[English] 日本語
Yorodumi
- EMDB-49637: SARS-CoV-2 nsp1 bound to the Rhinolophus lepidus 40S ribosome (co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-49637
TitleSARS-CoV-2 nsp1 bound to the Rhinolophus lepidus 40S ribosome (consensus map)
Map data
Sample
  • Complex: SARS-CoV-2 nsp1-Rhinolophus lepidus ribosome complex, consensus map
    • Complex: SARS-CoV-2 nsp1
      • Protein or peptide: x 1 types
    • Complex: Eukaryotic translation initiation factor 1
      • Protein or peptide: x 1 types
    • Organelle or cellular component: Rhinolophus lepidus 40S ribosomal subunit
      • Protein or peptide: x 21 types
      • RNA: x 1 types
  • Ligand: x 4 types
KeywordsSARS-CoV-2 / RIBOSOME / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


multi-eIF complex / translation factor activity, RNA binding / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / regulation of translational initiation / ribosomal small subunit binding / translation initiation factor activity / translational initiation / protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism ...multi-eIF complex / translation factor activity, RNA binding / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / regulation of translational initiation / ribosomal small subunit binding / translation initiation factor activity / translational initiation / 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) / Maturation of replicase proteins / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / 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 / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / SARS coronavirus main proteinase / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase 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 / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / symbiont-mediated suppression of host NF-kappaB cascade / DNA helicase / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / regulation of autophagy / host cell perinuclear region of cytoplasm / 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 / DNA-templated transcription / lipid binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / nucleus / membrane / cytoplasm
Similarity search - Function
Eukaryotic translation initiation factor SUI1 / SUI1 domain superfamily / Translation initiation factor SUI1 / Translation initiation factor SUI1 family profile. / SUI1 domain / 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 ...Eukaryotic translation initiation factor SUI1 / SUI1 domain superfamily / Translation initiation factor SUI1 / Translation initiation factor SUI1 family profile. / SUI1 domain / 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.
Similarity search - Domain/homology
Replicase polyprotein 1ab / Eukaryotic translation initiation factor 1
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human) / Rhinolophus lepidus (bat)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsGen R / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Veesler D
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Cell Rep / Year: 2025
Title: SARS-CoV-2 nsp1 mediates broad inhibition of translation in mammals.
Authors: Risako Gen / Amin Addetia / Daniel Asarnow / Young-Jun Park / Joel Quispe / Matthew C Chan / Jack T Brown / Jimin Lee / Melody G Campbell / Christopher P Lapointe / David Veesler /
Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) non-structural protein 1 (nsp1) promotes innate immune evasion by inhibiting host translation in human cells. However, the role of nsp1 in ...Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) non-structural protein 1 (nsp1) promotes innate immune evasion by inhibiting host translation in human cells. However, the role of nsp1 in other host species remains elusive, especially in bats-natural reservoirs of sarbecoviruses with a markedly different innate immune system than humans. We reveal that nsp1 potently inhibits translation in Rhinolophus lepidus bat cells, which belong to the same genus as known sarbecovirus reservoir hosts. We determined a cryoelectron microscopy structure of nsp1 bound to the R. lepidus 40S ribosomal subunit, showing that it blocks the mRNA entry channel by targeting a highly conserved site among mammals. Accordingly, we found that nsp1 blocked protein translation in mammalian cells from several species, underscoring its broadly inhibitory activity and conserved role in numerous SARS-CoV-2 hosts. Our findings illuminate the arms race between coronaviruses and mammalian host immunity, providing a foundation for understanding the determinants of viral maintenance in bat hosts and spillover.
History
DepositionMar 11, 2025-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_49637.png

Downloads & links

-
Map

FileDownload / File: emd_49637.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 424.448 Å		0.83 Å/pix.
x 512 pix.
= 424.448 Å		0.83 Å/pix.
x 512 pix.
= 424.448 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.829 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.0600686 - 0.3095081
Average (Standard dev.)0.0003220329 (±0.0071120374)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 424.448 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: #1

Fileemd_49637_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_49637_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_49637_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : SARS-CoV-2 nsp1-Rhinolophus lepidus ribosome complex, consensus map

EntireName: SARS-CoV-2 nsp1-Rhinolophus lepidus ribosome complex, consensus map
Components
  • Complex: SARS-CoV-2 nsp1-Rhinolophus lepidus ribosome complex, consensus map
    • Complex: SARS-CoV-2 nsp1
      • Protein or peptide: Host translation inhibitor nsp1
    • Complex: Eukaryotic translation initiation factor 1
      • Protein or peptide: Eukaryotic translation initiation factor 1
    • Organelle or cellular component: Rhinolophus lepidus 40S ribosomal subunit
      • Protein or peptide: 40S ribosomal protein uS5, RPS2
      • Protein or peptide: 40S ribosomal protein eS4 X isoform, RPS4
      • Protein or peptide: 40S ribosomal protein eS6, RPS6
      • Protein or peptide: 40S ribosomal protein eS8, RPS8
      • Protein or peptide: 40S ribosomal protein uS4, RPS9
      • Protein or peptide: 40S ribosomal protein uS15, RPS13
      • Protein or peptide: 40S ribosomal protein uS11, RPS14
      • Protein or peptide: 40S ribosomal protein uS8, RPS15a
      • Protein or peptide: 40S ribosomal protein eS17, RPS17
      • Protein or peptide: 40S ribosomal protein eS21, RPS21
      • Protein or peptide: 40S ribosomal protein uS12, RPS23
      • Protein or peptide: 40S ribosomal protein eS24, RPS24
      • Protein or peptide: 40S ribosomal protein eS26, RPS26
      • Protein or peptide: 40S ribosomal protein eS27, RPS27
      • Protein or peptide: 40S ribosomal protein eS32, L41
      • Protein or peptide: 40S ribosomal protein uS2, RPSA
      • Protein or peptide: 40S ribosomal protein eS7, RPS7
      • Protein or peptide: 40S ribosomal protein uS17, RPS11
      • Protein or peptide: 40S ribosomal protein eS30, RPS30
      • Protein or peptide: 40S ribosomal protein eS1, RPS3a
      • RNA: 18S ribosomal RNA
      • Protein or peptide: 40S ribosomal protein uS3, RPS3
  • Ligand: MAGNESIUM ION
  • Ligand: POTASSIUM ION
  • Ligand: ZINC ION
  • Ligand: water

+
Supramolecule #1: SARS-CoV-2 nsp1-Rhinolophus lepidus ribosome complex, consensus map

SupramoleculeName: SARS-CoV-2 nsp1-Rhinolophus lepidus ribosome complex, consensus map
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#24

+
Supramolecule #3: SARS-CoV-2 nsp1

SupramoleculeName: SARS-CoV-2 nsp1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #17
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

+
Supramolecule #4: Eukaryotic translation initiation factor 1

SupramoleculeName: Eukaryotic translation initiation factor 1 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #18
Source (natural)Organism: Homo sapiens (human)

+
Supramolecule #2: Rhinolophus lepidus 40S ribosomal subunit

SupramoleculeName: Rhinolophus lepidus 40S ribosomal subunit / type: organelle_or_cellular_component / ID: 2 / Parent: 1 / Macromolecule list: #1-#16, #19-#24
Source (natural)Organism: Rhinolophus lepidus (bat)

+
Macromolecule #1: 40S ribosomal protein uS5, RPS2

MacromoleculeName: 40S ribosomal protein uS5, RPS2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhinolophus lepidus (bat)
Molecular weightTheoretical: 31.257352 KDa
SequenceString: MADDAGAAGG AGAPGGPGLG GRGGFRGGFG SGVRGRGRGR GRGRGRGRGA RGGKAEDKEW IPVTKLGRLV KDMKIKSLEE IYLFSLPIK ESEIIDFFLG ASLKDEVLKI MPVQKQTRAG QRTRFKAFVA IGDYNGHVGL GVKCSKEVAT AIRGAIILAK L SIVPVRRG ...String:
MADDAGAAGG AGAPGGPGLG GRGGFRGGFG SGVRGRGRGR GRGRGRGRGA RGGKAEDKEW IPVTKLGRLV KDMKIKSLEE IYLFSLPIK ESEIIDFFLG ASLKDEVLKI MPVQKQTRAG QRTRFKAFVA IGDYNGHVGL GVKCSKEVAT AIRGAIILAK L SIVPVRRG YWGNKIGKPH TVPCKVTGRC GSVLVRLIPA PRGTGIVSAP VPKKLLMMAG IDDCYTSARG CTATLGNFAK AT FDAISKT YSYLTPDLWK ETVFTKSPYQ EFTDHLVKTH TRVSVQRTQA PAVATT

+
Macromolecule #2: 40S ribosomal protein eS4 X isoform, RPS4

MacromoleculeName: 40S ribosomal protein eS4 X isoform, RPS4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhinolophus lepidus (bat)
Molecular weightTheoretical: 29.640846 KDa
SequenceString: MARGPKKHLK RVAAPKHWML DKLTGVFAPR PSTGPHKLRE CLPLIIFLRN RLKYALTGDE VKKICMQRFI KIDGKVRTDV TYPAGFMDV ISIDKTGENF RLIYDTKGRF AVHRITPEEA KYKLCKVRKI FVGTKGIPHL VTHDARTIRY PDPLIKVNDT I QIDLETGK ...String:
MARGPKKHLK RVAAPKHWML DKLTGVFAPR PSTGPHKLRE CLPLIIFLRN RLKYALTGDE VKKICMQRFI KIDGKVRTDV TYPAGFMDV ISIDKTGENF RLIYDTKGRF AVHRITPEEA KYKLCKVRKI FVGTKGIPHL VTHDARTIRY PDPLIKVNDT I QIDLETGK ITDFIKFDTG NLCMVTGGAN LGRIGVITNR ERHPGSFDVV HVKDANGNSF ATRLSNIFVI GKGNKPWISL PR GKGIRLT IAEERDKRLA AKQSSG

+
Macromolecule #3: 40S ribosomal protein eS6, RPS6

MacromoleculeName: 40S ribosomal protein eS6, RPS6 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhinolophus lepidus (bat)
Molecular weightTheoretical: 28.751906 KDa
SequenceString: MKLNISFPAT GCQKLIEVDD ERKLRTFYEK RMATEVAADA LGEEWKGYVV RISGGNDKQG FPMKQGVLTH GRVRLLLSKG HSCYRPRRT GERKRKSVRG CIVDANLSVL NLVIVKKGEK DIPGLTDTTV PRRLGPKRAS RIRKLFNLSK EDDVRQYVVR K PLNKEGKK ...String:
MKLNISFPAT GCQKLIEVDD ERKLRTFYEK RMATEVAADA LGEEWKGYVV RISGGNDKQG FPMKQGVLTH GRVRLLLSKG HSCYRPRRT GERKRKSVRG CIVDANLSVL NLVIVKKGEK DIPGLTDTTV PRRLGPKRAS RIRKLFNLSK EDDVRQYVVR K PLNKEGKK PRTKAPKIQR LVTPRVLQHK RRRIALKKQR TKKNKEEAAE YAKLLAKRMK EAKEKRQEQI AKRRRLSSLR AS TSKSESS QK

+
Macromolecule #4: 40S ribosomal protein eS8, RPS8

MacromoleculeName: 40S ribosomal protein eS8, RPS8 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhinolophus lepidus (bat)
Molecular weightTheoretical: 24.249359 KDa
SequenceString: MGISRDNWHK RRKTGGKRKP YHKKRKYELG RPAANTKIGP RRIHTVRVRG GNKKYRALRL DVGNFSWGSE CCTRKTRIID VVYNASNNE LVRTKTLVKN CIVLVDSTPY RQWYESHYAL PLGRKKGAKL TPEEEEILNK KRSKKIQKKY DERKKNAKIS S LLEEQFQQ ...String:
MGISRDNWHK RRKTGGKRKP YHKKRKYELG RPAANTKIGP RRIHTVRVRG GNKKYRALRL DVGNFSWGSE CCTRKTRIID VVYNASNNE LVRTKTLVKN CIVLVDSTPY RQWYESHYAL PLGRKKGAKL TPEEEEILNK KRSKKIQKKY DERKKNAKIS S LLEEQFQQ GKLLACIASR PGQCGRADGY VLEGKELEFY LRKIKARKGK

+
Macromolecule #5: 40S ribosomal protein uS4, RPS9

MacromoleculeName: 40S ribosomal protein uS4, RPS9 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhinolophus lepidus (bat)
Molecular weightTheoretical: 22.641564 KDa
SequenceString: MPVARSWVCR KTYVTPRRPF EKSRLDQELK LIGEYGLRNK REVWRVKFTL AKIRKAAREL LTLDEKDPRR LFEGNALLRR LVRIGVLDE GKMKLDYILG LKIEDFLERR LQTQVFKLGL AKSIHHARVL IRQRHIRVRK QVVNIPSFIV RLDSQKHIDF S LRSPYGGG ...String:
MPVARSWVCR KTYVTPRRPF EKSRLDQELK LIGEYGLRNK REVWRVKFTL AKIRKAAREL LTLDEKDPRR LFEGNALLRR LVRIGVLDE GKMKLDYILG LKIEDFLERR LQTQVFKLGL AKSIHHARVL IRQRHIRVRK QVVNIPSFIV RLDSQKHIDF S LRSPYGGG RPGRVKRKNA KKGQGGAGAG DDEEED

+
Macromolecule #6: 40S ribosomal protein uS15, RPS13

MacromoleculeName: 40S ribosomal protein uS15, RPS13 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhinolophus lepidus (bat)
Molecular weightTheoretical: 17.259389 KDa
SequenceString:
MGRMHAPGKG LSQSALPYRR SVPTWLKLTS DDVKEQIYKL AKKGLTPSQI GVILRDSHGV AQVRFVTGNK ILRILKSKGL APDLPEDLY HLIKKAVAVR KHLERNRKDK DAKFRLILIE SRIHRLARYY KTKRVLPPNW KYESSTASAL VA

+
Macromolecule #7: 40S ribosomal protein uS11, RPS14

MacromoleculeName: 40S ribosomal protein uS11, RPS14 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhinolophus lepidus (bat)
Molecular weightTheoretical: 16.302772 KDa
SequenceString:
MAPRKGKEKK EEQVISLGPQ VAEGENVFGV CHIFASFNDT FVHVTDLSGK ETICRVTGGM KVKADRDESS PYAAMLAAQD VAQRCKELG ITALHIKLRA TGGNRTKTPG PGAQSALRAL ARSGMKIGRI EDVTPIPS(IAS)S TRRKGGRRGR RL

+
Macromolecule #8: 40S ribosomal protein uS8, RPS15a

MacromoleculeName: 40S ribosomal protein uS8, RPS15a / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhinolophus lepidus (bat)
Molecular weightTheoretical: 14.865555 KDa
SequenceString:
MVRMNVLADA LKSINNAEKR GKRQVLIRPC SKVIVRFLTV MMKHGYIGEF EIIDDHRAGK IVVNLTGRLN KCGVISPRFD VQLKDLEKW QNNLLPSRQF GFIVLTTSAG IMDHEEARRK HTGGKILGFF F

+
Macromolecule #9: 40S ribosomal protein eS17, RPS17

MacromoleculeName: 40S ribosomal protein eS17, RPS17 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhinolophus lepidus (bat)
Molecular weightTheoretical: 15.552119 KDa
SequenceString:
MGRVRTKTVK KAARVIIEKY YTRLGNDFHT NKRVCEEIAI IPSKKLRNKI AGYVTHLMKR IQRGPVRGIS IKLQEEERER RDNYVPEVS ALDQEIIEVD PDTKEMLKLL DFGSLSNLQV TQPTVGMNFK TPRGAV

+
Macromolecule #10: 40S ribosomal protein eS21, RPS21

MacromoleculeName: 40S ribosomal protein eS21, RPS21 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhinolophus lepidus (bat)
Molecular weightTheoretical: 9.150427 KDa
SequenceString:
(ACE)MQNDAGEFV DLYVPRKCSA SNRIIGAKDH ASIQMNVAEV DKVTGRFNGQ FKTYAICGAI RRMGESDDSI LRLAKA DGI VSKNF

+
Macromolecule #11: 40S ribosomal protein uS12, RPS23

MacromoleculeName: 40S ribosomal protein uS12, RPS23 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhinolophus lepidus (bat)
Molecular weightTheoretical: 15.860666 KDa
SequenceString:
MGKCRGLRTA RKLRSHRRDQ KWHDKQYKKA HLGTALKANP FGGASHAKGI VLEKVGVEAK Q(HY3)NSAIRKCV RVQLIK NGK KITAFVPNDG CLNFIEENDE VLVAGFGRKG HAVGDIPGVR FKVVKVANVS LLALYKGKKE RPRS

+
Macromolecule #12: 40S ribosomal protein eS24, RPS24

MacromoleculeName: 40S ribosomal protein eS24, RPS24 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhinolophus lepidus (bat)
Molecular weightTheoretical: 15.094926 KDa
SequenceString:
MNDTVTIRTR KFMTNRLLQR KQMVIDVLHP GKATVPKTEI REKLAKMYKT TPDVIFVFGF RTHFGGGKTT GFGMIYDSLD YAKKNEPKH RLARHGLYEK KKTSRKQRKE RKNRMKKVRG TAKATVGAGK K

+
Macromolecule #13: 40S ribosomal protein eS26, RPS26

MacromoleculeName: 40S ribosomal protein eS26, RPS26 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhinolophus lepidus (bat)
Molecular weightTheoretical: 13.047532 KDa
SequenceString:
MTKKRRNNGR AKKGRGHVQP IRCTNCARCV PKDKAIKKFV IRNIVEAAAV RDISEASVFD AYVLPKLYVK LHYCVSCAIH SKVVRNRSR EARKDRTPPP RFRPAGAAPR PPPKPM

+
Macromolecule #14: 40S ribosomal protein eS27, RPS27

MacromoleculeName: 40S ribosomal protein eS27, RPS27 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhinolophus lepidus (bat)
Molecular weightTheoretical: 9.480186 KDa
SequenceString:
MPLAKDLLHP SPEEEKRKHK KKRLVQSPNS YFMDVKCPGC YKITTVFSHA QTVVLCVGCS TVLCQPTGGK ARLTEGCSFR RKQH

+
Macromolecule #15: 40S ribosomal protein eS32, L41

MacromoleculeName: 40S ribosomal protein eS32, L41 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhinolophus lepidus (bat)
Molecular weightTheoretical: 3.473451 KDa
SequenceString:
MRAKWRKKRM RRLKRKRRKM RQRSK

+
Macromolecule #16: 40S ribosomal protein uS2, RPSA

MacromoleculeName: 40S ribosomal protein uS2, RPSA / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhinolophus lepidus (bat)
Molecular weightTheoretical: 32.75077 KDa
SequenceString: (ACE)SGALDVLQM KEEDVLKFLA AGTHLGGTNL DFQMEQYIYK RKSDGIYIIN LKRTWEKLLL AARAIVAIEN PADVSV ISS RNTGQRAVLK FAAATGATPI AGRFTPGTFT NQIQAAFREP RLLVVTDPRA DHQPLTEASY VNLPTIALCN TDSPLRY VD IAIPCNNKGA ...String:
(ACE)SGALDVLQM KEEDVLKFLA AGTHLGGTNL DFQMEQYIYK RKSDGIYIIN LKRTWEKLLL AARAIVAIEN PADVSV ISS RNTGQRAVLK FAAATGATPI AGRFTPGTFT NQIQAAFREP RLLVVTDPRA DHQPLTEASY VNLPTIALCN TDSPLRY VD IAIPCNNKGA HSVGLMWWML AREVLRMRGT ISREHAWEVM PDLYFYRDPE EIEKEEQAAA EKAVTKEEFQ GEWTAPAP E FTAAQPEVAD WSEGVQVPAV PIQQFPTEDW SAQPATEDWS AAPTAQATEW VGTTTEWS

+
Macromolecule #17: Host translation inhibitor nsp1

MacromoleculeName: Host translation inhibitor nsp1 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 19.859324 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MESLVPGFNE KTHVQLSLPV LQVRDVLVRG FGDSVEEVLS EARQHLKDGT CGLVEVEKGV LPQLEQPYVF IKRSDARTAP HGHVMVELV AELEGIQYGR SGETLGVLVP HVGEIPVAYR KVLLRKNGNK GAGGHSYGAD LKSFDLGDEL DTDPYEDFQE N WNTKHSSG VTRELMRELN GG

UniProtKB: Replicase polyprotein 1ab

+
Macromolecule #18: Eukaryotic translation initiation factor 1

MacromoleculeName: Eukaryotic translation initiation factor 1 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.752498 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSAIQNLHSF DPFADASKGD DLLPAGTEDY IHIRIQQRNG RKTLTTVQGI ADDYDKKKLV KAFKKKFACN GTVIEHPEYG EVIQLQGDQ RKNICQFLVE IGLAKDDQLK VHGF

UniProtKB: Eukaryotic translation initiation factor 1

+
Macromolecule #19: 40S ribosomal protein eS7, RPS7

MacromoleculeName: 40S ribosomal protein eS7, RPS7 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhinolophus lepidus (bat)
Molecular weightTheoretical: 22.168914 KDa
SequenceString: MFSSSAKIVK PNGEKPDEFE SGISQALLEL EMNSDLKAQL RELNITAAKE IEVGGGRKAI IIFVPVPQLK SFQKIQVRLV RELEKKFSG KHVVFIAQRR ILPKPTRKSR TKNKQKRPRS RTLTAVHDAI LEDLVFPSEI VGKRIRVKLD GSRLIKVHLD K AQQNNVEH ...String:
MFSSSAKIVK PNGEKPDEFE SGISQALLEL EMNSDLKAQL RELNITAAKE IEVGGGRKAI IIFVPVPQLK SFQKIQVRLV RELEKKFSG KHVVFIAQRR ILPKPTRKSR TKNKQKRPRS RTLTAVHDAI LEDLVFPSEI VGKRIRVKLD GSRLIKVHLD K AQQNNVEH KVETFSGVYK KLTGKDVNFE FPEFQL

+
Macromolecule #20: 40S ribosomal protein uS17, RPS11

MacromoleculeName: 40S ribosomal protein uS17, RPS11 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhinolophus lepidus (bat)
Molecular weightTheoretical: 18.468826 KDa
SequenceString:
MADIQTERAY QKQPTIFQNK KRVLLGETGK EKLPRYYKNI GLGFKTPKEA IEGTYIDKKC PFTGNVSIRG RILSGVVTKM KMQRTIVIR RDYLHYIRKY NRFEKRHKNM SVHLSPCFRD VQIGDIVTVG ECRPLSKTVR FNVLKVTKAA GTKKQFQKF

+
Macromolecule #21: 40S ribosomal protein eS30, RPS30

MacromoleculeName: 40S ribosomal protein eS30, RPS30 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhinolophus lepidus (bat)
Molecular weightTheoretical: 6.857185 KDa
SequenceString:
MGKVHGSLAR AGKVRGQTPK VAKQEKKKKK TGRAKRRMQY NRRFVNVVPT FGKKKGPNAN S

+
Macromolecule #22: 40S ribosomal protein eS1, RPS3a

MacromoleculeName: 40S ribosomal protein eS1, RPS3a / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhinolophus lepidus (bat)
Molecular weightTheoretical: 30.002061 KDa
SequenceString: MAVGKNKRLT KGGKKGAKKK VVDPFSKKDW YDVKAPAMFN IRNIGKTLVT RTQGTKIASD GLKGRVFEVS LADLQNDEVA FRKFKLITE DVQGKNCLTN FHGMDLTRDK MCSMVKKWQT MIEAHVDVKT TDGYLLRLFC VGFTKKRNNQ IRKTSYAQHQ Q VRQIRKKM ...String:
MAVGKNKRLT KGGKKGAKKK VVDPFSKKDW YDVKAPAMFN IRNIGKTLVT RTQGTKIASD GLKGRVFEVS LADLQNDEVA FRKFKLITE DVQGKNCLTN FHGMDLTRDK MCSMVKKWQT MIEAHVDVKT TDGYLLRLFC VGFTKKRNNQ IRKTSYAQHQ Q VRQIRKKM MEIMTREVQT NDLKEVVNKL IPDSIGKDIE KACQSIYPLH DVFVRKVKML KKPKFELGKL MELHGEGSSS GK ATGDETG AKVERADGYE PPVQESV

+
Macromolecule #24: 40S ribosomal protein uS3, RPS3

MacromoleculeName: 40S ribosomal protein uS3, RPS3 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhinolophus lepidus (bat)
Molecular weightTheoretical: 26.715344 KDa
SequenceString: MAVQISKKRK FVADGIFKAE LNEFLTRELA EDGYSGVEVR VTPTRTEIII LATRTQNVLG EKGRRIRELT AVVQKRFGFP EGSVELYAE KVATRGLCAI AQAESLRYKL LGGLAVRRAC YGVLRFIMES GAKGCEVVVS GKLRGQRAKS MKFVDGLMIH S GDPVNYYV ...String:
MAVQISKKRK FVADGIFKAE LNEFLTRELA EDGYSGVEVR VTPTRTEIII LATRTQNVLG EKGRRIRELT AVVQKRFGFP EGSVELYAE KVATRGLCAI AQAESLRYKL LGGLAVRRAC YGVLRFIMES GAKGCEVVVS GKLRGQRAKS MKFVDGLMIH S GDPVNYYV DTAVRHVLLR QGVLGIKVKI MLPWDPSGKI GPKKPLPDHV SIVEPKDEIL PTTPISEQKG GKPEPPAMPQ PV PTA

+
Macromolecule #23: 18S ribosomal RNA

MacromoleculeName: 18S ribosomal RNA / type: rna / ID: 23 / Number of copies: 1
Source (natural)Organism: Rhinolophus lepidus (bat)
Molecular weightTheoretical: 447.71275 KDa
SequenceString: UACCUGGUUG AUCCUGCCAG UAGCAU(A2M)UGC UUG(PSU)C(PSU)CAAA GAUUAAGCCA UGCAUGUCUA AGUACGCA C GGCUGGUACA GUGAAACUGC GAA(PSU)GGCUC(A2M) UUAAA(PSU)CAG(PSU) UAUGGU(OMU)CC(PSU) U (OMU)GGUCGCU ...String:
UACCUGGUUG AUCCUGCCAG UAGCAU(A2M)UGC UUG(PSU)C(PSU)CAAA GAUUAAGCCA UGCAUGUCUA AGUACGCA C GGCUGGUACA GUGAAACUGC GAA(PSU)GGCUC(A2M) UUAAA(PSU)CAG(PSU) UAUGGU(OMU)CC(PSU) U (OMU)GGUCGCU CGCUCCUCUC CUACUUGGAU AACUGUGGUA (A2M)UUCUAG(A2M)GC UAA(OMU)A(OMC)AUGC CG ACGGGCG CUGACCCCCC UCGCGGGGGG GAUGCGUGCA (PSU)UUAUCAGAU CAAAACCAAC CCGGUCAGCC UCCCCUCGG CCCCGGCCGG GGGGCGGGCG CCGGCGGCUU UGGUGACUCU AGAUAACCUC GGGCCGAUCG CACGCCCCCC GUGGCGGCGA CGACCCAUU CGAACGUC(OMU)G CCCUAUCAAC UUUCGAUGGU AGUCGCCGUG CCUACCAUGG UGACCACGGG (PSU)GA CGGGGA AUCAGGGUUC GAU(OMU)CCGGAG A(OMG)GGAGCCUG AGAAACGGCU ACCACAU(OMC)CA AGG(A2M)AGGC A GCAGGCGCGC (A2M)AAUUACCCA CUCCCGACCC GGGGA(OMG)GU(A2M)G UGA(OMC)GAAAAA UAACAAUACA GGA CUCUUU CGAGGCCCUG UAAUUGGAAU GAGUCCACU(PSU) UAA(A2M)UCCUUU AACGAGG(A2M)UC CAUUGGAG (OMG) GCAAGUC(PSU)GG UGCCAGCAGC CGCGG(OMU)AAUU CCAGCUCCAA UA(OMG)CGUA(PSU)A(PSU) UAAAG UUGC UGCAGUU(A2M)AA AAGCUCGUAG (PSU)U(OMG)GA(PSU)CUUG GGAGCGGGCG GGCGGUCCGC CGCGAGGCGA GCCACCGCC CGUCCCCGCC CCUUGCCUCU CGGCGCCCCC UCGAUGCUCU UAGCUGAGUG UCCCGCGGGG CCCGAAG (OMC)G (OMU)UUACUUUGA AAAAA(PSU)(PSU)AGA GUG(PSU)UCAAAG CAGGCCCGAG CCGCCUGGAU ACCGCAGC U AGGAA(PSU)AA(PSU)G GAAUAGGACC GCGGUUCUAU UUUGUUGGUU UUCGGAACUG AGGCCAUGAU UAAGAGGGAC G GCCGGGGG CAUUCGUAUU GCGCCGCUAG AGGUGAAAU(PSU) CUUGGACCGG CGCAAGACGG ACCAGAGCGA AAGCAUU (PSU)G CCAAGAAUGU UUUCAUUAAU CAAGA(A2M)CGAA AGUCGGAGG(PSU) (PSU)CGAAGACGA (PSU)CAGAUAC C GUCGUAGUUC CGACCA(PSU)AAA CGAUGCCGAC UGGCGAUGCG GCGGCGUUAU UCCCAUGACC CGCCGGGCAG C (PSU)UCCGGGA AACCAAAGUC UUUGGGUUCC GGGGGGAGUA (PSU)GG(PSU)UGCAAA GCUGAAACUU AAAGGAAUUG ACGGA(PSU)GUA CACACCG(OMC)CC GUCGCUACUA CCGAUUGGAU GGUUUAGUGA GGCCCUCGGA UCGGCCCCGC CGG GGUCGG CCCACGGCCC UGGCGGAGCG CUGAGAAGAC GGUCGAACU(OMU) GACUAUCUAG AGGAAGUAAA AGUCGUA (6MZ)C AAGGUUUC(4AC)G UAGGUG(MA6)(MA6)CC UGCGGAAGGA UCAUUA

+
Macromolecule #25: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 25 / Number of copies: 57 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #26: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 26 / Number of copies: 13 / Formula: K
Molecular weightTheoretical: 39.098 Da

+
Macromolecule #27: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 27 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #28: water

MacromoleculeName: water / type: ligand / ID: 28 / Number of copies: 1640 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 30.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: NONE / Details: Ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1205667
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more