation of Set2 enzymes promotes cancer progression, however, mechanisms of H3K36me are poorly understood. Set2 enzymes show spurious activity on histones and histone tails, and it is unknown how they obtain specificity to methylate H3K36 on the nucleosome. In this study, we present 3.8 Å cryo-EM structure of Set2 bound to the mimic of H2B ubiquitinated nucleosome. Our structure shows that Set2 makes extensive interactions with the H3 αN, the H3 tail, the H2A C-terminal tail and stabilizes DNA in the unwrapped conformation, which positions Set2 to specifically methylate H3K36. Moreover, we show that ubiquitin contributes to Set2 positioning on the nucleosome and stimulates the methyltransferase activity. Notably, our structure uncovers interfaces that can be targeted by small molecules for development of future cancer therapies.
History
DepositionFeb 14, 2019-
Header (metadata) releaseJul 17, 2019-
Map releaseAug 28, 2019-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6nzo
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0559.png

Downloads & links

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Map

FileDownload / File: emd_0559.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSet2 bound to the nucleosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 240 pix.
= 249.6 Å		1.04 Å/pix.
x 240 pix.
= 249.6 Å		1.04 Å/pix.
x 240 pix.
= 249.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012 / Movie #1: 0.012
Minimum - Maximum-0.049233016 - 0.07451724
Average (Standard dev.)0.00013642217 (±0.002860413)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 249.59999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z249.600249.600249.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0490.0750.000

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Supplemental data

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Sample components

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Entire : Set2 nucleosome complex

EntireName: Set2 nucleosome complex
Components
  • Complex: Set2 nucleosome complex
    • Complex: Histone-lysine N-methyltransferase
      • Protein or peptide: Histone-lysine N-methyltransferase
    • Complex: DNA
      • DNA: DNA (149-MER)
      • DNA: DNA (149-MER)
    • Complex: Histone H3, Histone H4, Ubiquitin-60S ribosomal protein L40,Histone H2A, Histone H2B 1.1
      • Protein or peptide: Histone H3
      • Protein or peptide: Histone H4
      • Protein or peptide: Ubiquitin-60S ribosomal protein L40,Histone H2A
      • Protein or peptide: Histone H2B 1.1
  • Ligand: ZINC ION

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Supramolecule #1: Set2 nucleosome complex

SupramoleculeName: Set2 nucleosome complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Molecular weightTheoretical: 240 KDa

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Supramolecule #2: Histone-lysine N-methyltransferase

SupramoleculeName: Histone-lysine N-methyltransferase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #7
Source (natural)Organism: Chaetomium thermophilum (fungus)

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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 H3, Histone H4, Ubiquitin-60S ribosomal protein L40,Histo...

SupramoleculeName: Histone H3, Histone H4, Ubiquitin-60S ribosomal protein L40,Histone H2A, Histone H2B 1.1
type: complex / ID: 4 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Macromolecule #1: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.437144 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVMKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEASEA YLVALFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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Macromolecule #3: Ubiquitin-60S ribosomal protein L40,Histone H2A

MacromoleculeName: Ubiquitin-60S ribosomal protein L40,Histone H2A / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 24.045436 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDSPDLHHHH HHGTLVPRGS MQIFVKTLTG KTITLEVESS DTIDNVKSKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHL VLRLRGTSSG GSGGSGGSGR SSRAGLQFPV GRVHRLLRKG NYAERVGAGA PVYLAAVLEY LTAEILELAG N AARDNKKT ...String:
MDSPDLHHHH HHGTLVPRGS MQIFVKTLTG KTITLEVESS DTIDNVKSKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHL VLRLRGTSSG GSGGSGGSGR SSRAGLQFPV GRVHRLLRKG NYAERVGAGA PVYLAAVLEY LTAEILELAG N AARDNKKT RIIPRHLQLA VRNDEELNKL LGRVTIAQGG VLPNIQSVLL PKKTESSKSA KSK

UniProtKB: Ubiquitin-ribosomal protein eL40B fusion protein, 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: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.655948 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAKSAPAPKK GSKKAVTKTQ KKDGKKRRKT RKESYAIYVY KVLKQVHPDT GISSKAMSIM NSFVNDVFER IAGEASRLAH YNKRSTITS REIQTAVRLL LPGELAKHAV SEGTKAVTKY TSAK

UniProtKB: Histone H2B 1.1

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Macromolecule #7: Histone-lysine N-methyltransferase

MacromoleculeName: Histone-lysine N-methyltransferase / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: histone-lysine N-methyltransferase
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 105.425906 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEASDRASGP TAGSKSEERT KQNGPRSKKE DASDSSTSTG SKSASRSSSA TTMSPDDAKP ADDSALAQEN GVAPKPSRKS SKLPPRNPP QLFNHLPDAT EEACRTFQVI SDCLYGSRNM GSSDHDALDC DCAEDWRDGK NHACGEDSDC INRATKIECV I GDCNCGEG ...String:
MEASDRASGP TAGSKSEERT KQNGPRSKKE DASDSSTSTG SKSASRSSSA TTMSPDDAKP ADDSALAQEN GVAPKPSRKS SKLPPRNPP QLFNHLPDAT EEACRTFQVI SDCLYGSRNM GSSDHDALDC DCAEDWRDGK NHACGEDSDC INRATKIECV I GDCNCGEG CQNQRFQRKQ YAKVSVIKTE KKGYGLRADT DLQPNDFIYE YVGEVINEPT FRSRMLKYDK EGIKHFYFMS LT KNEFVDA TKKGNLGRFC NHSCNPNCYV DKWVVGDKLR MGIFAARYIK AGEELVFNYN VDRYGADPQP CYCGEPNCVG FIG GKTQTE RATKLPLATI EALGIEDGDS WDTTVAKKPR KKKASETDEE YVNSLQPKAL DEDGVNKVMA TLMQCKEKWI AVKL LSRLQ ATQDDHLRHR VVRMHGYQIL KSTLNAFKHD NNVVLQVLDI LYNLPRITKN KISDSNIEAV VQPLASSSDE RVAFE AKRL LEEWDKLETA YRIPRKKDGR VVSAIANSFE EERRSNREEP TKPADPLANV VIPTGPRSNI PQRNANYYNG VRPRKP PTN LPEGWFVTVD KKTGKYYFYD VNGKVQWQRP TAPAITTPKP SVKAQQDQKA LQDIIDSLTK EPTPRQSAGH TPQRSST PA TEPKKEKWRS LPIEKQMKIY ENTLFPHVKY VMDKFHGKLP REDLKKFARD VNKKLVASDY KHNRVQDPTV PLSSKQAK K VRKYVYDFFD RALQKYLEYQ KRKAQYTSKE GMQSSQTEQN TATPTGTLGK DVDEVMSDVE APNSSPQSTS SAGRKRKRD DDQDGDHDMR SPADEDAATS SDPPSVKRIK EDDGTGNDVI PSPPPPPPPP AEIPMTEEER SMREQEEALM RENEEAQRLE DEAKRKQLE LQNGLAAAKN AGIELGSASF TVSGEPMDVD NDGPPPQEQA QQQKQAVMSH

UniProtKB: Histone-lysine N-methyltransferase, H3 lysine-36 specific

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Macromolecule #5: DNA (149-MER)

MacromoleculeName: DNA (149-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 45.764141 KDa
SequenceString: (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) ...String:
(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)

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Macromolecule #6: DNA (149-MER)

MacromoleculeName: DNA (149-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 46.222434 KDa
SequenceString: (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) ...String:
(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)

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Macromolecule #8: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 8 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: 7.5
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 75.0 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 65000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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