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- EMDB-12216: pre-50S-ObgE particle state 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-12216
Titlepre-50S-ObgE particle state 2
Map data
Sample
  • Complex: ribosomal pre-50S assembly intermediate state 2
    • RNA: x 2 types
    • Protein or peptide: x 29 types
  • Ligand: x 3 types
KeywordsRIBOSOME / pre-50S / ribosome biogenesis / ribosome assembly
Function / homology
Function and homology information


guanyl ribonucleotide binding / dormancy process / negative regulation of ribosome biogenesis / negative regulation of cytoplasmic translational initiation / guanosine tetraphosphate binding / stringent response / ribosomal large subunit binding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity ...guanyl ribonucleotide binding / dormancy process / negative regulation of ribosome biogenesis / negative regulation of cytoplasmic translational initiation / guanosine tetraphosphate binding / stringent response / ribosomal large subunit binding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translational termination / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / response to reactive oxygen species / chromosome segregation / regulation of cell growth / translational initiation / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / GDP binding / large ribosomal subunit / ribosome binding / 5S rRNA binding / large ribosomal subunit rRNA binding / transferase activity / ribosomal large subunit assembly / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / GTPase activity / mRNA binding / GTP binding / magnesium ion binding / DNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
GTP1/OBG, conserved site / GTP1/OBG family signature. / GTP1/OBG domain / GTP-binding protein Obg/CgtA / GTP1/OBG domain superfamily / OBG-type GTPase / GTP1/OBG / Obg domain profile. / Protein Iojap/ribosomal silencing factor RsfS / Ribosomal silencing factor during starvation ...GTP1/OBG, conserved site / GTP1/OBG family signature. / GTP1/OBG domain / GTP-binding protein Obg/CgtA / GTP1/OBG domain superfamily / OBG-type GTPase / GTP1/OBG / Obg domain profile. / Protein Iojap/ribosomal silencing factor RsfS / Ribosomal silencing factor during starvation / OBG-type guanine nucleotide-binding (G) domain / OBG-type guanine nucleotide-binding (G) domain profile. / 50S ribosome-binding GTPase / GTP binding domain / Ribosomal protein L25, short-form / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Nucleotidyltransferase superfamily / Ribosomal protein L11, conserved site / : / Ribosomal protein L11 signature. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L17 signature. / Ribosomal protein L11, N-terminal / Ribosomal L25p family / Ribosomal protein L11, N-terminal domain / Ribosomal protein L25 / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11, RNA binding domain / Ribosomal protein L11/L12 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L32p, bacterial type / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / : / : / Ribosomal protein L28 / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L5, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L20 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L34, conserved site / Ribosomal L28 family / Ribosomal protein L34 signature. / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 superfamily / Ribosomal protein L30, bacterial-type / : / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal L32p protein family
Similarity search - Domain/homology
Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL33 ...Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein uL13 / Ribosomal silencing factor RsfS / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / GTPase ObgE/CgtA / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein bL25
Similarity search - Component
Biological speciesEscherichia coli (strain K12) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsHilal T / Nikolay R
Funding support Germany, 3 items
OrganizationGrant numberCountry
German Research Foundation (DFG)FOR1805 Germany
German Research Foundation (DFG)SFB740 Germany
Human Frontier Science Program (HFSP)RPG0008/2014 Germany
CitationJournal: Mol Cell / Year: 2021
Title: Snapshots of native pre-50S ribosomes reveal a biogenesis factor network and evolutionary specialization.
Authors: Rainer Nikolay / Tarek Hilal / Sabine Schmidt / Bo Qin / David Schwefel / Carlos H Vieira-Vieira / Thorsten Mielke / Jörg Bürger / Justus Loerke / Kazuaki Amikura / Timo Flügel / Takuya ...Authors: Rainer Nikolay / Tarek Hilal / Sabine Schmidt / Bo Qin / David Schwefel / Carlos H Vieira-Vieira / Thorsten Mielke / Jörg Bürger / Justus Loerke / Kazuaki Amikura / Timo Flügel / Takuya Ueda / Matthias Selbach / Elke Deuerling / Christian M T Spahn /
Abstract: Ribosome biogenesis is a fundamental multi-step cellular process that culminates in the formation of ribosomal subunits, whose production and modification are regulated by numerous biogenesis factors. ...Ribosome biogenesis is a fundamental multi-step cellular process that culminates in the formation of ribosomal subunits, whose production and modification are regulated by numerous biogenesis factors. In this study, we analyze physiologic prokaryotic ribosome biogenesis by isolating bona fide pre-50S subunits from an Escherichia coli strain with the biogenesis factor ObgE, affinity tagged at its native gene locus. Our integrative structural approach reveals a network of interacting biogenesis factors consisting of YjgA, RluD, RsfS, and ObgE on the immature pre-50S subunit. In addition, our study provides mechanistic insight into how the GTPase ObgE, in concert with other biogenesis factors, facilitates the maturation of the 50S functional core and reveals both conserved and divergent evolutionary features of ribosome biogenesis between prokaryotes and eukaryotes.
History
DepositionJan 18, 2021-
Header (metadata) releaseMay 12, 2021-
Map releaseMay 12, 2021-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7bl3
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12216.png

Downloads & links

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Map

FileDownload / File: emd_12216.map.gz / Format: CCP4 / Size: 75.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.24 Å/pix.
x 270 pix.
= 334.8 Å		1.24 Å/pix.
x 270 pix.
= 334.8 Å		1.24 Å/pix.
x 270 pix.
= 334.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.24 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.5 / Movie #1: 2.5
Minimum - Maximum-6.1498947 - 12.748112000000001
Average (Standard dev.)0.034337554 (±0.8049399)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions270270270
Spacing270270270
CellA=B=C: 334.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.241.241.24
M x/y/z270270270
origin x/y/z0.0000.0000.000
length x/y/z334.800334.800334.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS270270270
D min/max/mean-6.15012.7480.034

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Supplemental data

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Sample components

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Entire : ribosomal pre-50S assembly intermediate state 2

EntireName: ribosomal pre-50S assembly intermediate state 2
Components
  • Complex: ribosomal pre-50S assembly intermediate state 2
    • RNA: 23S ribosomal RNA
    • RNA: 5S ribosomal RNA
    • Protein or peptide: GTPase ObgE/CgtA
    • Protein or peptide: 50S ribosomal protein L31
    • Protein or peptide: 50S ribosomal protein L2
    • Protein or peptide: 50S ribosomal protein L3
    • Protein or peptide: 50S ribosomal protein L4
    • Protein or peptide: 50S ribosomal protein L6
    • Protein or peptide: 50S ribosomal protein L13
    • Protein or peptide: 50S ribosomal protein L15
    • Protein or peptide: 50S ribosomal protein L17
    • Protein or peptide: 50S ribosomal protein L18
    • Protein or peptide: 50S ribosomal protein L20
    • Protein or peptide: 50S ribosomal protein L21
    • Protein or peptide: 50S ribosomal protein L22
    • Protein or peptide: 50S ribosomal protein L23
    • Protein or peptide: 50S ribosomal protein L24
    • Protein or peptide: 50S ribosomal protein L25
    • Protein or peptide: 50S ribosomal protein L27
    • Protein or peptide: 50S ribosomal protein L28
    • Protein or peptide: 50S ribosomal protein L29
    • Protein or peptide: 50S ribosomal protein L30
    • Protein or peptide: 50S ribosomal protein L32
    • Protein or peptide: 50S ribosomal protein L33
    • Protein or peptide: 50S ribosomal protein L34
    • Protein or peptide: 50S ribosomal protein L11
    • Protein or peptide: 50S ribosomal protein L14
    • Protein or peptide: 50S ribosomal protein L19
    • Protein or peptide: Ribosomal silencing factor RsfS
    • Protein or peptide: 50S ribosomal protein L9
    • Protein or peptide: 50S ribosomal protein L5
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: ribosomal pre-50S assembly intermediate state 2

SupramoleculeName: ribosomal pre-50S assembly intermediate state 2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#31
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Molecular weightTheoretical: 1.5 MDa

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Macromolecule #1: 23S ribosomal RNA

MacromoleculeName: 23S ribosomal RNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 946.4335 KDa
SequenceString: GUUGUAAGGU UAAGCGACUA AGCGUACACG GUGGAUGCCC UGGCAGUCAG AGGCGAUGAA GGACGUGCUA AUCUGCGAUA AGCGUCGGU AAGGUGAUAU GAACCGUUAU AACCGGCGAU UUCCGAAUGG GGAAACCCAG UGUGUUUCGA CACACUAUCA U UAACUGAA ...String:
GUUGUAAGGU UAAGCGACUA AGCGUACACG GUGGAUGCCC UGGCAGUCAG AGGCGAUGAA GGACGUGCUA AUCUGCGAUA AGCGUCGGU AAGGUGAUAU GAACCGUUAU AACCGGCGAU UUCCGAAUGG GGAAACCCAG UGUGUUUCGA CACACUAUCA U UAACUGAA UCCAUAGGUU AAUGAGGCGA ACCGGGGGAA CUGAAACAUC UAAGUACCCC GAGGAAAAGA AAUCAACCGA GA UUCCCCC AGUAGCGGCG AGCGAACGGG GAGCAGCCCA GAGCCUGAAU CAGUGUGUGU GUUAGUGGAA GCGUCUGGAA AGG CGCGCG AUACAGGGUG ACAGCCCCGU ACACAAAAAU GCACAUGCUG UGAGCUCGAU GAGUAGGGCG GGACACGUGG UAUC CUGUC UGAAUAUGGG GGGACCAUCC UCCAAGGCUA AAUACUCCUG ACUGACCGAU AGUGAACCAG UACCGUGAGG GAAAG GCGA AAAGAACCCC GGCGAGGGGA GUGAAAAAGA ACCUGAAACC GUGUACGUAC AAGCAGUGGG AGCACGCUUA GGCGUG UGA CUGCGUACCU UUUGUAUAAU GGGUCAGCGA CUUAUAUUCU GUAGCAAGGU UAACCGAAUA GGGGAGCCGA AGGGAAA CC GAGUCUUAAC UGGGCGUUAA GUUGCAGGGU AUAGACCCGA AACCCGGUGA UCUAGCCAUG GGCAGGUUGA AGGUUGGG U AACACUAACU GGAGGACCGA ACCGACUAAU GUUGAAAAAU UAGCGGAUGA CUUGUGGCUG GGGGUGAAAG GCCAAUCAA ACCGGGAGAU AGCUGGUUCU CCCCGAAAGC UAUUUAGGUA GCGCCUCGUG AAUUCAUCUC CGGGGGUAGA GCACUGUUUC GGCAAGGGG GUCAUCCCGA CUUACCAACC CGAUGCAAAC UGCGAAUACC GGAGAAUGUU AUCACGGGAG ACACACGGCG G GUGCUAAC GUCCGUCGUG AAGAGGGAAA CAACCCAGAC CGCCAGCUAA GGUCCCAAAG UCAUGGUUAA GUGGGAAACG AU GUGGGAA GGCCCAGACA GCCAGGAUGU UGGCUUAGAA GCAGCCAUCA UUUAAAGAAA GCGUAAUAGC UCACUGGUCG AGU CGGCCU GCGCGGAAGA UGUAACGGGG CUAAACCAUG CACCGAAGCU GCGGCAGCGA CGCUUAUGCG UUGUUGGGUA GGGG AGCGU UCUGUAAGCC UGCGAAGGUG UGCUGUGAGG CAUGCUGGAG GUAUCAGAAG UGCGAAUGCU GACAUAAGUA ACGAU AAAG CGGGUGAAAA GCCCGCUCGC CGGAAGACCA AGGGUUCCUG UCCAACGUUA AUCGGGGCAG GGUGAGUCGA CCCCUA AGG CGAGGCCGAA AGGCGUAGUC GAUGGGAAAC AGGUUAAUAU UCCUGUACUU GGUGUUACUG CGAAGGGGGG ACGGAGA AG GCUAUGUUGG CCGGGCGACG GUUGUCCCGG UUUAAGCGUG UAGGCUGGUU UUCCAGGCAA AUCCGGAAAA UCAAGGCU G AGGCGUGAUG ACGAGGCACU ACGGUGCUGA AGCAACAAAU GCCCUGCUUC CAGGAAAAGC CUCUAAGCAU CAGGUAACA UCAAAUCGUA CCCCAAACCG ACACAGGUGG UCAGGUAGAG AAUACCAAGG CGCUUGAGAG AACUCGGGUG AAGGAACUAG GCAAAAUGG UGCCGUAACU UCGGGAGAAG GCACGCUGAU AUGUAGGUGA GGUCCCUCGC GGAUGGAGCU GAAAUCAGUC G AAGAUACC AGCUGGCUGC AACUGUUUAU UAAAAACACA GCACUGUGCA AACACGAAAG UGGACGUAUA CGGUGUGACG CC UGCCCGG UGCCGGAAGG UUAAUUGAUG GGGUUAGCGC AAGCGAAGCU CUUGAUCGAA GCCCCGGUAA ACGGCGGCCG UAA CUAUAA CGGUCCUAAG GUAGCGAAAU UCCUUGUCGG GUAAGUUCCG ACCUGCACGA AUGGCGUAAU GAUGGCCAGG CUGU CUCCA CCCGAGACUC AGUGAAAUUG AACUCGCUGU GAAGAUGCAG UGUACCCGCG GCAAGACGGA AAGACCCCGU GAACC UUUA CUAUAGCUUG ACACUGAACA UUGAGCCUUG AUGUGUAGGA UAGGUGGGAG GCUUUGAAGU GUGGACGCCA GUCUGC AUG GAGCCGACCU UGAAAUACCA CCCUUUAAUG UUUGAUGUUC UAACGUUGAC CCGUAAUCCG GGUUGCGGAC AGUGUCU GG UGGGUAGUUU GACUGGGGCG GUCUCCUCCU AAAGAGUAAC GGAGGAGCAC GAAGGUUGGC UAAUCCUGGU CGGACAUC A GGAGGUUAGU GCAAUGGCAU AAGCCAGCUU GACUGCGAGC GUGACGGCGC GAGCAGGUGC GAAAGCAGGU CAUAGUGAU CCGGUGGUUC UGAAUGGAAG GGCCAUCGCU CAACGGAUAA AAGGUACUCC GGGGAUAACA GGCUGAUACC GCCCAAGAGU UCAUAUCGA CGGCGGUGUU UGGCACCUCG AUGUCGGCUC AUCACAUCCU GGGGCUGAAG UAGGUCCCAA GGGUAUGGCU G UUCGCCAU UUAAAGUGGU ACGCGAGCUG GGUUUAGAAC GUCGUGAGAC AGUUCGGUCC CUAUCUGCCG UGGGCGCUGG AG AACUGAG GGGGGCUGCU CCUAGUACGA GAGGACCGGA GUGGACGCAU CACUGGUGUU CGGGUUGUCA UGCCAAUGGC ACU GCCCGG UAGCUAAAUG CGGAAGAGAU AAGUGCUGAA AGCAUCUAAG CACGAAACUU GCCCCGAGAU GAGUUCUCCC UGAC CCUUU AAGGGUCCUG AAGGAACGUU GAAGACGACG ACGUUGAUAG GCCGGGUGUG UAAGCGCAGC GAUGCGUUGA GCUAA CCGG UACUAAUGAA CCGUGAGGCU UAACCUUACA ACGCC

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Macromolecule #2: 5S ribosomal RNA

MacromoleculeName: 5S ribosomal RNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 38.483926 KDa
SequenceString:
UGCCUGGCGG CCGUAGCGCG GUGGUCCCAC CUGACCCCAU GCCGAACUCA GAAGUGAAAC GCCGUAGCGC CGAUGGUAGU GUGGGGUCU CCCCAUGCGA GAGUAGGGAA CUGCCAGGCA

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Macromolecule #3: GTPase ObgE/CgtA

MacromoleculeName: GTPase ObgE/CgtA / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 43.340801 KDa
SequenceString: MKFVDEASIL VVAGDGGNGC VSFRREKYIP KGGPDGGDGG DGGDVWMEAD ENLNTLIDYR FEKSFRAERG QNGASRDCTG KRGKDVTIK VPVGTRVIDQ GTGETMGDMT KHGQRLLVAK GGWHGLGNTR FKSSVNRTPR QKTNGTPGDK RELLLELMLL A DVGMLGMP ...String:
MKFVDEASIL VVAGDGGNGC VSFRREKYIP KGGPDGGDGG DGGDVWMEAD ENLNTLIDYR FEKSFRAERG QNGASRDCTG KRGKDVTIK VPVGTRVIDQ GTGETMGDMT KHGQRLLVAK GGWHGLGNTR FKSSVNRTPR QKTNGTPGDK RELLLELMLL A DVGMLGMP NAGKSTFIRA VSAAKPKVAD YPFTTLVPSL GVVRMDNEKS FVVADIPGLI EGAAEGAGLG IRFLKHLERC RV LLHLIDI DPIDGTDPVE NARIIISELE KYSQDLATKP RWLVFNKIDL LDKVEAEEKA KAIAEALGWE DKYYLISAAS GLG VKDLCW DVMTFIIENP VVQAEEAKQP EKVEFMWDDY HRQQLEEIAE EDDEDWDDDW DEDDEEGVEF IYKR

UniProtKB: GTPase ObgE/CgtA

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Macromolecule #4: 50S ribosomal protein L31

MacromoleculeName: 50S ribosomal protein L31 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 7.887117 KDa
SequenceString:
MKKDIHPKYE EITASCSCGN VMKIRSTVGH DLNLDVCSKC HPFFTGKQRD VATGGRVDRF NKRFNIPGSK

UniProtKB: Large ribosomal subunit protein bL31

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Macromolecule #5: 50S ribosomal protein L2

MacromoleculeName: 50S ribosomal protein L2 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 29.923619 KDa
SequenceString: MAVVKCKPTS PGRRHVVKVV NPELHKGKPF APLLEKNSKS GGRNNNGRIT TRHIGGGHKQ AYRIVDFKRN KDGIPAVVER LEYDPNRSA NIALVLYKDG ERRYILAPKG LKAGDQIQSG VDAAIKPGNT LPMRNIPVGS TVHNVEMKPG KGGQLARSAG T YVQIVARD ...String:
MAVVKCKPTS PGRRHVVKVV NPELHKGKPF APLLEKNSKS GGRNNNGRIT TRHIGGGHKQ AYRIVDFKRN KDGIPAVVER LEYDPNRSA NIALVLYKDG ERRYILAPKG LKAGDQIQSG VDAAIKPGNT LPMRNIPVGS TVHNVEMKPG KGGQLARSAG T YVQIVARD GAYVTLRLRS GEMRKVEADC RATLGEVGNA EHMLRVLGKA GAARWRGVRP TVRGTAMNPV DHPHGGGEGR NF GKHPVTP WGVQTKGKKT RSNKRTDKFI VRRRSK

UniProtKB: Large ribosomal subunit protein uL2

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Macromolecule #6: 50S ribosomal protein L3

MacromoleculeName: 50S ribosomal protein L3 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 22.277535 KDa
SequenceString: MIGLVGKKVG MTRIFTEDGV SIPVTVIEVE ANRVTQVKDL ANDGYRAIQV TTGAKKANRV TKPEAGHFAK AGVEAGRGLW EFRLAEGEE FTVGQSISVE LFADVKKVDV TGTSKGKGFA GTVKRWNFRT QDATHGNSLS HRVPGSIGQN QTPGKVFKGK K MAGQMGNE ...String:
MIGLVGKKVG MTRIFTEDGV SIPVTVIEVE ANRVTQVKDL ANDGYRAIQV TTGAKKANRV TKPEAGHFAK AGVEAGRGLW EFRLAEGEE FTVGQSISVE LFADVKKVDV TGTSKGKGFA GTVKRWNFRT QDATHGNSLS HRVPGSIGQN QTPGKVFKGK K MAGQMGNE RVTVQSLDVV RVDAERNLLL VKGAVPGATG SDLIVKPAVK A

UniProtKB: Large ribosomal subunit protein uL3

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Macromolecule #7: 50S ribosomal protein L4

MacromoleculeName: 50S ribosomal protein L4 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
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 #8: 50S ribosomal protein L6

MacromoleculeName: 50S ribosomal protein L6 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 18.932791 KDa
SequenceString:
MSRVAKAPVV VPAGVDVKIN GQVITIKGKN GELTRTLNDA VEVKHADNTL TFGPRDGYAD GWAQAGTARA LLNSMVIGVT EGFTKKLQL VGVGYRAAVK GNVINLSLGF SHPVDHQLPA GITAECPTQT EIVLKGADKQ VIGQVAADLR AYRRPEPYKG K GVRYADEV VRTKEAKKK

UniProtKB: Large ribosomal subunit protein uL6

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Macromolecule #9: 50S ribosomal protein L13

MacromoleculeName: 50S ribosomal protein L13 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
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 #10: 50S ribosomal protein L15

MacromoleculeName: 50S ribosomal protein L15 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 15.008471 KDa
SequenceString:
MRLNTLSPAE GSKKAGKRLG RGIGSGLGKT GGRGHKGQKS RSGGGVRRGF EGGQMPLYRR LPKFGFTSRK AAITAEIRLS DLAKVEGGV VDLNTLKAAN IIGIQIEFAK VILAGEVTTP VTVRGLRVTK GARAAIEAAG GKIEE

UniProtKB: Large ribosomal subunit protein uL15

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Macromolecule #11: 50S ribosomal protein L17

MacromoleculeName: 50S ribosomal protein L17 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 14.393657 KDa
SequenceString:
MRHRKSGRQL NRNSSHRQAM FRNMAGSLVR HEIIKTTLPK AKELRRVVEP LITLAKTDSV ANRRLAFART RDNEIVAKLF NELGPRFAS RAGGYTRILK CGFRAGDNAP MAYIELVDRS EKAEAAAE

UniProtKB: Large ribosomal subunit protein bL17

+
Macromolecule #12: 50S ribosomal protein L18

MacromoleculeName: 50S ribosomal protein L18 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 12.794668 KDa
SequenceString:
MDKKSARIRR ATRARRKLQE LGATRLVVHR TPRHIYAQVI APNGSEVLVA ASTVEKAIAE QLKYTGNKDA AAAVGKAVAE RALEKGIKD VSFDRSGFQY HGRVQALADA AREAGLQF

UniProtKB: Large ribosomal subunit protein uL18

+
Macromolecule #13: 50S ribosomal protein L20

MacromoleculeName: 50S ribosomal protein L20 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 13.528024 KDa
SequenceString:
MARVKRGVIA RARHKKILKQ AKGYYGARSR VYRVAFQAVI KAGQYAYRDR RQRKRQFRQL WIARINAAAR QNGISYSKFI NGLKKASVE IDRKILADIA VFDKVAFTAL VEKAKAALA

UniProtKB: Large ribosomal subunit protein bL20

+
Macromolecule #14: 50S ribosomal protein L21

MacromoleculeName: 50S ribosomal protein L21 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 11.586374 KDa
SequenceString:
MYAVFQSGGK QHRVSEGQTV RLEKLDIATG ETVEFAEVLM IANGEEVKIG VPFVDGGVIK AEVVAHGRGE KVKIVKFRRR KHYRKQQGH RQWFTDVKIT GISA

UniProtKB: Large ribosomal subunit protein bL21

+
Macromolecule #15: 50S ribosomal protein L22

MacromoleculeName: 50S ribosomal protein L22 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 12.253359 KDa
SequenceString:
METIAKHRHA RSSAQKVRLV ADLIRGKKVS QALDILTYTN KKAAVLVKKV LESAIANAEH NDGADIDDLK VTKIFVDEGP SMKRIMPRA KGRADRILKR TSHITVVVSD R

UniProtKB: Large ribosomal subunit protein uL22

+
Macromolecule #16: 50S ribosomal protein L23

MacromoleculeName: 50S ribosomal protein L23 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 11.22216 KDa
SequenceString:
MIREERLLKV LRAPHVSEKA STAMEKSNTI VLKVAKDATK AEIKAAVQKL FEVEVEVVNT LVVKGKVKRH GQRIGRRSDW KKAYVTLKE GQNLDFVGGA E

UniProtKB: Large ribosomal subunit protein uL23

+
Macromolecule #17: 50S ribosomal protein L24

MacromoleculeName: 50S ribosomal protein L24 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 11.33925 KDa
SequenceString:
MAAKIRRDDE VIVLTGKDKG KRGKVKNVLS SGKVIVEGIN LVKKHQKPVP ALNQPGGIVE KEAAIQVSNV AIFNAATGKA DRVGFRFED GKKVRFFKSN SETIK

UniProtKB: Large ribosomal subunit protein uL24

+
Macromolecule #18: 50S ribosomal protein L25

MacromoleculeName: 50S ribosomal protein L25 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 10.713465 KDa
SequenceString:
MFTINAEVRK EQGKGASRRL RAANKFPAII YGGKEAPLAI ELDHDKVMNM QAKAEFYSEV LTIVVDGKEI KVKAQDVQRH PYKPKLQHI DFVRA

UniProtKB: Large ribosomal subunit protein bL25

+
Macromolecule #19: 50S ribosomal protein L27

MacromoleculeName: 50S ribosomal protein L27 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 9.14654 KDa
SequenceString:
MAHKKAGGST RNGRDSEAKR LGVKRFGGES VLAGSIIVRQ RGTKFHAGAN VGCGRDHTLF AKADGKVKFE VKGPKNRKFI SIEAE

UniProtKB: Large ribosomal subunit protein bL27

+
Macromolecule #20: 50S ribosomal protein L28

MacromoleculeName: 50S ribosomal protein L28 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 9.027551 KDa
SequenceString:
MSRVCQVTGK RPVTGNNRSH ALNATKRRFL PNLHSHRFWV ESEKRFVTLR VSAKGMRVID KKGIDTVLAE LRARGEKY

UniProtKB: Large ribosomal subunit protein bL28

+
Macromolecule #21: 50S ribosomal protein L29

MacromoleculeName: 50S ribosomal protein L29 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 7.286464 KDa
SequenceString:
MKAKELREKS VEELNTELLN LLREQFNLRM QAASGQLQQS HLLKQVRRDV ARVKTLLNEK AGA

UniProtKB: Large ribosomal subunit protein uL29

+
Macromolecule #22: 50S ribosomal protein L30

MacromoleculeName: 50S ribosomal protein L30 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 6.55482 KDa
SequenceString:
MAKTIKITQT RSAIGRLPKH KATLLGLGLR RIGHTVERED TPAIRGMINA VSFMVKVEE

UniProtKB: Large ribosomal subunit protein uL30

+
Macromolecule #23: 50S ribosomal protein L32

MacromoleculeName: 50S ribosomal protein L32 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 6.463445 KDa
SequenceString:
MAVQQNKPTR SKRGMRRSHD ALTAVTSLSV DKTSGEKHLR HHITADGYYR GRKVIAK

UniProtKB: Large ribosomal subunit protein bL32

+
Macromolecule #24: 50S ribosomal protein L33

MacromoleculeName: 50S ribosomal protein L33 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 6.388631 KDa
SequenceString:
MAKGIREKIK LVSSAGTGHF YTTTKNKRTK PEKLELKKFD PVVRQHVIYK EAKIK

UniProtKB: Large ribosomal subunit protein bL33

+
Macromolecule #25: 50S ribosomal protein L34

MacromoleculeName: 50S ribosomal protein L34 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 5.397463 KDa
SequenceString:
MKRTFQPSVL KRNRSHGFRA RMATKNGRQV LARRRAKGRA RLTVSK

UniProtKB: Large ribosomal subunit protein bL34

+
Macromolecule #26: 50S ribosomal protein L11

MacromoleculeName: 50S ribosomal protein L11 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 14.894362 KDa
SequenceString:
MAKKVQAYVK LQVAAGMANP SPPVGPALGQ QGVNIMEFCK AFNAKTDSIE KGLPIPVVIT VYADRSFTFV TKTPPAAVLL KKAAGIKSG SGKPNKDKVG KISRAQLQEI AQTKAADMTG ADIEAMTRSI EGTARSMGLV VED

UniProtKB: Large ribosomal subunit protein uL11

+
Macromolecule #27: 50S ribosomal protein L14

MacromoleculeName: 50S ribosomal protein L14 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 13.565067 KDa
SequenceString:
MIQEQTMLNV ADNSGARRVM CIKVLGGSHR RYAGVGDIIK ITIKEAIPRG KVKKGDVLKA VVVRTKKGVR RPDGSVIRFD GNACVLLNN NSEQPIGTRI FGPVTRELRS EKFMKIISLA PEVL

UniProtKB: Large ribosomal subunit protein uL14

+
Macromolecule #28: 50S ribosomal protein L19

MacromoleculeName: 50S ribosomal protein L19 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 13.159278 KDa
SequenceString:
MSNIIKQLEQ EQMKQDVPSF RPGDTVEVKV WVVEGSKKRL QAFEGVVIAI RNRGLHSAFT VRKISNGEGV ERVFQTHSPV VDSISVKRR GAVRKAKLYY LRERTGKAAR IKERLN

UniProtKB: Large ribosomal subunit protein bL19

+
Macromolecule #29: Ribosomal silencing factor RsfS

MacromoleculeName: Ribosomal silencing factor RsfS / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 11.594205 KDa
SequenceString:
MQGKALQDFV IDKIDDLKGQ DIIALDVQGK SSITDCMIIC TGTSSRHVMS IADHVVQESR AAGLLPLGVE GENSADWIVV DLGDVIVHV MQEESRRLYE LEKLWS

UniProtKB: Ribosomal silencing factor RsfS

+
Macromolecule #30: 50S ribosomal protein L9

MacromoleculeName: 50S ribosomal protein L9 / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 15.78902 KDa
SequenceString:
MQVILLDKVA NLGSLGDQVN VKAGYARNFL VPQGKAVPAT KKNIEFFEAR RAELEAKLAE VLAAANARAE KINALETVTI ASKAGDEGK LFGSIGTRDI ADAVTAAGVE VAKSEVRLPN GVLRTTGEHE VSFQVHSEVF AKVIVNVVAE

UniProtKB: Large ribosomal subunit protein bL9

+
Macromolecule #31: 50S ribosomal protein L5

MacromoleculeName: 50S ribosomal protein L5 / type: protein_or_peptide / ID: 31 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 20.333611 KDa
SequenceString:
MAKLHDYYKD EVVKKLMTEF NYNSVMQVPR VEKITLNMGV GEAIADKKLL DNAAADLAAI SGQKPLITKA RKSVAGFKIR QGYPIGCKV TLRGERMWEF FERLITIAVP RIRDFRGLSA KSFDGRGNYS MGVREQIIFP EIDYDKVDRV RGLDITITTT A KSDEEGRA LLAAFDFPFR K

UniProtKB: Large ribosomal subunit protein uL5

+
Macromolecule #32: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 32 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #33: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 33 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #34: water

MacromoleculeName: water / type: ligand / ID: 34 / Number of copies: 27 / 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

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus min: 2.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus min: 0.8 µm / Nominal magnification: 36000
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 287576
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 23445
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cisTEM
Final 3D classificationSoftware - Name: cisTEM
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7bl3:
pre-50S-ObgE particle state 2

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