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- EMDB-0510: Protein Phosphatase 2A (Aalpha-B56alpha-Calpha) holoenzyme in com... -

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Entry
Database: EMDB / ID: EMD-0510
TitleProtein Phosphatase 2A (Aalpha-B56alpha-Calpha) holoenzyme in complex with a Small Molecule Activator of PP2A (SMAP)
Map data
Sample
  • Complex: PP2A Aalpha-B56alpha-Calpha holoenzyme in complex with a Small Molecule Activator of PP2A (SMAP)
    • Protein or peptide: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
    • Protein or peptide: Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit alpha isoform
  • Protein or peptide: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
  • Ligand: N-[(1R,2R,3S)-2-hydroxy-3-(10H-phenoxazin-10-yl)cyclohexyl]-4-(trifluoromethoxy)benzene-1-sulfonamide
  • Ligand: MANGANESE (II) ION
KeywordsHoloenzyme complex / Phosphatase / Activator / HYDROLASE-ACTIVATOR complex
Function / homology
Function and homology information


meiotic spindle elongation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MASTL Facilitates Mitotic Progression / protein phosphatase type 2A complex / protein serine/threonine phosphatase complex / regulation of meiotic cell cycle process involved in oocyte maturation / peptidyl-threonine dephosphorylation ...meiotic spindle elongation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MASTL Facilitates Mitotic Progression / protein phosphatase type 2A complex / protein serine/threonine phosphatase complex / regulation of meiotic cell cycle process involved in oocyte maturation / peptidyl-threonine dephosphorylation / mitotic sister chromatid separation / meiotic sister chromatid cohesion, centromeric / INTAC complex / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / FAR/SIN/STRIPAK complex / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / female meiotic nuclear division / protein phosphatase regulator activity / GABA receptor binding / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / protein antigen binding / ERKs are inactivated / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / Initiation of Nuclear Envelope (NE) Reformation / RNA polymerase II transcription initiation surveillance / Co-stimulation by CD28 / regulation of growth / M band / Disassembly of the destruction complex and recruitment of AXIN to the membrane / negative regulation of epithelial to mesenchymal transition / Co-inhibition by CTLA4 / Platelet sensitization by LDL / protein-serine/threonine phosphatase / negative regulation of glycolytic process through fructose-6-phosphate / positive regulation of NLRP3 inflammasome complex assembly / ERK/MAPK targets / mesoderm development / protein serine/threonine phosphatase activity / vascular endothelial cell response to oscillatory fluid shear stress / T cell homeostasis / regulation of cell differentiation / phosphoprotein phosphatase activity / regulation of microtubule polymerization / regulation of G1/S transition of mitotic cell cycle / lateral plasma membrane / chromosome, centromeric region / DARPP-32 events / negative regulation of hippo signaling / negative regulation of protein localization to plasma membrane / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / protein dephosphorylation / Cyclin A/B1/B2 associated events during G2/M transition / spindle assembly / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / protein tyrosine phosphatase activity / Resolution of Sister Chromatid Cohesion / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / AURKA Activation by TPX2 / meiotic cell cycle / chromosome segregation / RHO GTPases Activate Formins / RAF activation / Spry regulation of FGF signaling / negative regulation of canonical Wnt signaling pathway / Degradation of beta-catenin by the destruction complex / PKR-mediated signaling / response to lead ion / kinase binding / tau protein binding / Z disc / spindle pole / Negative regulation of MAPK pathway / Cyclin D associated events in G1 / Separation of Sister Chromatids / Regulation of TP53 Degradation / Regulation of PLK1 Activity at G2/M Transition / mitotic cell cycle / microtubule cytoskeleton / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein-containing complex assembly / neuron projection / intracellular signal transduction / membrane raft
Similarity search - Function
Protein phosphatase 2A, regulatory B subunit, B56 / Protein phosphatase 2A regulatory B subunit (B56 family) / : / : / HEAT repeat / HEAT repeat / : / PPP2R1A-like HEAT repeat / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. ...Protein phosphatase 2A, regulatory B subunit, B56 / Protein phosphatase 2A regulatory B subunit (B56 family) / : / : / HEAT repeat / HEAT repeat / : / PPP2R1A-like HEAT repeat / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / HEAT repeat profile. / HEAT, type 2 / HEAT repeats / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform / Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform / Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit alpha isoform
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.63 Å
AuthorsHuang W / Taylor D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)DP2CA186571 United States
CitationJournal: Cell / Year: 2020
Title: Selective PP2A Enhancement through Biased Heterotrimer Stabilization.
Authors: Daniel Leonard / Wei Huang / Sudeh Izadmehr / Caitlin M O'Connor / Danica D Wiredja / Zhizhi Wang / Nilesh Zaware / Yinghua Chen / Daniela M Schlatzer / Janna Kiselar / Nikhil Vasireddi / ...Authors: Daniel Leonard / Wei Huang / Sudeh Izadmehr / Caitlin M O'Connor / Danica D Wiredja / Zhizhi Wang / Nilesh Zaware / Yinghua Chen / Daniela M Schlatzer / Janna Kiselar / Nikhil Vasireddi / Stefan Schüchner / Abbey L Perl / Matthew D Galsky / Wenqing Xu / David L Brautigan / Egon Ogris / Derek J Taylor / Goutham Narla /
Abstract: Impairment of protein phosphatases, including the family of serine/threonine phosphatases designated PP2A, is essential for the pathogenesis of many diseases, including cancer. The ability of PP2A to ...Impairment of protein phosphatases, including the family of serine/threonine phosphatases designated PP2A, is essential for the pathogenesis of many diseases, including cancer. The ability of PP2A to dephosphorylate hundreds of proteins is regulated by over 40 specificity-determining regulatory "B" subunits that compete for assembly and activation of heterogeneous PP2A heterotrimers. Here, we reveal how a small molecule, DT-061, specifically stabilizes the B56α-PP2A holoenzyme in a fully assembled, active state to dephosphorylate selective substrates, such as its well-known oncogenic target, c-Myc. Our 3.6 Å structure identifies molecular interactions between DT-061 and all three PP2A subunits that prevent dissociation of the active enzyme and highlight inherent mechanisms of PP2A complex assembly. Thus, our findings provide fundamental insights into PP2A complex assembly and regulation, identify a unique interfacial stabilizing mode of action for therapeutic targeting, and aid in the development of phosphatase-based therapeutics tailored against disease specific phospho-protein targets.
History
DepositionJan 30, 2019-
Header (metadata) releaseFeb 20, 2019-
Map releaseMay 6, 2020-
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: 0.3
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.3
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  • Surface view with fitted model
  • Atomic models: PDB-6nts
  • Surface level: 0.3
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0510.png

Downloads & links

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Map

FileDownload / File: emd_0510.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 336 pix.
= 357.504 Å		1.06 Å/pix.
x 336 pix.
= 357.504 Å		1.06 Å/pix.
x 336 pix.
= 357.504 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.064 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3 / Movie #1: 0.3
Minimum - Maximum-0.18912628 - 1.3795784
Average (Standard dev.)-0.0009118488 (±0.032503888)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 357.504 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0641.0641.064
M x/y/z336336336
origin x/y/z0.0000.0000.000
length x/y/z357.504357.504357.504
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS336336336
D min/max/mean-0.1891.380-0.001

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Supplemental data

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Mask #1

Fileemd_0510_msk_1.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Half map: #1

Fileemd_0510_half_map_1.map
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Half map: #2

Fileemd_0510_half_map_2.map
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Sample components

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Entire : PP2A Aalpha-B56alpha-Calpha holoenzyme in complex with a Small Mo...

EntireName: PP2A Aalpha-B56alpha-Calpha holoenzyme in complex with a Small Molecule Activator of PP2A (SMAP)
Components
  • Complex: PP2A Aalpha-B56alpha-Calpha holoenzyme in complex with a Small Molecule Activator of PP2A (SMAP)
    • Protein or peptide: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
    • Protein or peptide: Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit alpha isoform
  • Protein or peptide: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
  • Ligand: N-[(1R,2R,3S)-2-hydroxy-3-(10H-phenoxazin-10-yl)cyclohexyl]-4-(trifluoromethoxy)benzene-1-sulfonamide
  • Ligand: MANGANESE (II) ION

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Supramolecule #1: PP2A Aalpha-B56alpha-Calpha holoenzyme in complex with a Small Mo...

SupramoleculeName: PP2A Aalpha-B56alpha-Calpha holoenzyme in complex with a Small Molecule Activator of PP2A (SMAP)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit...

MacromoleculeName: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 65.378344 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAAADGDDSL YPIAVLIDEL RNEDVQLRLN SIKKLSTIAL ALGVERTRSE LLPFLTDTIY DEDEVLLALA EQLGTFTTLV GGPEYVHCL LPPLESLATV EETVVRDKAV ESLRAISHEH SPSDLEAHFV PLVKRLAGGD WFTSRTSACG LFSVCYPRVS S AVKAELRQ ...String:
MAAADGDDSL YPIAVLIDEL RNEDVQLRLN SIKKLSTIAL ALGVERTRSE LLPFLTDTIY DEDEVLLALA EQLGTFTTLV GGPEYVHCL LPPLESLATV EETVVRDKAV ESLRAISHEH SPSDLEAHFV PLVKRLAGGD WFTSRTSACG LFSVCYPRVS S AVKAELRQ YFRNLCSDDT PMVRRAAASK LGEFAKVLEL DNVKSEIIPM FSNLASDEQD SVRLLAVEAC VNIAQLLPQE DL EALVMPT LRQAAEDKSW RVRYMVADKF TELQKAVGPE ITKTDLVPAF QNLMKDCEAE VRAAASHKVK EFCENLSADC REN VIMSQI LPCIKELVSD ANQHVKSALA SVIMGLSPIL GKDNTIEHLL PLFLAQLKDE CPEVRLNIIS NLDCVNEVIG IRQL SQSLL PAIVELAEDA KWRVRLAIIE YMPLLAGQLG VEFFDEKLNS LCMAWLVDHV YAIREAATSN LKKLVEKFGK EWAHA TIIP KVLAMSGDPN YLHRMTTLFC INVLSEVCGQ DITTKHMLPT VLRMAGDPVA NVRFNVAKSL QKIGPILDNS TLQSEV KPI LEKLTQDQDV DVKYFAQEAL TVLSLA

UniProtKB: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform

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Macromolecule #2: Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit...

MacromoleculeName: Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit alpha isoform
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.266555 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSSSSPPAGA ASAAISASEK VDGFTRKSVR KAQRQKRSQG SSQFRSQGSQ AELHPLPQLK DATSNEQQEL FCQKLQQCCI LFDFMDSVS DLKSKEIKRA TLNELVEYVS TNRGVIVESA YSDIVKMISA NIFRTLPPSD NPDFDPEEDE PTLEASWPHI Q LVYEFFLR ...String:
MSSSSPPAGA ASAAISASEK VDGFTRKSVR KAQRQKRSQG SSQFRSQGSQ AELHPLPQLK DATSNEQQEL FCQKLQQCCI LFDFMDSVS DLKSKEIKRA TLNELVEYVS TNRGVIVESA YSDIVKMISA NIFRTLPPSD NPDFDPEEDE PTLEASWPHI Q LVYEFFLR FLESPDFQPS IAKRYIDQKF VQQLLELFDS EDPRERDFLK TVLHRIYGKF LGLRAFIRKQ INNIFLRFIY ET EHFNGVA ELLEILGSII NGFALPLKAE HKQFLMKVLI PMHTAKGLAL FHAQLAYCVV QFLEKDTTLT EPVIRGLLKF WPK TCSQKE VMFLGEIEEI LDVIEPTQFK KIEEPLFKQI SKCVSSSHFQ VAERALYFWN NEYILSLIEE NIDKILPIMF ASLY KISKE HWNPTIVALV YNVLKTLMEM NGKLFDDLTS SYKAERQREK KKELEREELW KKLEELKLKK ALEKQNSAYN MHSIL SNTS AE

UniProtKB: Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit alpha isoform

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Macromolecule #3: Serine/threonine-protein phosphatase 2A catalytic subunit alpha i...

MacromoleculeName: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: protein-serine/threonine phosphatase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.0215 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDEKVFTKEL DQWIEQLNEC KQLSESQVKS LCEKAKEILT KESNVQEVRC PVTVCGDVHG QFHDLMELFR IGGKSPDTNY LFMGDYVNR GYYSVETVTL LVALKVRYRE RITILRGNHE SRQITQVYGF YDECLRKYGN ANVWKYFTDL FDYLPLTALV D GQIFCLHG ...String:
MDEKVFTKEL DQWIEQLNEC KQLSESQVKS LCEKAKEILT KESNVQEVRC PVTVCGDVHG QFHDLMELFR IGGKSPDTNY LFMGDYVNR GYYSVETVTL LVALKVRYRE RITILRGNHE SRQITQVYGF YDECLRKYGN ANVWKYFTDL FDYLPLTALV D GQIFCLHG GLSPSIDTLD HIRALDRLQE VPHEGPMCDL LWSDPDDRGG WGISPRGAGY TFGQDISETF NHANGLTLVS RA HQLVMEG YNWCHDRNVV TIFSAPNYCY RCGNQAAIME LDDTLKYSFL QFDPAPRRGE PHVTYF(MLL)

UniProtKB: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform

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Macromolecule #4: N-[(1R,2R,3S)-2-hydroxy-3-(10H-phenoxazin-10-yl)cyclohexyl]-4-(tr...

MacromoleculeName: N-[(1R,2R,3S)-2-hydroxy-3-(10H-phenoxazin-10-yl)cyclohexyl]-4-(trifluoromethoxy)benzene-1-sulfonamide
type: ligand / ID: 4 / Number of copies: 1 / Formula: L2J
Molecular weightTheoretical: 520.521 Da
Chemical component information

ChemComp-L2J:
N-[(1R,2R,3S)-2-hydroxy-3-(10H-phenoxazin-10-yl)cyclohexyl]-4-(trifluoromethoxy)benzene-1-sulfonamide

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Macromolecule #5: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MN
Molecular weightTheoretical: 54.938 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: 7.02
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) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / 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: OTHER / Details: ab initio model generated by cryoSparc
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 83784
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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