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- EMDB-49636: SARS-CoV-2 nsp1 bound to the Rhinolophus lepidus 40S ribosome (lo... -

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Basic information

Entry
Database: EMDB / ID: EMD-49636
TitleSARS-CoV-2 nsp1 bound to the Rhinolophus lepidus 40S ribosome (local refinement of the 40S head)
Map data
Sample
  • Complex: SARS-CoV-2 nsp1-Rhinolophus lepidus ribosome complex, head map
    • Complex: SARS-CoV-2 nsp1
    • Complex: Eukaryotic translation initiation factor 1
    • Organelle or cellular component: Rhinolophus lepidus ribosome
      • Protein or peptide: x 15 types
      • RNA: x 1 types
  • Ligand: x 4 types
KeywordsSARS-CoV-2 / RIBOSOME / Seattle Structural Genomics Center for Infectious Disease / SSGCID
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

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Structure visualization

Supplemental images

emd_49636.png

Downloads & links

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Map

FileDownload / File: emd_49636.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)

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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-0.06252181 - 0.2698706
Average (Standard dev.)0.00033581076 (±0.005757029)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Additional map: #1

Fileemd_49636_additional_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_49636_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49636_half_map_2.map
Projections & Slices
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Sample components

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

EntireName: SARS-CoV-2 nsp1-Rhinolophus lepidus ribosome complex, head map
Components
  • Complex: SARS-CoV-2 nsp1-Rhinolophus lepidus ribosome complex, head map
    • Complex: SARS-CoV-2 nsp1
    • Complex: Eukaryotic translation initiation factor 1
    • Organelle or cellular component: Rhinolophus lepidus ribosome
      • Protein or peptide: 40S ribosomal protein uS3, RPS3
      • Protein or peptide: 40S ribosomal protein eS10, RPS10
      • Protein or peptide: 40S ribosomal protein eS12, RPS12
      • Protein or peptide: 40S ribosomal protein uS19, RPS15
      • Protein or peptide: 40S ribosomal protein uS9, RPS16
      • Protein or peptide: 40S ribosomal protein eS17, RPS17
      • Protein or peptide: 40S ribosomal protein uS13, RPS18
      • Protein or peptide: 40S ribosomal protein eS19, RPS19
      • Protein or peptide: 40S ribosomal protein uS10, RPS20
      • Protein or peptide: 40S ribosomal protein eS25, RPS25
      • Protein or peptide: 40S ribosomal protein eS31, RPS27a
      • Protein or peptide: 40S ribosomal protein eS28, RPS28
      • Protein or peptide: 40S ribosomal protein uS14, RPS29
      • RNA: 18S ribosomal RNA
      • Protein or peptide: 40S ribosomal protein uS7, RPS5
      • Protein or peptide: RACK1
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: POTASSIUM ION
  • Ligand: water

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

SupramoleculeName: SARS-CoV-2 nsp1-Rhinolophus lepidus ribosome complex, head map
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#16

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Supramolecule #3: SARS-CoV-2 nsp1

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

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Supramolecule #4: Eukaryotic translation initiation factor 1

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

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Supramolecule #2: Rhinolophus lepidus ribosome

SupramoleculeName: Rhinolophus lepidus ribosome / type: organelle_or_cellular_component / ID: 2 / Parent: 1 / Macromolecule list: #1-#16
Source (natural)Organism: Rhinolophus lepidus (bat)

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Macromolecule #1: 40S ribosomal protein uS3, RPS3

MacromoleculeName: 40S ribosomal protein uS3, RPS3 / type: protein_or_peptide / ID: 1 / 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

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Macromolecule #2: 40S ribosomal protein eS10, RPS10

MacromoleculeName: 40S ribosomal protein eS10, RPS10 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhinolophus lepidus (bat)
Molecular weightTheoretical: 18.933846 KDa
SequenceString:
MLMPKKNRIA IYELLFKEGV MVAKKDVHMP KHPELADKNV PNLHVMKAMQ SLKSRGYVKE QFAWRHFYWY LTNEGIQYLR DYLHLPPEI VPATLRRSRP ETGRPRPKGL EGERPARLTR GEADRDTYRR SAVPPGADKK AEAGAGSATE FQFRGGFGRG R GQPPQ

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Macromolecule #3: 40S ribosomal protein eS12, RPS12

MacromoleculeName: 40S ribosomal protein eS12, RPS12 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhinolophus lepidus (bat)
Molecular weightTheoretical: 14.538987 KDa
SequenceString:
MAEEGIAAGG VMDVNTALQE VLKTALIHDG LARGIREAAK ALDKRQAHLC VLASNCDEPM YVKLVEALCA EHQINLIKVD DNKKLGEWV GLCKIDREGK PRKVVGCSCV VVKDYGKESQ AKDVIEEYFK CKK

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Macromolecule #4: 40S ribosomal protein uS19, RPS15

MacromoleculeName: 40S ribosomal protein uS19, RPS15 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhinolophus lepidus (bat)
Molecular weightTheoretical: 17.076207 KDa
SequenceString:
MAEVEQKKKR TFRKFTYRGV DLDQLLDMSY EQLMQLYSAR QRRRLNRGLR RKQHSLLKRL RKAKKEAPPM EKPEVVKTHL RDMIILPEM VGSMVGVYNG KTFNQVEIKP EMIGHYLGEF SITYKPVKHG RPGIGATHSS RFIPLK

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Macromolecule #5: 40S ribosomal protein uS9, RPS16

MacromoleculeName: 40S ribosomal protein uS9, RPS16 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhinolophus lepidus (bat)
Molecular weightTheoretical: 16.477377 KDa
SequenceString:
MPSKGPLQSV QVFGRKKTAT AVAHCKRGNG LIKVNGRPLE MIEPRTLQYK LLEPVLLLGK ERFAGVDIRV RVKGGGHVAQ IYAIRQSIS KALVAYYQKY VDEASKKEIK DILIQYDRTL LVADPRRCES KKFGGPGARA RYQKSYR

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Macromolecule #6: 40S ribosomal protein eS17, RPS17

MacromoleculeName: 40S ribosomal protein eS17, RPS17 / type: protein_or_peptide / ID: 6 / 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

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Macromolecule #7: 40S ribosomal protein uS13, RPS18

MacromoleculeName: 40S ribosomal protein uS13, RPS18 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhinolophus lepidus (bat)
Molecular weightTheoretical: 17.759777 KDa
SequenceString:
MSLVIPEKFQ HILRVLNTNI DGRRKIAFAI TAIKGVGRRY AHVVLRKADI DLTKRAGELT EDEVERVITI MQNPRQYKIP DWFLNRQKD VKDGKYSQVL ANGLDNKLRE DLERLKKIRA HRGLRHFWGL RVRGQHTKTT GRRGRTVGVS KKK

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Macromolecule #8: 40S ribosomal protein eS19, RPS19

MacromoleculeName: 40S ribosomal protein eS19, RPS19 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhinolophus lepidus (bat)
Molecular weightTheoretical: 16.104579 KDa
SequenceString:
MPGVTVKDVN QQEFVRALAA FLKKSGKLKV PEWVDTVKLA KHKELAPYDE NWFYTRAAST ARHLYL(NMM)GGA GVGSMT KIY GGRQRNGVMP SHFSRGSKSV ARRVLQALEG LKMVEKDQDG GRKLTPQGQR DLDRIAGQVA AANKKH

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Macromolecule #9: 40S ribosomal protein uS10, RPS20

MacromoleculeName: 40S ribosomal protein uS10, RPS20 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhinolophus lepidus (bat)
Molecular weightTheoretical: 13.398763 KDa
SequenceString:
MAFKDTGKTP VEPEVAIHRI RITLTSRNVK SLEKVCADLI RGAKEKNLKV KGPVRMPTKT LRITTRKTPC GEGSKTWDRF QMRIHKRLI DLHSPSEIVK QITSISIEPG VEVEVTIADA

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Macromolecule #10: 40S ribosomal protein eS25, RPS25

MacromoleculeName: 40S ribosomal protein eS25, RPS25 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhinolophus lepidus (bat)
Molecular weightTheoretical: 13.776224 KDa
SequenceString:
MPPKDDKKKK DAGKSAKKDK DPVNKSGGKA KKKKWSKGKV RDKLNNLVLF DKATYDKLCK EVPNYKLITP AVVSERLKIR GSLARAALQ ELLSKGLIKL VSKHRAQVIY TRNTKGGDAP AAGEDA

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Macromolecule #11: 40S ribosomal protein eS31, RPS27a

MacromoleculeName: 40S ribosomal protein eS31, RPS27a / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhinolophus lepidus (bat)
Molecular weightTheoretical: 18.004041 KDa
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGGAKKR KKKSYTTPK KNKHKRKKVK LAVLKYYKVD ENGKISRLRR ECPSDECGAG VFMASHFDRH YCGKCCLTYC FNKPEDK

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Macromolecule #12: 40S ribosomal protein eS28, RPS28

MacromoleculeName: 40S ribosomal protein eS28, RPS28 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhinolophus lepidus (bat)
Molecular weightTheoretical: 7.855052 KDa
SequenceString:
MDTSRVQPIK LARVTKVLGR TGSQGQCTQV RVEFMDDTSR SIIRNVKGPV REGDVLTLLE SEREARRLR

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Macromolecule #13: 40S ribosomal protein uS14, RPS29

MacromoleculeName: 40S ribosomal protein uS14, RPS29 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhinolophus lepidus (bat)
Molecular weightTheoretical: 6.690821 KDa
SequenceString:
MGHQQLYWSH PRKFGQGSRS CRVCSNRHGL IRKYGLNMCR QCFRQYAKDI GFIKLD

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Macromolecule #15: 40S ribosomal protein uS7, RPS5

MacromoleculeName: 40S ribosomal protein uS7, RPS5 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhinolophus lepidus (bat)
Molecular weightTheoretical: 22.913453 KDa
SequenceString: MTEWETAAPA VAETPDIKLF GKWSTDDVQI NDISLQDYIA VKEKYAKYLP HSAGRYAAKR FRKAQCPIVE RLTNSMMMHG RNNGKKLMT VRIVKHAFEI IHLLTGENPL QVLVNAIINS GPREDSTRIG RAGTVRRQAV DVSPLRRVNQ AIWLLCTGAR E AAFRNIKT ...String:
MTEWETAAPA VAETPDIKLF GKWSTDDVQI NDISLQDYIA VKEKYAKYLP HSAGRYAAKR FRKAQCPIVE RLTNSMMMHG RNNGKKLMT VRIVKHAFEI IHLLTGENPL QVLVNAIINS GPREDSTRIG RAGTVRRQAV DVSPLRRVNQ AIWLLCTGAR E AAFRNIKT IAECLADELI NAAKGSSNSY AIKKKDELER VAKSNR

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Macromolecule #16: RACK1

MacromoleculeName: RACK1 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhinolophus lepidus (bat)
Molecular weightTheoretical: 35.115652 KDa
SequenceString: MTEQMTLRGT LKGHNGWVTQ IATTPQFPDM ILSASRDKTI IMWKLTRDET NYGIPQRALR GHSHFVSDVV ISSDGQFALS GSWDGTLRL WDLTTGTTTR RFVGHTKDVL SVAFSSDNRQ IVSGSRDKTI KLWNTLGVCK YTVQDESHSE WVSCVRFSPN S SNPIIVSC ...String:
MTEQMTLRGT LKGHNGWVTQ IATTPQFPDM ILSASRDKTI IMWKLTRDET NYGIPQRALR GHSHFVSDVV ISSDGQFALS GSWDGTLRL WDLTTGTTTR RFVGHTKDVL SVAFSSDNRQ IVSGSRDKTI KLWNTLGVCK YTVQDESHSE WVSCVRFSPN S SNPIIVSC GWDKLVKVWN LANCKLKTNH IGHTGYLNTV TVSPDGSLCA SGGKDGQAML WDLNEGKHLY TLDGGDIINA LC FSPNRYW LCAATGPSIK IWDLEGKIIV DELKQEVIST SSKAEPPQCT SLAWSADGQT LFAGYTDNLV RVWQVTIGTR

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Macromolecule #14: 18S ribosomal RNA

MacromoleculeName: 18S ribosomal RNA / type: rna / ID: 14 / Number of copies: 1
Source (natural)Organism: Rhinolophus lepidus (bat)
Molecular weightTheoretical: 603.611188 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 ACGGAAGGG CACCACCAGG AGUGGAGCC(PSU) GCGGC(PSU)UAAU U(PSU)GAC(B8N)CAAC ACGGGAAACC UCACC CGGC (OMC)CGGACACGG ACAGGA(OMU)UGA CAGAUUGAUA GCUCUUUUUC GAUUCCGUGG GUGG(OMU)G(OMG)UGC AUGGC(4AC)GUU CUUAGU(PSU)GGU GGAGCGAUUU GUCUGG(PSU)UAA UUCCGAUAAC GA(A2M)CGAGACU (OMC) UGGCAUGC UAACUAGUUA CGCGACCCCC GAGCGGUCGG CGUCCCCCAA CU(OMU)CU(PSU)A(OMG)AG GGACAAGUGG CGUUCAGCC ACCCGAGAUU GAGCAAUAAC A(OMG)GUCUGUGA UGCCCUUAGA UGUCCGGGGC UGCACGCGCG CUACACU GA CUGGCUCAGC GUGUGCCUAC CCUACGCCGG CAGGCGCGGG UAACCCGUUG AACCCCAUUC GUGAUGGGGA UCGGGGAU U GCAAUUAUUC CCCAUGAACG AG(G7M)AAUUCCC AGUAAGUGCG GGUCAUAAGC UUGCGUUGAU U(A2M)AGUCCCUG C CCUU(PSU)GUA CACACCG(OMC)CC GUCGCUACUA CCGAUUGGAU GGUUUAGUGA GGCCCUCGGA UCGGCCCCGC CGGG GUCGG CCCACGGCCC UGGCGGAGCG CUGAGAAGAC GGUCGAACU(OMU) GACUAUCUAG AGGAAGUAAA AGUCGUA (6MZ)C AAGGUUUC(4AC)G UAGGUG(MA6)(MA6)CC UGCGGAAGGA UCAUUA

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Macromolecule #17: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 17 / Number of copies: 21 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #18: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 18 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #19: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 19 / Number of copies: 9 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #20: water

MacromoleculeName: water / type: ligand / ID: 20 / Number of copies: 827 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 7.4
VitrificationCryogen name: ETHANE

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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

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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)

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  • 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

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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

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