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- EMDB-47303: iSAT-PNA-RA20, RA20-B-c class -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-47303
TitleiSAT-PNA-RA20, RA20-B-c class
Map dataiSAT-PNA-RA20, RA20-B-c class, reconstructed by 3D Flex in cryoSPARC
Sample
  • Complex: iSAT-PNA-RA20 50S ribosomal subunit assembly intermediate
    • RNA: x 1 types
    • Protein or peptide: x 13 types
Keywords50S subunit / assembly intermediate / RNA-protein complex / ribosome
Function / homology
Function and homology information


transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / negative regulation of cytoplasmic translation / translation repressor activity / assembly of large subunit precursor of preribosome / ribosome assembly / cytosolic ribosome assembly / DNA-templated transcription termination / mRNA 5'-UTR binding ...transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / negative regulation of cytoplasmic translation / translation repressor activity / assembly of large subunit precursor of preribosome / ribosome assembly / cytosolic ribosome assembly / DNA-templated transcription termination / mRNA 5'-UTR binding / large ribosomal subunit / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / : / Ribosomal protein L17 signature. / : / : / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type ...Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / : / Ribosomal protein L17 signature. / : / : / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / : / Ribosomal protein L20 / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 superfamily / Ribosomal protein L21 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L24 / Ribosomal protein L13, bacterial-type / Ribosomal protein L3, bacterial/organelle-type / 50S ribosomal protein uL4 / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L29, conserved site / Ribosomal protein L29 signature. / Ribosomal protein L13 signature. / Ribosomal protein L13, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein L22 signature. / Ribosomal protein L14P, conserved site / Ribosomal protein L14 signature. / Ribosomal L29 protein / Ribosomal protein L29/L35 / Ribosomal protein L29/L35 superfamily / Ribosomal protein L24 signature. / Ribosomal protein L24/L26, conserved site / KOW (Kyprides, Ouzounis, Woese) motif. / Ribosomal protein L13 / Ribosomal protein L13 / Ribosomal protein L13 superfamily / Ribosomal protein L23 / Ribosomal protein L25/L23 / Ribosomal protein L14p/L23e / Ribosomal protein L14P / Ribosomal protein L14 superfamily / Ribosomal protein L14p/L23e / Ribosomal protein L22/L17 / Ribosomal protein L22p/L17e / Ribosomal protein L22/L17 superfamily / Ribosomal protein L26/L24, KOW domain / Ribosomal protein L3, conserved site / Ribosomal protein L3 signature. / Ribosomal protein L3 / Ribosomal protein L3 / Ribosomal protein L4/L1e / Ribosomal protein L4 domain superfamily / Ribosomal protein L4/L1 family / Translation protein SH3-like domain superfamily / Ribosomal protein L23/L15e core domain superfamily / KOW motif / KOW / Translation protein, beta-barrel domain superfamily / Ribosomal protein L2, domain 2 / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL17 ...Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL22
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.27 Å
AuthorsSheng K / Dong X / Lee J
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM136412 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM053757 United States
CitationJournal: To Be Published
Title: Domain consolidation in bacterial 50S assembly revealed by anti-sense oligonucleotide probing
Authors: Sheng K / Dong X / Aiyer S / Lee J / Djordjevic-Marquardt S / Lyumkis D / Williamson JR
History
DepositionOct 14, 2024-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47303.png

Downloads & links

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Map

FileDownload / File: emd_47303.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationiSAT-PNA-RA20, RA20-B-c class, reconstructed by 3D Flex in cryoSPARC
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 400 pix.
= 420. Å		1.05 Å/pix.
x 400 pix.
= 420. Å		1.05 Å/pix.
x 400 pix.
= 420. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00642
Minimum - Maximum-0.009091184 - 0.030919734
Average (Standard dev.)0.00015070429 (±0.0012981895)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 419.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_47303_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_47303_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : iSAT-PNA-RA20 50S ribosomal subunit assembly intermediate

EntireName: iSAT-PNA-RA20 50S ribosomal subunit assembly intermediate
Components
  • Complex: iSAT-PNA-RA20 50S ribosomal subunit assembly intermediate
    • RNA: 23S rRNA
    • Protein or peptide: Large ribosomal subunit protein bL34
    • Protein or peptide: Large ribosomal subunit protein uL3
    • Protein or peptide: Large ribosomal subunit protein uL4
    • Protein or peptide: Large ribosomal subunit protein uL13
    • Protein or peptide: Large ribosomal subunit protein uL14
    • Protein or peptide: Large ribosomal subunit protein bL17
    • Protein or peptide: Large ribosomal subunit protein bL19
    • Protein or peptide: Large ribosomal subunit protein bL20
    • Protein or peptide: Large ribosomal subunit protein bL21
    • Protein or peptide: Large ribosomal subunit protein uL22
    • Protein or peptide: Large ribosomal subunit protein uL23
    • Protein or peptide: Large ribosomal subunit protein uL24
    • Protein or peptide: Large ribosomal subunit protein uL29

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Supramolecule #1: iSAT-PNA-RA20 50S ribosomal subunit assembly intermediate

SupramoleculeName: iSAT-PNA-RA20 50S ribosomal subunit assembly intermediate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600

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Macromolecule #1: 23S rRNA

MacromoleculeName: 23S rRNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 565.405812 KDa
SequenceString: UAAGCGACUA AGCGUACACG GUGGAUGCCC UGGCAGUCAG AGGCGAUGAA GGACGUGCUA AUCUGCGAUA AGCGUCGGUA AGGUGAUAU GAACCGUUAU AACCGGCGAU UUCCGAAUGG GGAAACCCAG UGUGUUUCGA CACACUAUCA UUAACUGAAU C CAUAGGUU ...String:
UAAGCGACUA AGCGUACACG GUGGAUGCCC UGGCAGUCAG AGGCGAUGAA GGACGUGCUA AUCUGCGAUA AGCGUCGGUA AGGUGAUAU GAACCGUUAU AACCGGCGAU UUCCGAAUGG GGAAACCCAG UGUGUUUCGA CACACUAUCA UUAACUGAAU C CAUAGGUU AAUGAGGCGA ACCGGGGGAA CUGAAACAUC UAAGUACCCC GAGGAAAAGA AAUCAACCGA GAUUCCCCCA GU AGCGGCG AGCGAACGGG GAGCAGCCCA GAGCCUGAAU CAGUGUGUGU GUUAGUGGAA GCGUCUGGAA AGGCGCGCGA UAC AGGGUG ACAGCCCCGU ACACAAAAAU GCACAUGCUG UGAGCUCGAU GAGUAGGGCG GGAGGUAUCC UGUCUGAAUA UGGG GGGAC CAUCCUCCAA GGCUAAAUAC UCCUGACUGA CCGAUAGUGA ACCAGUACCG UGAGGGAAAG GCGAAAAGAA CCCCG GCGA GGGGAGUGAA AAAGAACCUG AAACCGUGUA CGUACAAGCA GUGGGAGCAC GCUUAGGCGU GUGACUGCGU UAAUGG GUC AGCGACUUAU AUUCUGUAGC AAGGUUAACC GAAUAGGGGA GCCGAAGGGA AACCGAGUCU UAACUGGGCG UUAAGUU GC AGGGUAUAGA CCCGAAACCC GGUGAUCUAG CCUCAAACCG GGAGAUAGCU GGUUCUCCCC GAAAGCUAUU UAGGUAGC G CCUCGUGAAU UCAUCGAAUG UUAUCACGGG AGACACACGG CGGG(PSU)GCUAA CGUCCGUCGU GAAGAGGGAA ACAAC CCAG ACCGCCAGCU AAGGUCCCAA AGUCAUGGUU AAGUGGGAAA CGGGGCUAAA CCAUGCACCG AAGCUGCGGC AGCGAC GCU UAUGCGUUGU UGGGUAGGGG AGCGUUCUGU AAGCCUGCGA AGGUGUGCUG UGAGGCAUGC UGGAGGUAUC AGAAGUG CG AAUGCUGACA UAAGUAACGA UAAAGCGGGU GAAAAGCCCG CUCGCCGGAA GACCAAGGGU UCCUGUCCAA CGUUAAUC G GGGCAGGGUG AGUCGACCCC UAAGGCGAGG CCGAAAGGCG UAGUCGAUGG GAAACAGGUU AAUAUUCCUG UACUUGGUG UUACUGCGAA GGGGGGACGG AGAAGGCUAU GUUGGCCGGG CGACGGUUGU CCCGGUUUAA GCGUGUAGGC UGGUUUUCCA GGCAAAUCC GGAAAAUCAA GGCUGAGGCG UGAUGACGAG GCACUACGGU GCUGAAGCAA CAAAUGCCCU GCUUCCAGGA A AAGCCUCU AAGCAUCAGG UAACAUCAAA UCGUACCCCA AACCGACAC(6MZ) GGUGGUCAGG UAGAGAAUAC CAAGGCGC U UGAGAGAACU CGGGUGAAGG AACUAGGCAA AAUGGUGCCG UGCACGCUGA UAUGUAGGUG AGGUCCCUCG CGGAUGGAG CUGAAAUCAG UCGAAGAUAC CAGCUGGCUG AUGGCCAGGC UGUCUCCACC CGAGACUCAG UGCUGGAGAA CUGAGGGGGG CUGCUCCUA GUACGAGAGG ACCGGAGUGG ACGCAUCACU GGUGUUCGGG UUGUCAUGCC AAUGGCACUG CCCGGUAGCU A AAUGCGGA AGAGAUAAGG AAACUUGCCC CGAGAUGAGU UCUCCCUGAC CCUUUAAGGG UCCUGAAGGA ACGUUGAAGA CG ACGACGU UGAUAGGCCG GGUGUGUAAG CGCAGCGAUG CGUUGAGCUA ACCGGUACUA AUGAACCGUG AGG

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Macromolecule #2: Large ribosomal subunit protein bL34

MacromoleculeName: Large ribosomal subunit protein bL34 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 4.290116 KDa
SequenceString:
VLKRNRSHGF RARMATKNGR QVLARRRAKG RARLTVS

UniProtKB: Large ribosomal subunit protein bL34

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Macromolecule #3: Large ribosomal subunit protein uL3

MacromoleculeName: Large ribosomal subunit protein uL3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 21.76384 KDa
SequenceString: GKKVGMTRIF TEDGVSIPVT VIEVEANRVT QVKDLANDGY RAIQVTTGAK KANRVTKPEA GHFAKAGVEA GRGLWEFRLA EGEEFTVGQ SISVELFADV KKVDVTGTSK GKGFAGTVKR WNFRTQDATH GNSLSHRVPG SIGQNQTPGK VFKGKKMAGQ M GNERVTVQ ...String:
GKKVGMTRIF TEDGVSIPVT VIEVEANRVT QVKDLANDGY RAIQVTTGAK KANRVTKPEA GHFAKAGVEA GRGLWEFRLA EGEEFTVGQ SISVELFADV KKVDVTGTSK GKGFAGTVKR WNFRTQDATH GNSLSHRVPG SIGQNQTPGK VFKGKKMAGQ M GNERVTVQ SLDVVRVDAE RNLLLVKGAV PGATGSDLIV KPAVKA

UniProtKB: Large ribosomal subunit protein uL3

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Macromolecule #4: Large ribosomal subunit protein uL4

MacromoleculeName: Large ribosomal subunit protein uL4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 22.121566 KDa
SequenceString: MELVLKDAQS ALTVSETTFG RDFNEALVHQ VVVAYAAGAR QGTRAQKTRA EVTGSGKKPW RQKGTGRARS GSIKSPIWRS GGVTFAARP QDHSQKVNKK MYRGALKSIL SELVRQDRLI VVEKFSVEAP KTKLLAQKLK DMALEDVLII TGELDENLFL A ARNLHKVD ...String:
MELVLKDAQS ALTVSETTFG RDFNEALVHQ VVVAYAAGAR QGTRAQKTRA EVTGSGKKPW RQKGTGRARS GSIKSPIWRS GGVTFAARP QDHSQKVNKK MYRGALKSIL SELVRQDRLI VVEKFSVEAP KTKLLAQKLK DMALEDVLII TGELDENLFL A ARNLHKVD VRDATGIDPV SLIAFDKVVM TADAVKQVEE MLA

UniProtKB: Large ribosomal subunit protein uL4

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Macromolecule #5: Large ribosomal subunit protein uL13

MacromoleculeName: Large ribosomal subunit protein uL13 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 16.050606 KDa
SequenceString:
MKTFTAKPET VKRDWYVVDA TGKTLGRLAT ELARRLRGKH KAEYTPHVDT GDYIIVLNAD KVAVTGNKRT DKVYYHHTGH IGGIKQATF EEMIARRPER VIEIAVKGML PKGPLGRAMF RKLKVYAGNE HNHAAQQPQV LDI

UniProtKB: Large ribosomal subunit protein uL13

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Macromolecule #6: Large ribosomal subunit protein uL14

MacromoleculeName: Large ribosomal subunit protein uL14 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 12.080289 KDa
SequenceString:
NVADNSGARR VMCIKVLGGS HRRYAGVGDI IKITIKEAIP RGKVKKGDVL KAVVVRTKKG VRRPDGSVIR FDGNACVLLN NNSEQPIGT RIFGPVTREL RSEKFMKIIS L

UniProtKB: Large ribosomal subunit protein uL14

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Macromolecule #7: Large ribosomal subunit protein bL17

MacromoleculeName: Large ribosomal subunit protein bL17 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 13.721938 KDa
SequenceString:
MRHRKSGRQL NRNSSHRQAM FRNMAGSLVR HEIIKTTLPK AKELRRVVEP LITLAKTDSV ANRRLAFART RDNEIVAKLF NELGPRFAS RAGGYTRILK CGFRAGDNAP MAYIELVDRS E

UniProtKB: Large ribosomal subunit protein bL17

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Macromolecule #8: Large ribosomal subunit protein bL19

MacromoleculeName: Large ribosomal subunit protein bL19 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 12.941005 KDa
SequenceString:
NIIKQLEQEQ MKQDVPSFRP GDTVEVKVWV VEGSKKRLQA FEGVVIAIRN RGLHSAFTVR KISNGEGVER VFQTHSPVVD SISVKRRGA VRKAKLYYLR ERTGKAARIK ERLN

UniProtKB: Large ribosomal subunit protein bL19

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Macromolecule #9: Large ribosomal subunit protein bL20

MacromoleculeName: Large ribosomal subunit protein bL20 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 13.396828 KDa
SequenceString:
ARVKRGVIAR ARHKKILKQA KGYYGARSRV YRVAFQAVIK AGQYAYRDRR QRKRQFRQLW IARINAAARQ NGISYSKFIN GLKKASVEI DRKILADIAV FDKVAFTALV EKAKAALA

UniProtKB: Large ribosomal subunit protein bL20

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Macromolecule #10: Large ribosomal subunit protein bL21

MacromoleculeName: Large ribosomal subunit protein bL21 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 11.586374 KDa
SequenceString:
MYAVFQSGGK QHRVSEGQTV RLEKLDIATG ETVEFAEVLM IANGEEVKIG VPFVDGGVIK AEVVAHGRGE KVKIVKFRRR KHYRKQQGH RQWFTDVKIT GISA

UniProtKB: Large ribosomal subunit protein bL21

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Macromolecule #11: Large ribosomal subunit protein uL22

MacromoleculeName: Large ribosomal subunit protein uL22 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 12.253359 KDa
SequenceString:
METIAKHRHA RSSAQKVRLV ADLIRGKKVS QALDILTYTN KKAAVLVKKV LESAIANAEH NDGADIDDLK VTKIFVDEGP SMKRIMPRA KGRADRILKR TSHITVVVSD R

UniProtKB: Large ribosomal subunit protein uL22

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Macromolecule #12: Large ribosomal subunit protein uL23

MacromoleculeName: Large ribosomal subunit protein uL23 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 10.546472 KDa
SequenceString:
MIREERLLKV LRAPHVSEKA STAMEKSNTI VLKVAKDATK AEIKAAVQKL FEVEVEVVNT LVVKGKVKRH GQRIGRRSDW KKAYVTLKE GQNL

UniProtKB: Large ribosomal subunit protein uL23

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Macromolecule #13: Large ribosomal subunit protein uL24

MacromoleculeName: Large ribosomal subunit protein uL24 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 11.078874 KDa
SequenceString:
AAKIRRDDEV IVLTGKDKGK RGKVKNVLSS GKVIVEGINL VKKHQKPVPA LNQPGGIVEK EAAIQVSNVA IFNAATGKAD RVGFRFEDG KKVRFFKSNS ETI

UniProtKB: Large ribosomal subunit protein uL24

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Macromolecule #14: Large ribosomal subunit protein uL29

MacromoleculeName: Large ribosomal subunit protein uL29 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 7.286464 KDa
SequenceString:
MKAKELREKS VEELNTELLN LLREQFNLRM QAASGQLQQS HLLKQVRRDV ARVKTLLNEK AGA

UniProtKB: Large ribosomal subunit protein uL29

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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
Component:
ConcentrationFormulaName
50.0 mMC4H11NO3Tris Hydrochloride
100.0 mMNH4ClAmmonium Chloride
10.0 mMMgCl2Magnesium Chloride
0.5 mMC10H16N2O8Ethylenediaminetetraacetic Acid
6.0 mMC2H6OSBeta-mercaptoethanol

Details: Most of the sucrose was removed by spin concentration.
GridModel: Au-flat 1.2/1.3 / Material: GOLD
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV / Details: 3 microliter of the sample was added..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average exposure time: 2.0 sec. / Average electron dose: 25.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Homogeneous refinement in CryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.27 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 9000
Initial angle assignmentType: OTHER / Details: Homogeneous refinement in CryoSPARC
Final angle assignmentType: OTHER / Details: 3D Flex model in cryoSAPRC

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Atomic model buiding 1

Initial model
PDB IDChain

4ybb

chain_id: CA, source_name: PDB, initial_model_type: experimental model

8rpy

chain_id: D, source_name: PDB, initial_model_type: experimental model

8rpy

chain_id: E, source_name: PDB, initial_model_type: experimental model

8rpy

chain_id: J, source_name: PDB, initial_model_type: experimental model

8rpy

chain_id: K, source_name: PDB, initial_model_type: experimental model

8rpy

chain_id: N, source_name: PDB, initial_model_type: experimental model

8rpy

chain_id: P, source_name: PDB, initial_model_type: experimental model

8rpy

chain_id: Q, source_name: PDB, initial_model_type: experimental model

8rpy

chain_id: R, source_name: PDB, initial_model_type: experimental model

8rpy

chain_id: S, source_name: PDB, initial_model_type: experimental model

8rpy

chain_id: T, source_name: PDB, initial_model_type: experimental model

8rpy

chain_id: U, source_name: PDB, initial_model_type: experimental model

8rpy

chain_id: Y, source_name: PDB, initial_model_type: experimental model

8rpy

chain_id: 2, source_name: PDB, initial_model_type: experimental model
DetailsThe atomic model was fitted into a low resolution (5 Angstrom) EM map; therefore the coordinates should only serve as a general visual representation and should not be looked into detail. Initial docking of the atomic model was done in ChimeraX. Coot and Phenix were used for real-space refinements. Geometry minimization in Phenix was used to improve the RNA atomic model.
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 120.42 / Target criteria: Comprehensive validation (cryo-EM)
Output model

PDB-9dyg:
iSAT-PNA-RA20, RA20-B-c class

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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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