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- EMDB-10390: Structure of a human nucleosome at 3.2 A resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-10390
TitleStructure of a human nucleosome at 3.2 A resolution
Map dataStructure of a human nucleosome at 3.2A
Sample
  • Complex: Nucleosome
    • Complex: Proteins
      • Protein or peptide: Histone H3.2
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1-B/E
      • Protein or peptide: Histone H2B type 1-K
    • Complex: DNA
      • DNA: DNA (147-MER)
      • DNA: DNA (147-MER)
KeywordsNucleosome / DNA / histones / NUCLEAR PROTEIN
Function / homology
Function and homology information


negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine ...negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / telomere organization / Meiotic synapsis / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / innate immune response in mucosa / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / HDMs demethylate histones / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / heterochromatin formation / nucleosome assembly / antimicrobial humoral immune response mediated by antimicrobial peptide / structural constituent of chromatin / UCH proteinases / antibacterial humoral response / nucleosome / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / defense response to Gram-negative bacterium / Estrogen-dependent gene expression / killing of cells of another organism / chromosome, telomeric region / defense response to Gram-positive bacterium / Ub-specific processing proteases / protein heterodimerization activity / Amyloid fiber formation / negative regulation of cell population proliferation / protein-containing complex / DNA binding / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane / cytosol
Similarity search - Function
: / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A ...: / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / 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 type 1-K / Histone H2A type 1-B/E / Histone H4 / Histone H3.2
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsDodonova SO / Zhu F
Funding support Germany, 3 items
OrganizationGrant numberCountry
European Research Council693023 Germany
European Molecular Biology OrganizationALTF-949-2016 Germany
Volkswagen Foundation Germany
CitationJournal: Nature / Year: 2020
Title: Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function.
Authors: Svetlana O Dodonova / Fangjie Zhu / Christian Dienemann / Jussi Taipale / Patrick Cramer /
Abstract: 'Pioneer' transcription factors are required for stem-cell pluripotency, cell differentiation and cell reprogramming. Pioneer factors can bind nucleosomal DNA to enable gene expression from regions ...'Pioneer' transcription factors are required for stem-cell pluripotency, cell differentiation and cell reprogramming. Pioneer factors can bind nucleosomal DNA to enable gene expression from regions of the genome with closed chromatin. SOX2 is a prominent pioneer factor that is essential for pluripotency and self-renewal of embryonic stem cells. Here we report cryo-electron microscopy structures of the DNA-binding domains of SOX2 and its close homologue SOX11 bound to nucleosomes. The structures show that SOX factors can bind and locally distort DNA at superhelical location 2. The factors also facilitate detachment of terminal nucleosomal DNA from the histone octamer, which increases DNA accessibility. SOX-factor binding to the nucleosome can also lead to a repositioning of the N-terminal tail of histone H4 that includes residue lysine 16. We speculate that this repositioning is incompatible with higher-order nucleosome stacking, which involves contacts of the H4 tail with a neighbouring nucleosome. Our results indicate that pioneer transcription factors can use binding energy to initiate chromatin opening, and thereby facilitate nucleosome remodelling and subsequent transcription.
History
DepositionOct 21, 2019-
Header (metadata) releaseOct 30, 2019-
Map releaseApr 29, 2020-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6t79
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10390.png

Downloads & links

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Map

FileDownload / File: emd_10390.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of a human nucleosome at 3.2A
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 140 pix.
= 147. Å		1.05 Å/pix.
x 140 pix.
= 147. Å		1.05 Å/pix.
x 140 pix.
= 147. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.07724066 - 0.16049513
Average (Standard dev.)0.0009965262 (±0.009815395)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions140140140
Spacing140140140
CellA=B=C: 147.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z140140140
origin x/y/z0.0000.0000.000
length x/y/z147.000147.000147.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ350350350
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS140140140
D min/max/mean-0.0770.1600.001

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Supplemental data

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Half map: half-map 2, nucleosome

Fileemd_10390_half_map_1.map
Annotationhalf-map 2, nucleosome
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map 1, nucleosome

Fileemd_10390_half_map_2.map
Annotationhalf-map 1, nucleosome
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Nucleosome

EntireName: Nucleosome
Components
  • Complex: Nucleosome
    • Complex: Proteins
      • Protein or peptide: Histone H3.2
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1-B/E
      • Protein or peptide: Histone H2B type 1-K
    • Complex: DNA
      • DNA: DNA (147-MER)
      • DNA: DNA (147-MER)

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Supramolecule #1: Nucleosome

SupramoleculeName: Nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Nucleosome
Molecular weightTheoretical: 205 KDa

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Supramolecule #2: Proteins

SupramoleculeName: Proteins / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4 / Details: Proteins
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: DNA

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

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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: Homo sapiens (human)
Molecular weightTheoretical: 15.389036 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEASEA YLVGLFEDTN LAAIHAKRVT IMPKDIQLAR RIRGERA

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: Homo sapiens (human)
Molecular weightTheoretical: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A type 1-B/E

MacromoleculeName: Histone H2A type 1-B/E / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.707277 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MGSSHHHHHH ENLYFQSNAP WMSGRGKQGG KARAKAKTRS SRAGLQFPVG RVHRLLRKGN YSERVGAGAP VYLAAVLEYL TAEILELAG NAARDNKKTR IIPRHLQLAI RNDEELNKLL GRVTIAQGGV LPNIQAVLLP KKTESHHKAK GK

UniProtKB: Histone H2A type 1-B/E

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Macromolecule #4: Histone H2B type 1-K

MacromoleculeName: Histone H2B type 1-K / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.921213 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSV YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSAK

UniProtKB: Histone H2B type 1-K

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Macromolecule #5: DNA (147-MER)

MacromoleculeName: DNA (147-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 45.240848 KDa
SequenceString: (DA)(DT)(DC)(DT)(DA)(DC)(DA)(DC)(DG)(DA) (DC)(DG)(DC)(DT)(DC)(DT)(DT)(DC)(DC)(DG) (DA)(DT)(DC)(DT)(DA)(DA)(DT)(DT)(DT) (DA)(DT)(DG)(DT)(DT)(DT)(DG)(DT)(DT)(DA) (DG) (DC)(DG)(DT)(DT)(DA)(DT) ...String:
(DA)(DT)(DC)(DT)(DA)(DC)(DA)(DC)(DG)(DA) (DC)(DG)(DC)(DT)(DC)(DT)(DT)(DC)(DC)(DG) (DA)(DT)(DC)(DT)(DA)(DA)(DT)(DT)(DT) (DA)(DT)(DG)(DT)(DT)(DT)(DG)(DT)(DT)(DA) (DG) (DC)(DG)(DT)(DT)(DA)(DT)(DA)(DC) (DT)(DA)(DT)(DT)(DC)(DT)(DA)(DA)(DT)(DT) (DC)(DT) (DT)(DT)(DG)(DT)(DT)(DT)(DC) (DG)(DG)(DT)(DG)(DG)(DT)(DA)(DT)(DT)(DG) (DT)(DT)(DT) (DA)(DT)(DT)(DT)(DT)(DG) (DT)(DT)(DC)(DC)(DT)(DT)(DT)(DG)(DT)(DG) (DC)(DG)(DT)(DT) (DC)(DA)(DG)(DC)(DT) (DT)(DA)(DA)(DT)(DG)(DC)(DC)(DT)(DA)(DA) (DC)(DG)(DA)(DC)(DA) (DC)(DT)(DC)(DG) (DG)(DA)(DG)(DA)(DT)(DC)(DG)(DG)(DA)(DA) (DG)(DA)(DG)(DC)(DA)(DC) (DA)(DC)(DG) (DT)(DG)(DA)(DT)

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Macromolecule #6: DNA (147-MER)

MacromoleculeName: DNA (147-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 45.484273 KDa
SequenceString: (DA)(DT)(DC)(DA)(DC)(DG)(DT)(DG)(DT)(DG) (DC)(DT)(DC)(DT)(DT)(DC)(DC)(DG)(DA)(DT) (DC)(DT)(DC)(DC)(DG)(DA)(DG)(DT)(DG) (DT)(DC)(DG)(DT)(DT)(DA)(DG)(DG)(DC)(DA) (DT) (DT)(DA)(DA)(DG)(DC)(DT) ...String:
(DA)(DT)(DC)(DA)(DC)(DG)(DT)(DG)(DT)(DG) (DC)(DT)(DC)(DT)(DT)(DC)(DC)(DG)(DA)(DT) (DC)(DT)(DC)(DC)(DG)(DA)(DG)(DT)(DG) (DT)(DC)(DG)(DT)(DT)(DA)(DG)(DG)(DC)(DA) (DT) (DT)(DA)(DA)(DG)(DC)(DT)(DG)(DA) (DA)(DC)(DG)(DC)(DA)(DC)(DA)(DA)(DA)(DG) (DG)(DA) (DA)(DC)(DA)(DA)(DA)(DA)(DT) (DA)(DA)(DA)(DC)(DA)(DA)(DT)(DA)(DC)(DC) (DA)(DC)(DC) (DG)(DA)(DA)(DA)(DC)(DA) (DA)(DA)(DG)(DA)(DA)(DT)(DT)(DA)(DG)(DA) (DA)(DT)(DA)(DG) (DT)(DA)(DT)(DA)(DA) (DC)(DG)(DC)(DT)(DA)(DA)(DC)(DA)(DA)(DA) (DC)(DA)(DT)(DA)(DA) (DA)(DT)(DT)(DA) (DG)(DA)(DT)(DC)(DG)(DG)(DA)(DA)(DG)(DA) (DG)(DC)(DG)(DT)(DC)(DG) (DT)(DG)(DT) (DA)(DG)(DA)(DT)

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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

Concentration0.15 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
20.0 mMHEPES
30.0 mMNaCl
1.0 mMEDTA
2.0 mMDTT
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa / Details: 0.39 mB, 25 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV
Details: The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen ...Details: The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 30 eV
DetailsAt least 50% of the data were collected at 25* stage tilt in order to partially compensate for preferred orientation of particles on the grid, and to improve angular distribution.
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average electron dose: 1.125 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
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

Startup modelType of model: OTHER
Details: The initial reference from the free-nucleosome set was obtained ab initio in cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 368270
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6fq5


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 75
Output model

PDB-6t79:
Structure of a human nucleosome at 3.2 A resolution

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