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- EMDB-0693: Cryo-EM structure of human MLL3-ubNCP complex (4.0 angstrom) -

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Entry
Database: EMDB / ID: EMD-0693
TitleCryo-EM structure of human MLL3-ubNCP complex (4.0 angstrom)
Map data
SampleHuman MLL3 complex associated with an H2B-monoubiquitinated nucleosome (4.0 angstrom)
  • Human MLL3KMT2C
  • H2B-monoubiquitinated nucleosome
  • Histone H3
  • Histone H4
  • Histone H2A
  • Histone H2B 1.1
  • (nucleic-acidNucleic acid) x 2
  • Histone-lysine N-methyltransferase 2C
  • Retinoblastoma-binding protein 5
  • Ubiquitin
  • WD repeat-containing protein 5
  • Set1/Ash2 histone methyltransferase complex subunit ASH2
  • ligand
Function / homology
Function and homology information


euchromatin binding / histone H3-K4 monomethylation / histone methyltransferase activity (H3-K4 specific) / [histone H3]-lysine4 N-trimethyltransferase / Set1C/COMPASS complex / MLL3/4 complex / histone H4-K5 acetylation / histone H4-K8 acetylation / Ada2/Gcn5/Ada3 transcription activator complex / histone H3-K4 methylation ...euchromatin binding / histone H3-K4 monomethylation / histone methyltransferase activity (H3-K4 specific) / [histone H3]-lysine4 N-trimethyltransferase / Set1C/COMPASS complex / MLL3/4 complex / histone H4-K5 acetylation / histone H4-K8 acetylation / Ada2/Gcn5/Ada3 transcription activator complex / histone H3-K4 methylation / histone H4-K16 acetylation / histone methyltransferase activity / transferase activity, transferring acyl groups / negative regulation of histone H3-K4 methylation / MLL1 complex / beta-catenin-TCF complex assembly / positive regulation of gluconeogenesis / euchromatin => GO:0000791 / positive regulation of histone H3-K4 methylation / SRP-dependent cotranslational protein targeting to membrane / hemopoiesis / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / viral transcription / histone acetyltransferase complex / histone H3 acetylation / translational initiation / MyD88-independent toll-like receptor signaling pathway / histone methyltransferase complex / nucleotide-binding oligomerization domain containing signaling pathway / nucleotide-excision repair, DNA gap filling / nucleotide-excision repair, DNA damage recognition / methylated histone binding / nucleotide-excision repair, DNA duplex unwinding / TRIF-dependent toll-like receptor signaling pathway / DNA-templated transcription, initiation / global genome nucleotide-excision repair / host cell / nucleotide-excision repair, preincision complex assembly / intracellular transport of virus / MyD88-dependent toll-like receptor signaling pathway / nucleotide-excision repair, DNA incision, 5'-to lesion / endosomal transport / regulation of megakaryocyte differentiation / skeletal system development / DNA damage response, detection of DNA damage / error-free translesion synthesis / nucleotide-excision repair, DNA incision / modification-dependent protein catabolic process / protein targeting to peroxisome / JNK cascade / nucleosome / interstrand cross-link repair / endocytic vesicle membrane / protein tag / stress-activated MAPK cascade / error-prone translesion synthesis / interleukin-1-mediated signaling pathway / regulation of transcription from RNA polymerase II promoter in response to hypoxia / I-kappaB kinase/NF-kappaB signaling / neuron projection development / viral life cycle / transcription-coupled nucleotide-excision repair / negative regulation of transforming growth factor beta receptor signaling pathway / beta-catenin binding / translesion synthesis / transforming growth factor beta receptor signaling pathway / anaphase-promoting complex-dependent catabolic process / virion assembly / cytosolic small ribosomal subunit / transmembrane transport / regulation of mRNA stability / small ribosomal subunit / post-translational protein modification / membrane organization / protein polyubiquitination / histone binding / Wnt signaling pathway / mitochondrial outer membrane / vesicle / transcription coactivator activity / activation of MAPK activity / structural constituent of ribosome / response to estrogen / endosome membrane / transcription regulatory region sequence-specific DNA binding / positive regulation of NF-kappaB transcription factor activity / protein ubiquitination / protein deubiquitination / translation / protein heterodimerization activity / positive regulation of apoptotic process / cytokine-mediated signaling pathway / cellular response to DNA damage stimulus / cellular protein metabolic process / nucleolus / endoplasmic reticulum membrane / ubiquitin protein ligase binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / host cell nucleus
Zinc-binding ribosomal protein / Histone H2A / Histone-fold / High mobility group box domain / Histone H2A/H2B/H3 / TATA box binding protein associated factor (TAF) / FY-rich, C-terminal / FY-rich, N-terminal / SPRY domain / Post-SET domain ...Zinc-binding ribosomal protein / Histone H2A / Histone-fold / High mobility group box domain / Histone H2A/H2B/H3 / TATA box binding protein associated factor (TAF) / FY-rich, C-terminal / FY-rich, N-terminal / SPRY domain / Post-SET domain / Ribosomal protein S27a / Zinc finger, PHD-type / Zinc finger, RING/FYVE/PHD-type / Histone H4 / B30.2/SPRY domain / Zinc finger, RING-type / WD40 repeat / SET domain / HMG-I/HMG-Y, DNA-binding, conserved site / Ubiquitin-like domain / Histone H2B / Histone H3/CENP-A / Zinc finger, FYVE/PHD-type / Concanavalin A-like lectin/glucanase domain superfamily / Histone H2A conserved site / WD40/YVTN repeat-like-containing domain superfamily / Histone-lysine N-methyltransferase 2C / in:ipr037866: / Retinoblastoma-binding protein 5/Swd1 / Histone methyltransferase complex subunit ASH2 / High mobility group box domain superfamily / WD40-repeat-containing domain superfamily / CENP-T/Histone H4, histone fold / Extended PHD (ePHD) domain / Histone H2A, C-terminal domain / KMT2C, ePHD1 / Ubiquitin-like domain superfamily / G-protein beta WD-40 repeat / Ubiquitin domain / Ubiquitin conserved site / Histone H4, conserved site / Zinc finger, PHD-finger / WD40 repeat, conserved site / WD40-repeat-containing domain / KMT2C, ePHD2 / S27a-like superfamily
Histone H3 / Histone H2B 1.1 / Histone H2A type 1 / WD repeat-containing protein 5 / Histone H4 / Ubiquitin-40S ribosomal protein S27a / Histone H3.2 / Retinoblastoma-binding protein 5 / Histone H2A / Histone-lysine N-methyltransferase 2C / Set1/Ash2 histone methyltransferase complex subunit ASH2
Biological speciesHomo sapiens (human) / Xenopus laevis (African clawed frog) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsHuang J / Xue H / Yao T
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (China) China
CitationJournal: Nature / Year: 2019
Title: Structural basis of nucleosome recognition and modification by MLL methyltransferases.
Authors: Han Xue / Tonghui Yao / Mi Cao / Guanjun Zhu / Yan Li / Guiyong Yuan / Yong Chen / Ming Lei / Jing Huang /
Abstract: Methyltransferases of the mixed-lineage leukaemia (MLL) family-which include MLL1, MLL2, MLL3, MLL4, SET1A and SET1B-implement methylation of histone H3 on lysine 4 (H3K4), and have critical and ...Methyltransferases of the mixed-lineage leukaemia (MLL) family-which include MLL1, MLL2, MLL3, MLL4, SET1A and SET1B-implement methylation of histone H3 on lysine 4 (H3K4), and have critical and distinct roles in the regulation of transcription in haematopoiesis, adipogenesis and development. The C-terminal catalytic SET (Su(var.)3-9, enhancer of zeste and trithorax) domains of MLL proteins are associated with a common set of regulatory factors (WDR5, RBBP5, ASH2L and DPY30) to achieve specific activities. Current knowledge of the regulation of MLL activity is limited to the catalysis of histone H3 peptides, and how H3K4 methyl marks are deposited on nucleosomes is poorly understood. H3K4 methylation is stimulated by mono-ubiquitination of histone H2B on lysine 120 (H2BK120ub1), a prevalent histone H2B mark that disrupts chromatin compaction and favours open chromatin structures, but the underlying mechanism remains unknown. Here we report cryo-electron microscopy structures of human MLL1 and MLL3 catalytic modules associated with nucleosome core particles that contain H2BK120ub1 or unmodified H2BK120. These structures demonstrate that the MLL1 and MLL3 complexes both make extensive contacts with the histone-fold and DNA regions of the nucleosome; this allows ease of access to the histone H3 tail, which is essential for the efficient methylation of H3K4. The H2B-conjugated ubiquitin binds directly to RBBP5, orienting the association between MLL1 or MLL3 and the nucleosome. The MLL1 and MLL3 complexes display different structural organizations at the interface between the WDR5, RBBP5 and MLL1 (or the corresponding MLL3) subunits, which accounts for the opposite roles of WDR5 in regulating the activity of the two enzymes. These findings transform our understanding of the structural basis for the regulation of MLL activity at the nucleosome level, and highlight the pivotal role of nucleosome regulation in histone-tail modification.
Validation ReportPDB-ID: 6kiw

SummaryFull reportAbout validation report
History
DepositionJul 20, 2019-
Header (metadata) releaseSep 11, 2019-
Map releaseSep 11, 2019-
UpdateNov 6, 2019-
Current statusNov 6, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.019
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.019
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6kiw
  • Surface level: 0.019
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_0693.map.gz / Format: CCP4 / Size: 75.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 270 pix.
= 294.3 Å
1.09 Å/pix.
x 270 pix.
= 294.3 Å
1.09 Å/pix.
x 270 pix.
= 294.3 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.019
Minimum - Maximum-0.22871779 - 0.33579835
Average (Standard dev.)-0.0002659313 (±0.012194572)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions270270270
Spacing270270270
CellA=B=C: 294.30002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z270270270
origin x/y/z0.0000.0000.000
length x/y/z294.300294.300294.300
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS270270270
D min/max/mean-0.1140.1660.000

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Supplemental data

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Segmentation: #1

Fileemd_0693_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: Additional EM map shows good density of WDR5.

Fileemd_0693_additional_1.map
AnnotationAdditional EM map shows good density of WDR5.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: Additional EM map shows the major binding mode...

Fileemd_0693_additional_2.map
AnnotationAdditional EM map shows the major binding mode of H2BK120ub1 to RBBP5.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Additional map: Additional EM map shows the minor binding mode...

Fileemd_0693_additional_3.map
AnnotationAdditional EM map shows the minor binding mode 1 of H2BK120ub1 to RBBP5.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: Additional EM map shows the minor binding mode...

Fileemd_0693_additional_4.map
AnnotationAdditional EM map shows the minor binding mode 2 of H2BK120ub1 to RBBP5.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: Additional EM map shows the minor binding mode...

Fileemd_0693_additional_5.map
AnnotationAdditional EM map shows the minor binding mode 3 of H2BK120ub1 to RBBP5.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: Additional EM map shows good density of ASH2L.

Fileemd_0693_additional_6.map
AnnotationAdditional EM map shows good density of ASH2L.
Projections & Slices
AxesZYX

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Sample components

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Entire Human MLL3 complex associated with an H2B-monoubiquitinated nucle...

EntireName: Human MLL3 complex associated with an H2B-monoubiquitinated nucleosome (4.0 angstrom)
Number of components: 15

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Component #1: protein, Human MLL3 complex associated with an H2B-monoubiquitina...

ProteinName: Human MLL3 complex associated with an H2B-monoubiquitinated nucleosome (4.0 angstrom)
Recombinant expression: No

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Component #2: protein, Human MLL3

ProteinName: Human MLL3KMT2C / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, H2B-monoubiquitinated nucleosome

ProteinName: H2B-monoubiquitinated nucleosome / Recombinant expression: No
SourceSpecies: Xenopus laevis (African clawed frog)

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Component #4: protein, Histone H3

ProteinName: Histone H3 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 15.30393 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #5: protein, Histone H4

ProteinName: Histone H4 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 11.263231 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #6: protein, Histone H2A

ProteinName: Histone H2A / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.978241 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #7: protein, Histone H2B 1.1

ProteinName: Histone H2B 1.1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.498715 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #8: nucleic-acid, DNA (144-MER)

nucleic acidName: DNA (144-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DC)(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) ...Sequence:
(DC)(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)(DG)(DA)
MassTheoretical: 44.217172 kDa
SourceSpecies: synthetic construct (others)

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Component #9: nucleic-acid, DNA (145-MER)

nucleic acidName: DNA (145-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DT)(DC)(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) ...Sequence:
(DT)(DC)(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)(DG)(DA)
MassTheoretical: 44.992648 kDa
SourceSpecies: synthetic construct (others)

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Component #10: protein, Histone-lysine N-methyltransferase 2C

ProteinName: Histone-lysine N-methyltransferase 2C / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.642941 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #11: protein, Retinoblastoma-binding protein 5

ProteinName: Retinoblastoma-binding protein 5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 59.223477 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #12: protein, Ubiquitin

ProteinName: Ubiquitin / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.622922 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #13: protein, WD repeat-containing protein 5

ProteinName: WD repeat-containing protein 5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 36.635438 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #14: protein, Set1/Ash2 histone methyltransferase complex subunit ASH2

ProteinName: Set1/Ash2 histone methyltransferase complex subunit ASH2
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 60.288758 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #15: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 81945
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Output model

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