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- EMDB-72127: Cryo-EM structure of SARS-CoV-2 nsp10-nsp14 E191A mutant-T20P14-R... -

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Entry
Database: EMDB / ID: EMD-72127
TitleCryo-EM structure of SARS-CoV-2 nsp10-nsp14 E191A mutant-T20P14-R complex
Map dataRaw map
Sample
  • Complex: Complex of SARS-CoV-2 nsp10-nsp14 E191A mutant with a synthetic T20P14-R and P7 RNA
    • Protein or peptide: Non-structural protein 10
    • Protein or peptide: Proofreading exoribonuclease
    • RNA: T20P14-R RNA
    • RNA: RNA (5'-R(*A*UP*UP*CP*CP*CP*C)-3')
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
KeywordsSARS-CoV-2 / replication and transcription / mismatch / proofreading exoribonuclease / VIRAL PROTEIN / VIRAL PROTEIN-RNA complex
Function / homology
Function and homology information


protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / ISG15-specific peptidase activity / TRAF3-dependent IRF activation pathway ...protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / ISG15-specific peptidase activity / TRAF3-dependent IRF activation pathway / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / snRNP Assembly / Replication of the SARS-CoV-2 genome / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease activity / host cell endosome / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / mRNA (guanine-N7)-methyltransferase / SARS-CoV-2 modulates host translation machinery / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated suppression of host NF-kappaB cascade / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / regulation of autophagy / viral protein processing / lyase activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / copper ion binding / viral translational frameshifting / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / lipid binding / DNA-templated transcription / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / NSP12 RNA-dependent RNA polymerase, coronavirus / : ...RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / NSP12 RNA-dependent RNA polymerase, coronavirus / : / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus Nsp12 Interface domain profile. / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Nidovirus 2-O-methyltransferase / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, N-terminal oligomerization / Nonstructural protein 15, middle domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / : / Lipocalin signature. / DNA2/NAM7 helicase-like, C-terminal / AAA domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, N-terminal, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Betacoronavirus replicase NSP3, N-terminal / NSP1 globular domain superfamily, betacoronavirus / Non-structural protein 2, SARS-CoV-like / Carbamoyl-phosphate synthase subdomain signature 2. / Betacoronavirus Nsp3c-M domain profile. / NSP1, globular domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Betacoronavirus replicase NSP1 / Betacoronavirus single-stranded poly(A) binding domain / NSP1, C-terminal domain, betacoronavirus / : / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile. / Betacoronavirus Nsp3c-C domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Papain-like viral protease, palm and finger domains, coronavirus / Papain-like protease, N-terminal domain superfamily, coronavirus / Coronavirus replicase NSP2, N-terminal / : / Coronavirus replicase NSP2, C-terminal / Coronavirus (CoV) Nsp2 middle domain profile. / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / Nonstructural protein 2, N-terminal domain, coronavirus / Non-structural protein 2, C-terminal domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Peptidase family C16 domain profile. / : / : / Coronavirus replicase NSP7 / Coronavirus 3Ecto domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile.
Similarity search - Domain/homology
Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 2.81 Å
AuthorsYang Y / Liu C / Liu B
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM150607 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)DP2AI177906 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Molecular basis of SARS-CoV-2 proofreading enzyme-mediated resistance to remdesivir.
Authors: Yang Yang / Yu Li / Scott T Becker / Ayesha Khan / Gloria Luo / Bin Liu / Chang Liu /
Abstract: SARS-CoV-2's remarkable resistance to nucleotide analog antivirals such as remdesivir, which thwarts RNA synthesis by inhibiting viral polymerase (RdRp), challenges available therapies. We reveal ...SARS-CoV-2's remarkable resistance to nucleotide analog antivirals such as remdesivir, which thwarts RNA synthesis by inhibiting viral polymerase (RdRp), challenges available therapies. We reveal that remdesivir incorporation destabilizes RdRp-RNA complex while enhancing RNA binding to the proofreading exoribonuclease (ExoN), facilitating remdesivir excision. Conserved ExoN determinants for remdesivir recognition and excision underpin ExoN-mediated resistance across all coronaviruses. These findings inform the design of next-generation antivirals and combination therapies capable of overcoming ExoN-mediated resistance.
History
DepositionAug 14, 2025-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateOct 15, 2025-
Current statusOct 15, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72127.png

Downloads & links

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Map

FileDownload / File: emd_72127.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRaw map
Projections & slices

Image control

Size
Brightness
Contrast
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AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 384 pix.
= 336.026 Å		0.88 Å/pix.
x 384 pix.
= 336.026 Å		0.88 Å/pix.
x 384 pix.
= 336.026 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.87507 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0926
Minimum - Maximum-0.24790107 - 0.5993895
Average (Standard dev.)0.0010005669 (±0.015439122)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 336.02557 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72127_msk_1.map
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Additional map: DeepEMhancer-postprocessed map

Fileemd_72127_additional_1.map
AnnotationDeepEMhancer-postprocessed map
Projections & Slices
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Additional map: Resolve density-modified map

Fileemd_72127_additional_2.map
AnnotationResolve density-modified map
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Half map: Half map A

Fileemd_72127_half_map_1.map
AnnotationHalf map A
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Half map: Half map B

Fileemd_72127_half_map_2.map
AnnotationHalf map B
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Sample components

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Entire : Complex of SARS-CoV-2 nsp10-nsp14 E191A mutant with a synthetic T...

EntireName: Complex of SARS-CoV-2 nsp10-nsp14 E191A mutant with a synthetic T20P14-R and P7 RNA
Components
  • Complex: Complex of SARS-CoV-2 nsp10-nsp14 E191A mutant with a synthetic T20P14-R and P7 RNA
    • Protein or peptide: Non-structural protein 10
    • Protein or peptide: Proofreading exoribonuclease
    • RNA: T20P14-R RNA
    • RNA: RNA (5'-R(*A*UP*UP*CP*CP*CP*C)-3')
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Complex of SARS-CoV-2 nsp10-nsp14 E191A mutant with a synthetic T...

SupramoleculeName: Complex of SARS-CoV-2 nsp10-nsp14 E191A mutant with a synthetic T20P14-R and P7 RNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Macromolecule #1: Non-structural protein 10

MacromoleculeName: Non-structural protein 10 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 14.80293 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AGNATEVPAN STVLSFCAFA VDAAKAYKDY LASGGQPITN CVKMLCTHTG TGQAITVTPE ANMDQESFGG ASCCLYCRCH IDHPNPKGF CDLKGKYVQI PTTCANDPVG FTLKNTVCTV CGMWKGYGCS CDQLREPMLQ

UniProtKB: Replicase polyprotein 1ab

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Macromolecule #2: Proofreading exoribonuclease

MacromoleculeName: Proofreading exoribonuclease / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
EC number: Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 59.829441 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AENVTGLFKD CSKVITGLHP TQAPTHLSVD TKFKTEGLCV DIPGIPKDMT YRRLISMMGF KMNYQVNGYP NMFITREEAI RHVRAWIGF DVEGCHATRE AVGTNLPLQL GFSTGVNLVA VPTGYVDTPN NTDFSRVSAK PPPGDQFKHL IPLMYKGLPW N VVRIKIVQ ...String:
AENVTGLFKD CSKVITGLHP TQAPTHLSVD TKFKTEGLCV DIPGIPKDMT YRRLISMMGF KMNYQVNGYP NMFITREEAI RHVRAWIGF DVEGCHATRE AVGTNLPLQL GFSTGVNLVA VPTGYVDTPN NTDFSRVSAK PPPGDQFKHL IPLMYKGLPW N VVRIKIVQ MLSDTLKNLS DRVVFVLWAH GFALTSMKYF VKIGPERTCC LCDRRATCFS TASDTYACWH HSIGFDYVYN PF MIDVQQW GFTGNLQSNH DLYCQVHGNA HVASCDAIMT RCLAVHECFV KRVDWTIEYP IIGDELKINA ACRKVQHMVV KAA LLADKF PVLHDIGNPK AIKCVPQADV EWKFYDAQPC SDKAYKIEEL FYSYATHSDK FTDGVCLFWN CNVDRYPANS IVCR FDTRV LSNLNLPGCD GGSLYVNKHA FHTPAFDKSA FVNLKQLPFF YYSDSPCESH GKQVVSDIDY VPLKSATCIT RCNLG GAVC RHHANEYRLY LDAYNMMISA GFSLWVYKQF DTYNLWNTFT RLQ

UniProtKB: Replicase polyprotein 1ab

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Macromolecule #3: T20P14-R RNA

MacromoleculeName: T20P14-R RNA / type: rna / ID: 3 / Number of copies: 2
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 12.541466 KDa
SequenceString:
GGGAAUGGGA UUUUAAUAGC UUCGGCUAUU AAAAUCCC(F86)

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Macromolecule #4: RNA (5'-R(*A*UP*UP*CP*CP*CP*C)-3')

MacromoleculeName: RNA (5'-R(*A*UP*UP*CP*CP*CP*C)-3') / type: rna / ID: 4 / Number of copies: 2
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 2.117307 KDa
SequenceString:
AUUCCCC

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 20 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 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: 7.5
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS 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 exposure time: 2.0 sec. / Average electron dose: 51.54 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 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

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 102206
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7n0d


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9q1j:
Cryo-EM structure of SARS-CoV-2 nsp10-nsp14 E191A mutant-T20P14-R complex

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