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- EMDB-11692: Nsp7-Nsp8-Nsp12 SARS-CoV2 RNA-dependent RNA polymerase in complex... -

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Entry
Database: EMDB / ID: EMD-11692
TitleNsp7-Nsp8-Nsp12 SARS-CoV2 RNA-dependent RNA polymerase in complex with template:primer dsRNA and favipiravir-RTP
Map data
SampleNsp7-Nsp8-Nsp12 SARS-CoV2 RNA-directed RNA polymerase in complex with template:primer dsRNA and favipiravir-RTP
  • Nsp7-Nsp8-Nsp12 SARS-CoV2 RNA-directed RNA polymerase
  • RNA
  • (Non-structural protein ...Viral nonstructural protein) x 3
  • (nucleic-acidNucleic acid) x 2
  • (ligand) x 4
Function / homology
Function and homology information


Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-2 sgRNAs / host cell endosome / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Translation of Replicase and Assembly of the Replication Transcription Complex / exoribonuclease activity / RNA phosphodiester bond hydrolysis, exonucleolytic / modulation by virus of host autophagy / mRNA methylation ...Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-2 sgRNAs / host cell endosome / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Translation of Replicase and Assembly of the Replication Transcription Complex / exoribonuclease activity / RNA phosphodiester bond hydrolysis, exonucleolytic / modulation by virus of host autophagy / mRNA methylation / double membrane vesicle viral factory outer membrane / suppression by virus of host translation / ISG15-specific protease activity / host cell Golgi apparatus / Replication of the SARS-CoV-2 genome / suppression by virus of host type I interferon production / host cell endoplasmic reticulum / induction by virus of catabolism of host mRNA / SARS coronavirus main proteinase / cytoplasmic viral factory / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / G-quadruplex RNA binding / 3'-5'-exoribonuclease activity / suppression by virus of host ISG15-protein conjugation / host cell endoplasmic reticulum-Golgi intermediate compartment / protein K48-linked deubiquitination / suppression by virus of host toll-like receptor signaling pathway / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / transcription, RNA-templated / suppression by virus of host NF-kappaB cascade / modulation by virus of host protein ubiquitination / protein K63-linked deubiquitination / positive stranded viral RNA replication / protein autoprocessing / cysteine-type peptidase activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / viral genome replication / suppression by virus of host TRAF activity / helicase activity / viral transcription / Transferases; Transferring one-carbon groups; Methyltransferases / ubiquitinyl hydrolase 1 / methyltransferase activity / DNA helicase / thiol-dependent deubiquitinase / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / DNA helicase activity / single-stranded RNA binding / host cell perinuclear region of cytoplasm / methylation / RNA helicase / induction by virus of host autophagy / endonuclease activity / RNA-directed RNA polymerase / RNA helicase activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / viral protein processing / suppression by virus of host type I interferon-mediated signaling pathway / Hydrolases; Acting on ester bonds / transcription, DNA-templated / host cell cytoplasm / protein dimerization activity / protein homodimerization activity / zinc ion binding / integral component of membrane / ATP binding / identical protein binding / cytosol
Similarity search - Function
RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nonstructural protein 14, betacoronavirus / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. ...RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nonstructural protein 14, betacoronavirus / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Viral (Superfamily 1) RNA helicase / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / RNA polymerase, N-terminal, coronavirus / Coronavirus 2'-O-methyltransferase / Non-structural protein 14, coronavirus / Coronavirus replicase NSP15, middle domain / Non-structural protein NSP16, coronavirus-like / Coronavirus proofreading exoribonuclease / Coronavirus replicase NSP15, N-terminal oligomerisation / Non-structural protein NSP15, middle domain superfamily / Coronavirus RNA-dependent RNA polymerase, N-terminal / Coronavirus replicase NSP15, N-terminal oligomerisation / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Coronavirus replicase NSP15, middle domain / Coronaviridae zinc-binding (CV ZBD) domain profile. / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, N-terminal, betacoronavirus / Betacoronavirus SUD-C domain / Betacoronavirus replicase NSP3, N-terminal / Non-structural protein 2, SARS-CoV-like / Polyprotein cleavage domain PL2pro superfamily, coronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Non-structural protein NSP1 superfamily, betacoronavirus / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / Endoribonuclease EndoU-like / Carbamoyl-phosphate synthase subdomain signature 2. / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Betacoronavirus Nsp3c-M domain profile. / Betacoronavirus Nsp3c-C domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Betacoronavirus single-stranded poly(A) binding domain / Betacoronavirus replicase NSP1 / Non-structural protein NSP1, betacoronavirus / Replicase polyprotein, nucleic acid-binding domain superfamily / Coronavirus (CoV) Nsp1 globular domain profile. / Non-structural protein 6, betacoronavirus / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3A domain-like superfamily / Papain-like protease, N-terminal domain superfamily, coronavirus / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Papain-like protease, thumb domain superfamily, coronavirus / Lipocalin signature. / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Coronavirus replicase NSP2, N-terminal / Nonstructural protein 2, N-terminal domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Papain-like viral protease, palm and finger domains, coronavirus / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Peptidase family C16 domain profile. / Non-structural protein NSP7, coronavirus / Non-structural protein NSP7 superfamily, coronavirus / Coronavirus replicase NSP7 / Coronavirus papain-like peptidase / Coronavirus replicase NSP4, C-terminal / Coronavirus replicase NSP6 / Coronavirus RNA synthesis protein NSP10 / Coronavirus endopeptidase C30 / Coronavirus replicase NSP3, C-terminal / Coronavirus replicase NSP8 / Non-structural protein NSP4, C-terminal superfamily, coronavirus / Coronavirus replicase NSP4, N-terminal / RNA synthesis protein NSP10, coronavirus / Coronavirus replicase NSP3, C-terminal / Coronavirus main protease (M-pro) domain profile. / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus / Coronavirus replicase NSP4, N-terminal / Peptidase C30, coronavirus / Non-structural protein NSP4, C-terminal, coronavirus / Non-structural protein NSP8 superfamily, coronavirus / Non-structural protein 6, coronavirus / Peptidase C30, domain 3, coronavirus
Similarity search - Domain/homology
Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsNaydenova K / Muir KW / Wu LF / Zhang Z / Coscia F / Peet M / Castro-Hartman P / Qian P / Sader K / Dent K ...Naydenova K / Muir KW / Wu LF / Zhang Z / Coscia F / Peet M / Castro-Hartman P / Qian P / Sader K / Dent K / Kimanius D / Sutherland JD / Loewe J / Barford D / Russo CJ
Funding support United Kingdom, 6 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_120117 United Kingdom
Medical Research Council (MRC, United Kingdom)U105184326 United Kingdom
Wellcome Trust202754/Z/16/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UP_A024_1009 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UP_1201/6 United Kingdom
Cancer Research UKC576/A14109 United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: Structure of the SARS-CoV-2 RNA-dependent RNA polymerase in the presence of favipiravir-RTP.
Authors: Katerina Naydenova / Kyle W Muir / Long-Fei Wu / Ziguo Zhang / Francesca Coscia / Mathew J Peet / Pablo Castro-Hartmann / Pu Qian / Kasim Sader / Kyle Dent / Dari Kimanius / John D ...Authors: Katerina Naydenova / Kyle W Muir / Long-Fei Wu / Ziguo Zhang / Francesca Coscia / Mathew J Peet / Pablo Castro-Hartmann / Pu Qian / Kasim Sader / Kyle Dent / Dari Kimanius / John D Sutherland / Jan Löwe / David Barford / Christopher J Russo /
Abstract: The RNA polymerase inhibitor favipiravir is currently in clinical trials as a treatment for infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), despite limited information ...The RNA polymerase inhibitor favipiravir is currently in clinical trials as a treatment for infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), despite limited information about the molecular basis for its activity. Here we report the structure of favipiravir ribonucleoside triphosphate (favipiravir-RTP) in complex with the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) bound to a template:primer RNA duplex, determined by electron cryomicroscopy (cryoEM) to a resolution of 2.5 Å. The structure shows clear evidence for the inhibitor at the catalytic site of the enzyme, and resolves the conformation of key side chains and ions surrounding the binding pocket. Polymerase activity assays indicate that the inhibitor is weakly incorporated into the RNA primer strand, and suppresses RNA replication in the presence of natural nucleotides. The structure reveals an unusual, nonproductive binding mode of favipiravir-RTP at the catalytic site of SARS-CoV-2 RdRp, which explains its low rate of incorporation into the RNA primer strand. Together, these findings inform current and future efforts to develop polymerase inhibitors for SARS coronaviruses.
History
DepositionSep 4, 2020-
Header (metadata) releaseSep 23, 2020-
Map releaseSep 23, 2020-
UpdateFeb 24, 2021-
Current statusFeb 24, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7aap
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
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Supplemental images

Downloads & links

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Map

FileDownload / File: emd_11692.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 320 pix.
= 208. Å
0.65 Å/pix.
x 320 pix.
= 208. Å
0.65 Å/pix.
x 320 pix.
= 208. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.012
Minimum - Maximum-0.047219016 - 0.11504151
Average (Standard dev.)0.00018596314 (±0.0031760929)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 208.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.650.650.65
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z208.000208.000208.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ428428428
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0470.1150.000

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Supplemental data

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Segmentation: #1

Fileemd_11692_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Additional map: Unsharpened EM density map

Fileemd_11692_additional.map
AnnotationUnsharpened EM density map
Projections & Slices
AxesZYX

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Slices (1/2)
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Half map: EM density half map 1

Fileemd_11692_half_map_1.map
AnnotationEM density half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: EM density half map 2

Fileemd_11692_half_map_2.map
AnnotationEM density half map 2
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Sample components

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Entire Nsp7-Nsp8-Nsp12 SARS-CoV2 RNA-directed RNA polymerase in complex ...

EntireName: Nsp7-Nsp8-Nsp12 SARS-CoV2 RNA-directed RNA polymerase in complex with template:primer dsRNA and favipiravir-RTP
Number of Components: 12

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Component #1: protein, Nsp7-Nsp8-Nsp12 SARS-CoV2 RNA-directed RNA polymerase in...

ProteinName: Nsp7-Nsp8-Nsp12 SARS-CoV2 RNA-directed RNA polymerase in complex with template:primer dsRNA and favipiravir-RTP
Recombinant expression: No

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Component #2: protein, Nsp7-Nsp8-Nsp12 SARS-CoV2 RNA-directed RNA polymerase

ProteinName: Nsp7-Nsp8-Nsp12 SARS-CoV2 RNA-directed RNA polymerase / Recombinant expression: No
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #3: protein, RNA

ProteinName: RNA / Recombinant expression: No
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: synthetic construct (others)

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Component #4: protein, Non-structural protein 12

ProteinName: Non-structural protein 12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 110.521938 kDa
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #5: protein, Non-structural protein 8

ProteinName: Non-structural protein 8 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 21.903047 kDa
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #6: protein, Non-structural protein 7

ProteinName: Non-structural protein 7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.248804 kDa
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #7: nucleic-acid, RNA (5'-R(P*UP*UP*AP*AP*GP*UP*UP*AP*U)-3')

nucleic acidName: RNA (5'-R(P*UP*UP*AP*AP*GP*UP*UP*AP*U)-3') / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
CAGUGCUAUG UGAGAUUAAG UUAU
MassTheoretical: 7.696575 kDa
SourceSpecies: Severe acute respiratory syndrome coronavirus 2

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Component #8: nucleic-acid, RNA (5'-R(P*UP*UP*CP*AP*UP*AP*AP*CP*UP*UP*AP*A)-3')

nucleic acidName: RNA (5'-R(P*UP*UP*CP*AP*UP*AP*AP*CP*UP*UP*AP*A)-3') / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UUUUUCAUAA CUUAAUCUCA CAUAGCACUG
MassTheoretical: 9.418569 kDa
SourceSpecies: Severe acute respiratory syndrome coronavirus 2

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Component #9: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Component #10: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #11: ligand, PYROPHOSPHATE 2-

LigandName: PYROPHOSPHATE 2- / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.175959 kDa

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Component #12: ligand, [[(2~{R},3~{S},4~{R},5~{R})-5-(3-aminocarbonyl-5-fluorany...

LigandName: [[(2~{R},3~{S},4~{R},5~{R})-5-(3-aminocarbonyl-5-fluoranyl-2-oxidanylidene-pyrazin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.529157 kDa

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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: TFS KRIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 24.72 e/Å2 / Illumination Mode: FLOOD BEAM
LensImaging Mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Number of Projections: 40828
3D reconstructionResolution: 2.5 Å / Resolution Method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement space: REAL
Input PDB model: 7BV2
Output model

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