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- EMDB-4380: 50S ribosomal subunit assembly intermediate state 3 -

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Entry
Database: EMDB / ID: 4380
Title50S ribosomal subunit assembly intermediate state 3
Map data
Sample50S ribosomal assembly intermediate state 3:
(50S ribosomal protein ...) x 24 / (nucleic-acidNucleic acid) x 2
Function / homologyRibosomal protein L18e/L15P / Ribosomal protein L13, conserved site / Ribosomal protein L34, conserved site / Ribosomal protein L9, C-terminal domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2, C-terminal / Ribosomal protein L2, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal protein L4 domain superfamily / Ribosomal protein L5, conserved site ...Ribosomal protein L18e/L15P / Ribosomal protein L13, conserved site / Ribosomal protein L34, conserved site / Ribosomal protein L9, C-terminal domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2, C-terminal / Ribosomal protein L2, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal protein L4 domain superfamily / Ribosomal protein L5, conserved site / Ribosomal protein L28/L24 / Ribosomal protein L21-like / Ribosomal protein L25 / Ribosomal protein L15 / Ribosomal protein L5, C-terminal / Ribosomal protein L5, N-terminal / L28p-like / Ribosomal protein L5, bacterial-type / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L29/L35 superfamily / Ribosomal protein L27, conserved site / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L30, conserved site / Ribosomal protein L29, conserved site / Ribosomal protein L19, conserved site / Ribosomal protein L21, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein L6, bacterial-type / Ribosomal protein L9, N-terminal / Ribosomal protein L3, conserved site / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L14P, conserved site / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L25, short-form / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L9, C-terminal / Ribosomal protein L20, C-terminal / L21-like superfamily / Ribosomal protein L2, domain 2 / Ribosomal prokaryotic L21 protein / KOW motif / Ribosomal protein L34 / Ribosomal protein L13 / Ribosomal protein L4/L1 family / ribosomal L5P family C-terminus / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal L28 family / Ribosomal protein L6 / Ribosomal L29 protein / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal L27 protein / Ribosomal protein L17 / Ribosomal protein L19 / Ribosomal protein L9, N-terminal domain / Ribosomal L25p family / Ribosomal protein L20 / Ribosomal protein L30p/L7e / Ribosomal L18e/L15P superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L17 superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L14 superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L3 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L19 superfamily / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L22p/L17e / Ribosomal protein L14p/L23e / Ribosomal protein L23 / Ribosomal protein L5 / Ribosomal protein L2, domain 3 / Ribosomal protein L25/L23 / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L2 signature. / Ribosomal protein L22/L17 / Ribosomal protein L23/L25, conserved site / Ribosomal protein L6 / Ribosomal protein L3 / 50S ribosomal protein uL4 / Ribosomal protein L34 / Ribosomal protein L9 / Ribosomal protein L14P / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L14 signature. / Ribosomal protein L23 signature. / Ribosomal protein L5 signature. / Ribosomal protein L22 signature. / Ribosomal protein L3 signature. / Ribosomal protein L28 / Ribosomal protein L15 signature. / Ribosomal protein L6 signature 1. / Ribosomal protein L29 signature. / Ribosomal protein L30 signature. / Ribosomal protein L9 signature. / Ribosomal protein L13 signature. / Ribosomal protein L34 signature.
Function and homology information
SourceEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / 4.3 Å resolution
AuthorsNikolay R / Hilal T / Qin B / Loerke J / Buerger J / Mielke T / Spahn CMT
CitationJournal: Mol. Cell / Year: 2018
Title: Structural Visualization of the Formation and Activation of the 50S Ribosomal Subunit during In Vitro Reconstitution.
Authors: Rainer Nikolay / Tarek Hilal / Bo Qin / Thorsten Mielke / Jörg Bürger / Justus Loerke / Kathrin Textoris-Taube / Knud H Nierhaus / Christian M T Spahn
Abstract: The assembly of ribosomal subunits is an essential prerequisite for protein biosynthesis in all domains of life. Although biochemical and biophysical approaches have advanced our understanding of ...The assembly of ribosomal subunits is an essential prerequisite for protein biosynthesis in all domains of life. Although biochemical and biophysical approaches have advanced our understanding of ribosome assembly, our mechanistic comprehension of this process is still limited. Here, we perform an in vitro reconstitution of the Escherichia coli 50S ribosomal subunit. Late reconstitution products were subjected to high-resolution cryo-electron microscopy and multiparticle refinement analysis to reconstruct five distinct precursors of the 50S subunit with 4.3-3.8 Å resolution. These assembly intermediates define a progressive maturation pathway culminating in a late assembly particle, whose structure is more than 96% identical to a mature 50S subunit. Our structures monitor the formation and stabilization of structural elements in a nascent particle in unprecedented detail and identify the maturation of the rRNA-based peptidyl transferase center as the final critical step along the 50S assembly pathway.
Validation ReportPDB-ID: 6gc4

SummaryFull reportAbout validation report
DateDeposition: Apr 17, 2018 / Header (metadata) release: May 23, 2018 / Map release: Jul 4, 2018 / Last update: Jul 4, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6gc4
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_4380.map.gz (map file in CCP4 format, 78733 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
270 pix
1.24 Å/pix.
= 334.8 Å
270 pix
1.24 Å/pix.
= 334.8 Å
270 pix
1.24 Å/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
Contour Level:4.5 (by author), 4.5 (movie #1):
Minimum - Maximum-13.797888 - 29.942157999999999
Average (Standard dev.)0.16376425 (1.3029556)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions270270270
Origin0.0.0.
Limit269.269.269.
Spacing270270270
CellA=B=C: 334.8 Å
α=β=γ: 90.0 deg.

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
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS270270270
D min/max/mean-13.79829.9420.164

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Supplemental data

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Sample components

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Entire 50S ribosomal assembly intermediate state 3

EntireName: 50S ribosomal assembly intermediate state 3 / Number of components: 27

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Component #1: protein, 50S ribosomal assembly intermediate state 3

ProteinName: 50S ribosomal assembly intermediate state 3 / Recombinant expression: No
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #2: protein, 50S ribosomal protein L25

ProteinName: 50S ribosomal protein L25 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.713465 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #3: nucleic-acid, 23S ribosomal RNA

Nucleic-acidName: 23S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GGUUAAGCGA CUAAGCGUAC ACGGUGGAUG CCCUGGCAGU CAGAGGCGAU GAAGGACGUG CUAAUCUGCG AUAAGCGUCG GUAAGGUGAU AUGAACCGUU AUAACCGGCG AUUUCCGAAU GGGGAAACCC AGUGUGUUUC GACACACUAU CAUUAACUGA AUCCAUAGGU UAAUGAGGCG AACCGGGGGA ACUGAAACAU CUAAGUACCC CGAGGAAAAG AAAUCAACCG AGAUUCCCCC AGUAGCGGCG AGCGAACGGG GAGCAGCCCA GAGCCUGAAU CAGUGUGUGU GUUAGUGGAA GCGUCUGGAA AGGCGCGCGA UACAGGGUGA CAGCCCCGUA CACAAAAAUG CACAUGCUGU GAGCUCGAUG AGUAGGGCGG GACACGUGGU AUCCUGUCUG AAUAUGGGGG GACCAUCCUC CAAGGCUAAA UACUCCUGAC UGACCGAUAG UGAACCAGUA CCGUGAGGGA AAGGCGAAAA GAACCCCGGC GAGGGGAGUG AAAAAGAACC UGAAACCGUG UACGUACAAG CAGUGGGAGC ACGCUUAGGC GUGUGACUGC GUACCUUUUG UAUAAUGGGU CAGCGACUUA UAUUCUGUAG CAAGGUUAAC CGAAUAGGGG AGCCGAAGGG AAACCGAGUC UUAACUGGGC GUUAAGUUGC AGGGUAUAGA CCCGAAACCC GGUGAUCUAG CCAUGGGCAG GUUGAAGGUU GGGUAACACU AACUGGAGGA CCGAACCGAC UAAUGUUGAA AAAUUAGCGG AUGACUUGUG GCUGGGGGUG AAAGGCCAAU CAAACCGGGA GAUAGCUGGU UCUCCCCGAA AGCUAUUUAG GUAGCGCCUC GUGAAUUCAU CUCCGGGGGU AGAGCACUGU UUCGGCAAGG GGGUCAUCCC GACUUACCAA CCCGAUGCAA ACUGCGAAUA CCGGAGAAUG UUAUCACGGG AGACACACGG CGGGUGCUAA CGUCCGUCGU GAAGAGGGAA ACAACCCAGA CCGCCAGCUA AGGUCCCAAA GUCAUGGUUA AGUGGGAAAC GAUGUGGGAA GGCCCAGACA GCCAGGAUGU UGGCUUAGAA GCAGCCAUCA UUUAAAGAAA GCGUAAUAGC UCACUGGUCG AGUCGGCCUG CGCGGAAGAU GUAACGGGGC UAAACCAUGC ACCGAAGCUG CGGCAGCGAC GCUUAUGCGU UGUUGGGUAG GGGAGCGUUC UGUAAGCCUG CGAAGGUGUG CUGUGAGGCA UGCUGGAGGU AUCAGAAGUG CGAAUGCUGA CAUAAGUAAC GAUAAAGCGG GUGAAAAGCC CGCUCGCCGG AAGACCAAGG GUUCCUGUCC AACGUUAAUC GGGGCAGGGU GAGUCGACCC CUAAGGCGAG GCCGAAAGGC GUAGUCGAUG GGAAACAGGU UAAUAUUCCU GUACUUGGUG UUACUGCGAA GGGGGGACGG AGAAGGCUAU GUUGGCCGGG CGACGGUUGU CCCGGUUUAA GCGUGUAGGC UGGUUUUCCA GGCAAAUCCG GAAAAUCAAG GCUGAGGCGU GAUGACGAGG CACUACGGUG CUGAAGCAAC AAAUGCCCUG CUUCCAGGAA AAGCCUCUAA GCAUCAGGUA ACAUCAAAUC GUACCCCAAA CCGACACAGG UGGUCAGGUA GAGAAUACCA AGGCGCUUGA GAGAACUCGG GUGAAGGAAC UAGGCAAAAU GGUGCCGUAA CUUCGGGAGA AGGCACGCUG AUAUGUAGGU GAGGUCCCUC GCGGAUGGAG CUGAAAUCAG UCGAAGAUAC CAGCUGGCUG CAACUGUUUA UUAAAAACAC AGCACUGUGC AAACACGAAA GUGGACGUAU ACGGUGUGAC GCCUGCCCGG UGCCGGAAGG UUAAUUGAUG GGGUUAGCGC AAGCGAAGCU CUUGAUCGAA GCCCCGGUAA ACGGCGGCCG UAACUAUAAC GGUCCUAAGG UAGCGAAAUU CCUUGUCGGG UAAGUUCCGA CCUGCACGAA UGGCGUAAUG AUGGCCAGGC UGUCUCCACC CGAGACUCAG UGAAAUUGAA CUCGCUGUGA AGAUGCAGUG UACCCGCGGC AAGACGGAAA GACCCCGUGA ACCUUUACUA UAGCUUGACA CUGAACAUUG AGCCUUGAUG UGUAGGAUAG GUGGGAGGCU UUGAAGUGUG GACGCCAGUC UGCAUGGAGC CGACCUUGAA AUACCACCCU UUAAUGUUUG AUGUUCUAAC GUUGACCCGU AAUCCGGGUU GCGGACAGUG UCUGGUGGGU AGUUUGACUG GGGCGGUCUC CUCCUAAAGA GUAACGGAGG AGCACGAAGG UUGGCUAAUC CUGGUCGGAC AUCAGGAGGU UAGUGCAAUG GCAUAAGCCA GCUUGACUGC GAGCGUGACG GCGCGAGCAG GUGCGAAAGC AGGUCAUAGU GAUCCGGUGG UUCUGAAUGG AAGGGCCAUC GCUCAACGGA UAAAAGGUAC UCCGGGGAUA ACAGGCUGAU ACCGCCCAAG AGUUCAUAUC GACGGCGGUG UUUGGCACCU CGAUGUCGGC UCAUCACAUC CUGGGGCUGA AGUAGGUCCC AAGGGUAUGG CUGUUCGCCA UUUAAAGUGG UACGCGAGCU GGGUUUAGAA CGUCGUGAGA CAGUUCGGUC CCUAUCUGCC GUGGGCGCUG GAGAACUGAG GGGGGCUGCU CCUAGUACGA GAGGACCGGA GUGGACGCAU CACUGGUGUU CGGGUUGUCA UGCCAAUGGC ACUGCCCGGU AGCUAAAUGC GGAAGAGAUA AGUGCUGAAA GCAUCUAAGC ACGAAACUUG CCCCGAGAUG AGUUCUCCCU GACCCUUUAA GGGUCCUGAA GGAACGUUGA AGACGACGAC GUUGAUAGGC CGGGUGUGUA AGCGCAGCGA UGCGUUGAGC UAACCGGUAC UAAUGAACCG UGAGGCUUAA CCUU
MassTheoretical: 941.612375 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #4: protein, 50S ribosomal protein L2

ProteinName: 50S ribosomal protein L2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.663244 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #5: protein, 50S ribosomal protein L3

ProteinName: 50S ribosomal protein L3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.277535 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #6: protein, 50S ribosomal protein L4

ProteinName: 50S ribosomal protein L4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.121566 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #7: protein, 50S ribosomal protein L6

ProteinName: 50S ribosomal protein L6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.801598 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #8: protein, 50S ribosomal protein L13

ProteinName: 50S ribosomal protein L13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.050606 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #9: protein, 50S ribosomal protein L14

ProteinName: 50S ribosomal protein L14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.45191 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #10: protein, 50S ribosomal protein L15

ProteinName: 50S ribosomal protein L15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.877273 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #11: protein, 50S ribosomal protein L17

ProteinName: 50S ribosomal protein L17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.721938 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #12: protein, 50S ribosomal protein L19

ProteinName: 50S ribosomal protein L19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.028082 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #13: protein, 50S ribosomal protein L20

ProteinName: 50S ribosomal protein L20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.396828 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #14: protein, 50S ribosomal protein L21

ProteinName: 50S ribosomal protein L21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.586374 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #15: protein, 50S ribosomal protein L22

ProteinName: 50S ribosomal protein L22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.253359 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #16: protein, 50S ribosomal protein L23

ProteinName: 50S ribosomal protein L23 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.546472 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #17: protein, 50S ribosomal protein L24

ProteinName: 50S ribosomal protein L24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.078874 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #18: protein, 50S ribosomal protein L28

ProteinName: 50S ribosomal protein L28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.896354 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #19: protein, 50S ribosomal protein L29

ProteinName: 50S ribosomal protein L29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.286464 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #20: protein, 50S ribosomal protein L32

ProteinName: 50S ribosomal protein L32 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.332249 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #21: protein, 50S ribosomal protein L34

ProteinName: 50S ribosomal protein L34 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.397463 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #22: protein, 50S ribosomal protein L18

ProteinName: 50S ribosomal protein L18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.663471 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #23: protein, 50S ribosomal protein L5

ProteinName: 50S ribosomal protein L5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.073234 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #24: nucleic-acid, 5S ribosomal RNA

Nucleic-acidName: 5S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UGCCUGGCGG CCGUAGCGCG GUGGUCCCAC CUGACCCCAU GCCGAACUCA GAAGUGAAAC GCCGUAGCGC CGAUGGUAGU GUGGGGUCUC CCCAUGCGAG AGUAGGGAAC UGCCAGGCA
MassTheoretical: 38.483926 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #25: protein, 50S ribosomal protein L30

ProteinName: 50S ribosomal protein L30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.423625 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #26: protein, 50S ribosomal protein L9

ProteinName: 50S ribosomal protein L9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.467367 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #27: protein, 50S ribosomal protein L27

ProteinName: 50S ribosomal protein L27 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.275498 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 80645. X (nominal) / Imaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 26665
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL
Output model

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