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- EMDB-45578: Cryo-EM structure of an HMGB1 box bound to nucleosome at SHL-2 -

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Basic information

Entry
Database: EMDB / ID: EMD-45578
TitleCryo-EM structure of an HMGB1 box bound to nucleosome at SHL-2
Map dataNU-Refine map from cryoSPARC (unsharpened)
Sample
  • Complex: Complex of nucleosome with HMGB1
    • Complex: 0/10 nucleosome with Xenopus laevis histones
      • Protein or peptide: Histone H3.2
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1
      • Protein or peptide: Histone H2B
      • DNA: Widom 601 DNA reverse strand (147-mer)
      • DNA: Widom 601 DNA forward strand (147-mer)
    • Complex: High mobility group protein B1
      • Protein or peptide: High mobility group protein B1
Keywordsnucleosome / high-mobility group box 1 / HMGB1 / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


regulation of restriction endodeoxyribonuclease activity / regulation of tolerance induction / positive regulation of mismatch repair / regulation of T cell mediated immune response to tumor cell / negative regulation of apoptotic cell clearance / negative regulation of RNA polymerase II transcription preinitiation complex assembly / myeloid dendritic cell activation / T-helper 1 cell activation / T-helper 1 cell differentiation / positive regulation of dendritic cell differentiation ...regulation of restriction endodeoxyribonuclease activity / regulation of tolerance induction / positive regulation of mismatch repair / regulation of T cell mediated immune response to tumor cell / negative regulation of apoptotic cell clearance / negative regulation of RNA polymerase II transcription preinitiation complex assembly / myeloid dendritic cell activation / T-helper 1 cell activation / T-helper 1 cell differentiation / positive regulation of dendritic cell differentiation / C-X-C chemokine binding / negative regulation of CD4-positive, alpha-beta T cell differentiation / positive regulation of toll-like receptor 9 signaling pathway / neutrophil clearance / DNA geometric change / RAGE receptor binding / positive regulation of interleukin-1 production / Regulation of TLR by endogenous ligand / bubble DNA binding / V(D)J recombination / alphav-beta3 integrin-HMGB1 complex / Apoptosis induced DNA fragmentation / inflammatory response to antigenic stimulus / positive regulation of monocyte chemotaxis / MyD88 deficiency (TLR2/4) / positive regulation of chemokine (C-X-C motif) ligand 2 production / apoptotic cell clearance / supercoiled DNA binding / positive regulation of vascular endothelial cell proliferation / dendritic cell chemotaxis / DNA binding, bending / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / positive regulation of DNA binding / phosphatidylserine binding / chemoattractant activity / endoplasmic reticulum-Golgi intermediate compartment / positive regulation of activated T cell proliferation / TRAF6 mediated NF-kB activation / negative regulation of type II interferon production / DNA topological change / negative regulation of blood vessel endothelial cell migration / Advanced glycosylation endproduct receptor signaling / positive regulation of interleukin-10 production / positive regulation of blood vessel endothelial cell migration / Pyroptosis / four-way junction DNA binding / condensed chromosome / DNA polymerase binding / positive regulation of autophagy / transcription repressor complex / positive regulation of interleukin-12 production / activation of innate immune response / cytokine activity / positive regulation of interleukin-8 production / positive regulation of JNK cascade / lipopolysaccharide binding / TAK1-dependent IKK and NF-kappa-B activation / double-strand break repair via nonhomologous end joining / autophagy / positive regulation of interleukin-6 production / neuron projection development / transcription corepressor activity / positive regulation of tumor necrosis factor production / structural constituent of chromatin / integrin binding / nucleosome / heterochromatin formation / double-strand break repair / nucleosome assembly / single-stranded DNA binding / ER-Phagosome pathway / cellular response to lipopolysaccharide / positive regulation of cytosolic calcium ion concentration / double-stranded DNA binding / secretory granule lumen / DNA-binding transcription factor binding / DNA recombination / RNA polymerase II-specific DNA-binding transcription factor binding / ficolin-1-rich granule lumen / damaged DNA binding / transcription coactivator activity / positive regulation of viral entry into host cell / positive regulation of ERK1 and ERK2 cascade / transcription cis-regulatory region binding / positive regulation of MAPK cascade / endosome / lyase activity / positive regulation of apoptotic process / inflammatory response / receptor ligand activity / protein heterodimerization activity / innate immune response / Neutrophil degranulation / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / cell surface / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / DNA binding
Similarity search - Function
HMG box A DNA-binding domain, conserved site / HMG box A DNA-binding domain signature. / : / HMG-box domain / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / : ...HMG box A DNA-binding domain, conserved site / HMG box A DNA-binding domain signature. / : / HMG-box domain / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain 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 / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
Histone H2B 1.1 / Histone H2A type 1 / High mobility group protein B1 / Histone H4 / Histone H3.2
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog) / Homo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsChio US / Saunders HS / Narlikar GJ / Cheng Y
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM127020 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM140847 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM137463 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: Competition between HMGB1 and H1 on nucleosomes tunes dynamics within condensed chromatin
Authors: Saunders HS / Chio US / Moore CM / Ramani V / Cheng Y / Narlikar GJ
History
DepositionJun 28, 2024-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45578.png

Downloads & links

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Map

FileDownload / File: emd_45578.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNU-Refine map from cryoSPARC (unsharpened)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 288 pix.
= 240.192 Å		0.83 Å/pix.
x 288 pix.
= 240.192 Å		0.83 Å/pix.
x 288 pix.
= 240.192 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.834 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.27
Minimum - Maximum-0.0 - 1.2903076
Average (Standard dev.)0.009273748 (±0.042639513)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 240.192 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 1 from cryoSPARC

Fileemd_45578_half_map_1.map
AnnotationHalf map 1 from cryoSPARC
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 from cryoSPARC

Fileemd_45578_half_map_2.map
AnnotationHalf map 2 from cryoSPARC
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of nucleosome with HMGB1

EntireName: Complex of nucleosome with HMGB1
Components
  • Complex: Complex of nucleosome with HMGB1
    • Complex: 0/10 nucleosome with Xenopus laevis histones
      • Protein or peptide: Histone H3.2
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1
      • Protein or peptide: Histone H2B
      • DNA: Widom 601 DNA reverse strand (147-mer)
      • DNA: Widom 601 DNA forward strand (147-mer)
    • Complex: High mobility group protein B1
      • Protein or peptide: High mobility group protein B1

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Supramolecule #1: Complex of nucleosome with HMGB1

SupramoleculeName: Complex of nucleosome with HMGB1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Details: Individual histones were recombinantly expressed and purified from E. coli BL21(DE3) pLysS as lyopholized powder. Histone octamer was refolded using urea and dialysis and then purified. ...Details: Individual histones were recombinantly expressed and purified from E. coli BL21(DE3) pLysS as lyopholized powder. Histone octamer was refolded using urea and dialysis and then purified. Widom 601 147-mer DNA with 10 base pairs flanking DNA was generated by PCR. Nucleosome was generated through salt-gradient dialysis of reconstituted histone octamer with DNA. Full-length HMGB1 was recombinantly expressed and purified from E. coli BL21(DE3) Rosetta.
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Supramolecule #2: 0/10 nucleosome with Xenopus laevis histones

SupramoleculeName: 0/10 nucleosome with Xenopus laevis histones / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#6
Details: Histones recombinantly expressed in E. coli. DNA generated by PCR.
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Supramolecule #3: High mobility group protein B1

SupramoleculeName: High mobility group protein B1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #7 / Details: Recombinantly expressed and purified from E. coli.
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: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.271863 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEASEAY LVALFEDTNL AAIHAKRVTI 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: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.263231 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A type 1

MacromoleculeName: Histone H2A type 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.978241 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
SGRGKQGGKT RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAVRN DEELNKLLGR VTIAQGGVLP NIQSVLLPKK TESSKSAKSK

UniProtKB: Histone H2A type 1

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Macromolecule #4: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.524752 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
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: High mobility group protein B1

MacromoleculeName: High mobility group protein B1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.092049 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GSMGKGDPKK PRGKMSSYAF FVQTCREEHK KKHPDASVNF SEFSKKCSER WKTMSAKEKG KFEDMAKADK ARYEREMKTY IPPKGETKK KFKDPNAPKR PPSAFFLFCS EYRPKIKGEH PGLSIGDVAK KLGEMWNNTA ADDKQPYEKK AAKLKEKYEK D IAAYRAKG ...String:
GSMGKGDPKK PRGKMSSYAF FVQTCREEHK KKHPDASVNF SEFSKKCSER WKTMSAKEKG KFEDMAKADK ARYEREMKTY IPPKGETKK KFKDPNAPKR PPSAFFLFCS EYRPKIKGEH PGLSIGDVAK KLGEMWNNTA ADDKQPYEKK AAKLKEKYEK D IAAYRAKG KPDAAKKGVV KAEKSKKKKE EEEDEEDEED EEEEEDEEDE DEEEDDDDE

UniProtKB: High mobility group protein B1

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Macromolecule #5: Widom 601 DNA reverse strand (147-mer)

MacromoleculeName: Widom 601 DNA reverse strand (147-mer) / type: dna / ID: 5 / Details: 10 base pairs flanking DNA / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 47.746418 KDa
SequenceString: (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) ...String:
(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)

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Macromolecule #6: Widom 601 DNA forward strand (147-mer)

MacromoleculeName: Widom 601 DNA forward strand (147-mer) / type: dna / ID: 6 / Details: 10 base pairs flanking DNA / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 47.328148 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)(DA)(DT)(DG)(DT) (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
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
25.0 mMKClpotassium chloride
1.0 mMC10H16N2O8EDTA
2.0 mMC4H10O2S2DTT
1.5 %C3H8O3glycerol
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV / Details: 3 uL of sample was applied to grid..
Details1 uM nucleosome was mixed with 12 uM HMGB1 prior to plunge freezing.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 8259 / Average exposure time: 2.024 sec. / Average electron dose: 43.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. v4.1.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab initio reconstruction from cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.1) / Software - details: Non-uniform Refinement / Number images used: 42115
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 4.1.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.1) / Software - details: Non-uniform Refinement
FSC plot (resolution estimation)

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