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- EMDB-34195: Human menin in complex with H3K79Me2 nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-34195
TitleHuman menin in complex with H3K79Me2 nucleosome
Map data
Sample
  • Complex: Human menin in complex with nH3K79 dimethylated nucleosome
    • Complex: nH3K79 dimethylated nucleosome
      • Protein or peptide: Histone H3.2
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1
      • Protein or peptide: Histone H2B 1.1
    • Complex: DNA (177-MER)
      • DNA: DNA (177-MER)
      • DNA: DNA (177-MER)
    • Complex: Isoform 2 of Menin
      • Protein or peptide: Isoform 2 of Menin
Function / homology
Function and homology information


Y-form DNA binding / : / negative regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of JNK cascade / T-helper 2 cell differentiation / MLL1/2 complex / osteoblast development / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / positive regulation of transforming growth factor beta receptor signaling pathway ...Y-form DNA binding / : / negative regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of JNK cascade / T-helper 2 cell differentiation / MLL1/2 complex / osteoblast development / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / positive regulation of transforming growth factor beta receptor signaling pathway / R-SMAD binding / cleavage furrow / MLL1 complex / negative regulation of cell cycle / negative regulation of osteoblast differentiation / RHO GTPases activate IQGAPs / response to UV / four-way junction DNA binding / transcription repressor complex / negative regulation of protein phosphorylation / transcription initiation-coupled chromatin remodeling / response to gamma radiation / Deactivation of the beta-catenin transactivating complex / Post-translational protein phosphorylation / phosphoprotein binding / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Formation of the beta-catenin:TCF transactivating complex / negative regulation of DNA-binding transcription factor activity / nuclear matrix / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / structural constituent of chromatin / MAPK cascade / nucleosome / nucleosome assembly / protein-macromolecule adaptor activity / double-stranded DNA binding / chromosome, telomeric region / transcription cis-regulatory region binding / protein heterodimerization activity / negative regulation of cell population proliferation / endoplasmic reticulum lumen / DNA repair / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Menin / Menin / 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 ...Menin / Menin / 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
Menin / Histone H2B 1.1 / Histone H2A type 1 / Histone H4 / Histone H3.2
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLin J / Yu D / Lam WH / Dang S / Zhai Y / Li XD
Funding support Hong Kong, 1 items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC) Hong Kong
CitationJournal: Science / Year: 2023
Title: Menin "reads" H3K79me2 mark in a nucleosomal context.
Authors: Jianwei Lin / Yiping Wu / Gaofei Tian / Daqi Yu / Eunjeong Yang / Wai Hei Lam / Zheng Liu / Yihang Jing / Shangyu Dang / Xiucong Bao / Jason Wing Hon Wong / Yuanliang Zhai / Xiang David Li /
Abstract: Methylation of histone H3 lysine-79 (H3K79) is an epigenetic mark for gene regulation in development, cellular differentiation, and disease progression. However, how this histone mark is translated ...Methylation of histone H3 lysine-79 (H3K79) is an epigenetic mark for gene regulation in development, cellular differentiation, and disease progression. However, how this histone mark is translated into downstream effects remains poorly understood owing to a lack of knowledge about its readers. We developed a nucleosome-based photoaffinity probe to capture proteins that recognize H3K79 dimethylation (H3K79me2) in a nucleosomal context. In combination with a quantitative proteomics approach, this probe identified menin as a H3K79me2 reader. A cryo-electron microscopy structure of menin bound to an H3K79me2 nucleosome revealed that menin engages with the nucleosome using its fingers and palm domains and recognizes the methylation mark through a π-cation interaction. In cells, menin is selectively associated with H3K79me2 on chromatin, particularly in gene bodies.
History
DepositionAug 26, 2022-
Header (metadata) releaseFeb 15, 2023-
Map releaseFeb 15, 2023-
UpdateMar 1, 2023-
Current statusMar 1, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34195.png

Downloads & links

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Map

FileDownload / File: emd_34195.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.4100922 - 1.0380092
Average (Standard dev.)0.0027450013 (±0.037650652)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 271.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_34195_msk_1.map
Projections & Slices
AxesZYX

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Additional map: #1

Fileemd_34195_additional_1.map
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Half map: #2

Fileemd_34195_half_map_1.map
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Half map: #1

Fileemd_34195_half_map_2.map
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Sample components

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Entire : Human menin in complex with nH3K79 dimethylated nucleosome

EntireName: Human menin in complex with nH3K79 dimethylated nucleosome
Components
  • Complex: Human menin in complex with nH3K79 dimethylated nucleosome
    • Complex: nH3K79 dimethylated nucleosome
      • Protein or peptide: Histone H3.2
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1
      • Protein or peptide: Histone H2B 1.1
    • Complex: DNA (177-MER)
      • DNA: DNA (177-MER)
      • DNA: DNA (177-MER)
    • Complex: Isoform 2 of Menin
      • Protein or peptide: Isoform 2 of Menin

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Supramolecule #1: Human menin in complex with nH3K79 dimethylated nucleosome

SupramoleculeName: Human menin in complex with nH3K79 dimethylated nucleosome
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 300 KDa

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Supramolecule #2: nH3K79 dimethylated nucleosome

SupramoleculeName: nH3K79 dimethylated nucleosome / type: complex / ID: 2 / Chimera: Yes / Parent: 1 / Macromolecule list: #1-#4

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Supramolecule #3: DNA (177-MER)

SupramoleculeName: DNA (177-MER) / type: complex / ID: 3 / Chimera: Yes / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: Isoform 2 of Menin

SupramoleculeName: Isoform 2 of Menin / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #7

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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: 15.448147 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDF (MLY)TDLRFQSSA VMALQEASEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

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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 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

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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: 13.993295 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MSGRGKQGGK TRAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAVR NDEELNKLLG GVTIAQGGVL PNIQSVLLPK KTESAKSAKS K

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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: 13.965265 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MPEPAKSAPA PKKGSKKAVT KTQKKDGKKR RKSRKESYAI YVYKVLKQVH PDTGISSKAM SIMNSFVNDV FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSAK

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Macromolecule #7: Isoform 2 of Menin

MacromoleculeName: Isoform 2 of Menin / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 67.665711 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: SMGLKAAQKT LFPLRSIDDV VRLFAAELGR EEPDLVLLSL VLGFVEHFLA VNRVIPTNVP ELTFQPSPAP DPPGGLTYFP VADLSIIAA LYARFTAQIR GAVDLSLYPR EGGVSSRELV KKVSDVIWNS LSRSYFKDRA HIQSLFSFIT GTKLDSSGVA F AVVGACQA ...String:
SMGLKAAQKT LFPLRSIDDV VRLFAAELGR EEPDLVLLSL VLGFVEHFLA VNRVIPTNVP ELTFQPSPAP DPPGGLTYFP VADLSIIAA LYARFTAQIR GAVDLSLYPR EGGVSSRELV KKVSDVIWNS LSRSYFKDRA HIQSLFSFIT GTKLDSSGVA F AVVGACQA LGLRDVHLAL SEDHAWVVFG PNGEQTAEVT WHGKGNEDRR GQTVNAGVAE RSWLYLKGSY MRCDRKMEVA FM VCAINPS IDLHTDSLEL LQLQQKLLWL LYDLGHLERY PMALGNLADL EELEPTPGRP DPLTLYHKGI ASAKTYYRDE HIY PYMYLA GYHCRNRNVR EALQAWADTA TVIQDYNYCR EDEEIYKEFF EVANDVIPNL LKEAASLLEA GEERPGEQSQ GTQS QGSAL QDPECFAHLL RFYDGICKWE EGSPTPVLHV GWATFLVQSL GRFEGQVRQK VRIVSREAEA AEAEEPWGEE AREGR RRGP RRESKPEEPP PPKKPALDKG LGTGQGAVSG PPRKPPGTVA GTARGPEGGS TAQVPAPTAS PPPEGPVLTF QSEKMK GMK ELLVATKINS SAIKLQLTAQ SQVQMKKQKV STPSDYTLSF LKRQRKGL

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Macromolecule #5: DNA (177-MER)

MacromoleculeName: DNA (177-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.295562 KDa
SequenceString: (DA)(DT)(DC)(DC)(DA)(DT)(DC)(DC)(DG)(DG) (DA)(DT)(DC)(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) ...String:
(DA)(DT)(DC)(DC)(DA)(DT)(DC)(DC)(DG)(DG) (DA)(DT)(DC)(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)(DC)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DC)(DA)(DT)(DC)(DC)(DT) (DG)(DT) (DT)(DC)(DC)(DA)(DG)(DT)(DG)(DC)(DC)(DG) (DG)(DA)(DG)(DA)(DT)

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Macromolecule #6: DNA (177-MER)

MacromoleculeName: DNA (177-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.994016 KDa
SequenceString: (DA)(DT)(DC)(DT)(DC)(DC)(DG)(DG)(DC)(DA) (DC)(DT)(DG)(DG)(DA)(DA)(DC)(DA)(DG)(DG) (DA)(DT)(DG)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DG)(DT)(DG)(DA)(DC)(DA)(DC)(DG)(DT) (DG) (DC)(DC)(DT)(DG)(DG)(DA) ...String:
(DA)(DT)(DC)(DT)(DC)(DC)(DG)(DG)(DC)(DA) (DC)(DT)(DG)(DG)(DA)(DA)(DC)(DA)(DG)(DG) (DA)(DT)(DG)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DG)(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)(DG)(DA)(DT)(DC)(DC)(DG)(DG)(DA) (DT)(DG)(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

BufferpH: 7.5
Component:
ConcentrationFormulaName
100.0 mMNaClSodium chloride
25.0 mMHEPESHEPES
VitrificationCryogen name: ETHANE

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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) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 47170 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
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

Particle selectionNumber selected: 4888359
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 45950
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final 3D classificationNumber classes: 8 / Avg.num./class: 31468 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-8gpn:
Human menin in complex with H3K79Me2 nucleosome

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