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- EMDB-3903: Polyproline-stalled ribosome in the presence of elongation-factor... -

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Basic information

Entry
Database: EMDB / ID: 3903
TitlePolyproline-stalled ribosome in the presence of elongation-factor P (EF-P)
Map dataPolyproline stalled ribosome in presence of EF-P with a truncated mRNA in the A-site.
SamplePolyproline stalled ribosome in the absence of elongation factor P:
(nucleic-acidNucleic acid) x 5 / (30S ribosomal protein ...) x 20 / (50S ribosomal protein ...) x 30 / Elongation factor P / ligand
Function / homologyRibosomal protein L5 domain superfamily / Ribosomal protein L25 / Ribosomal protein S6 superfamily / Ribosomal protein L36 superfamily / Ribosomal protein L20, C-terminal / L28p-like / Ribosomal protein L5, N-terminal / Ribosomal protein L5, C-terminal / Ribosomal protein L15 / Ribosomal protein L21-like ...Ribosomal protein L5 domain superfamily / Ribosomal protein L25 / Ribosomal protein S6 superfamily / Ribosomal protein L36 superfamily / Ribosomal protein L20, C-terminal / L28p-like / Ribosomal protein L5, N-terminal / Ribosomal protein L5, C-terminal / Ribosomal protein L15 / Ribosomal protein L21-like / Ribosomal protein L29/L35 superfamily / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L31 type A / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / Ribosomal protein L28/L24 / Ribosomal protein S16 domain superfamily / Ribosomal protein S7 domain / Ribosomal protein L1-like / Ribosomal protein S8 superfamily / L21-like superfamily / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S18 superfamily / Ribosomal protein L35 superfamily / Ribosomal protein L28/L24 superfamily / RNA-binding S4 domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L14 superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein S20 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L17 superfamily / Ribosomal protein L1, conserved site / Ribosomal protein S19, superfamily / Ribosomal protein L33 superfamily / Ribosomal protein S13, bacterial-type / Ribosomal protein L9, N-terminal / Ribosomal protein L9, C-terminal / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25, short-form / Ribosomal protein L6, alpha-beta domain / 30S ribosomal protein S17 / Ribosomal protein S11, bacterial-type / Ribosomal protein S17, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein L14P, conserved site / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L3, conserved site / Ribosomal protein L6, bacterial-type / Ribosomal protein S3, conserved site / Ribosomal protein S21, conserved site / Ribosomal protein S18, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S16, conserved site / Ribosomal protein L4 domain superfamily / Ribosomal protein L18e/L15P / Ribosomal protein L13, conserved site / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4/S9 / Ribosomal protein L2, conserved site / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L35 / Ribosomal protein L34, conserved site / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein S19 conserved site / Ribosomal protein L5, bacterial-type / Ribosomal protein L5, conserved site / Ribosomal protein S6, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L16, conserved site / Ribosomal protein S7, conserved site / Translation elongation factor P/YeiP / Ribosomal protein S21 superfamily / Ribosomal protein L19 superfamily / Ribosomal protein S10, conserved site / Ribosomal protein S5, C-terminal domain / Ribosomal protein L14 signature. / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Elongation factor P, C-terminal / Elongation factor P (EF-P) KOW-like domain / KH domain / Ribosomal protein L9, C-terminal domain / Ribosomal Proteins L2, C-terminal domain / Ribosomal L32p protein family / Ribosomal protein S7 signature. / Ribosomal protein S20 / Ribosomal protein L35 / S4 domain
Function and homology information
SourceEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / 3.1 Å resolution
AuthorsHuter P / Arenz S
CitationJournal: Mol. Cell / Year: 2017
Title: Structural Basis for Polyproline-Mediated Ribosome Stalling and Rescue by the Translation Elongation Factor EF-P.
Authors: Paul Huter / Stefan Arenz / Lars V Bock / Michael Graf / Jan Ole Frister / Andre Heuer / Lauri Peil / Agata L Starosta / Ingo Wohlgemuth / Frank Peske / Jiří Nováček / Otto Berninghausen / Helmut Grubmüller / Tanel Tenson / Roland Beckmann / Marina V Rodnina / Andrea C Vaiana / Daniel N Wilson
Abstract: Ribosomes synthesizing proteins containing consecutive proline residues become stalled and require rescue via the action of uniquely modified translation elongation factors, EF-P in bacteria, or ...Ribosomes synthesizing proteins containing consecutive proline residues become stalled and require rescue via the action of uniquely modified translation elongation factors, EF-P in bacteria, or archaeal/eukaryotic a/eIF5A. To date, no structures exist of EF-P or eIF5A in complex with translating ribosomes stalled at polyproline stretches, and thus structural insight into how EF-P/eIF5A rescue these arrested ribosomes has been lacking. Here we present cryo-EM structures of ribosomes stalled on proline stretches, without and with modified EF-P. The structures suggest that the favored conformation of the polyproline-containing nascent chain is incompatible with the peptide exit tunnel of the ribosome and leads to destabilization of the peptidyl-tRNA. Binding of EF-P stabilizes the P-site tRNA, particularly via interactions between its modification and the CCA end, thereby enforcing an alternative conformation of the polyproline-containing nascent chain, which allows a favorable substrate geometry for peptide bond formation.
Validation ReportPDB-ID: 6enu

SummaryFull reportAbout validation report
DateDeposition: Oct 6, 2017 / Header (metadata) release: Nov 22, 2017 / Map release: Nov 22, 2017 / Last update: Jan 31, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.108
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.108
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6enu
  • Surface level: 0.108
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3903.map.gz (map file in CCP4 format, 186625 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
360 pix
1.08 Å/pix.
= 390.24 Å
360 pix
1.08 Å/pix.
= 390.24 Å
360 pix
1.08 Å/pix.
= 390.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.084 Å
Density
Contour Level:0.108 (by author), 0.108 (movie #1):
Minimum - Maximum-0.3255747 - 0.6687987
Average (Standard dev.)0.0021238856 (0.0230238)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions360360360
Origin000
Limit359359359
Spacing360360360
CellA=B=C: 390.24 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0841.0841.084
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z390.240390.240390.240
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.3260.6690.002

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Supplemental data

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Sample components

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Entire Polyproline stalled ribosome in the absence of elongation factor P

EntireName: Polyproline stalled ribosome in the absence of elongation factor P
Number of components: 58
MassTheoretical: 3 MDa

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Component #1: protein, Polyproline stalled ribosome in the absence of elongatio...

ProteinName: Polyproline stalled ribosome in the absence of elongation factor P
Recombinant expression: No
MassTheoretical: 3 MDa
SourceSpecies: Escherichia coli (E. coli)

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Component #2: nucleic-acid, 16S ribosomal RNA

Nucleic-acidName: 16S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AAUUGAAGAG UUUGAUCAUG GCUCAGAUUG AACGCUGGCG GCAGGCCUAA CACAUGCAAG UCGAACGGUA ACAGGAAGAA GCUUGCUUCU UUGCUGACGA GUGGCGGACG GGUGAGUAAU GUCUGGGAAA CUGCCUGAUG GAGGGGGAUA ACUACUGGAA ACGGUAGCUA AUACCGCAUA ACGUCGCAAG ACCAAAGAGG GGGACCUUCG GGCCUCUUGC CAUCGGAUGU GCCCAGAUGG GAUUAGCUAG UAGGUGGGGU AACGGCUCAC CUAGGCGACG AUCCCUAGCU GGUCUGAGAG GAUGACCAGC CACACUGGAA CUGAGACACG GUCCAGACUC CUACGGGAGG CAGCAGUGGG GAAUAUUGCA CAAUGGGCGC AAGCCUGAUG CAGCCAUGCC GCGUGUAUGA AGAAGGCCUU CGGGUUGUAA AGUACUUUCA GCGGGGAGGA AGGGAGUAAA GUUAAUACCU UUGCUCAUUG ACGUUACCCG CAGAAGAAGC ACCGGCUAAC UCCGUGCCAG CAGCCGCGGU AAUACGGAGG GUGCAAGCGU UAAUCGGAAU UACUGGGCGU AAAGCGCACG CAGGCGGUUU GUUAAGUCAG AUGUGAAAUC CCCGGGCUCA ACCUGGGAAC UGCAUCUGAU ACUGGCAAGC UUGAGUCUCG UAGAGGGGGG UAGAAUUCCA GGUGUAGCGG UGAAAUGCGU AGAGAUCUGG AGGAAUACCG GUGGCGAAGG CGGCCCCCUG GACGAAGACU GACGCUCAGG UGCGAAAGCG UGGGGAGCAA ACAGGAUUAG AUACCCUGGU AGUCCACGCC GUAAACGAUG UCGACUUGGA GGUUGUGCCC UUGAGGCGUG GCUUCCGGAG CUAACGCGUU AAGUCGACCG CCUGGGGAGU ACGGCCGCAA GGUUAAAACU CAAAUGAAUU GACGGGGGCC CGCACAAGCG GUGGAGCAUG UGGUUUAAUU CGAUGCAACG CGAAGAACCU UACCUGGUCU UGACAUCCAC GGAAGUUUUC AGAGAUGAGA AUGUGCCUUC GGGAACCGUG AGACAGGUGC UGCAUGGCUG UCGUCAGCUC GUGUUGUGAA AUGUUGGGUU AAGUCCCGCA ACGAGCGCAA CCCUUAUCCU UUGUUGCCAG CGGUCCGGCC GGGAACUCAA AGGAGACUGC CAGUGAUAAA CUGGAGGAAG GUGGGGAUGA CGUCAAGUCA UCAUGGCCCU UACGACCAGG GCUACACACG UGCUACAAUG GCGCAUACAA AGAGAAGCGA CCUCGCGAGA GCAAGCGGAC CUCAUAAAGU GCGUCGUAGU CCGGAUUGGA GUCUGCAACU CGACUCCAUG AAGUCGGAAU CGCUAGUAAU CGUGGAUCAG AAUGCCACGG UGAAUACGUU CCCGGGCCUU GUACACACCG CCCGUCACAC CAUGGGAGUG GGUUGCAAAA GAAGUAGGUA GCUUAACCUU CGGGAGGGCG CUUACCACUU UGUGAUUCAU GACUGGGGUG AAGUCGUAAC AAGGUAACCG UAGGGGAACC UGCGGUUGGA UCACCUCCU
MassTheoretical: 498.725406 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #3: protein, 30S ribosomal protein S2

ProteinName: 30S ribosomal protein S2 / Recombinant expression: No
MassTheoretical: 24.253943 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #4: protein, 30S ribosomal protein S3

ProteinName: 30S ribosomal protein S3 / Recombinant expression: No
MassTheoretical: 23.078785 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #5: protein, 30S ribosomal protein S4

ProteinName: 30S ribosomal protein S4 / Recombinant expression: No
MassTheoretical: 23.383002 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #6: protein, 30S ribosomal protein S5

ProteinName: 30S ribosomal protein S5 / Recombinant expression: No
MassTheoretical: 16.532088 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #7: protein, 30S ribosomal protein S6

ProteinName: 30S ribosomal protein S6 / Recombinant expression: No
MassTheoretical: 11.669371 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #8: protein, 30S ribosomal protein S7

ProteinName: 30S ribosomal protein S7 / Recombinant expression: No
MassTheoretical: 16.861523 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #9: protein, 30S ribosomal protein S8

ProteinName: 30S ribosomal protein S8 / Recombinant expression: No
MassTheoretical: 14.015361 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #10: protein, 30S ribosomal protein S9

ProteinName: 30S ribosomal protein S9 / Recombinant expression: No
MassTheoretical: 14.554882 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #11: protein, 30S ribosomal protein S10

ProteinName: 30S ribosomal protein S10 / Recombinant expression: No
MassTheoretical: 11.196988 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #12: protein, 30S ribosomal protein S11

ProteinName: 30S ribosomal protein S11 / Recombinant expression: No
MassTheoretical: 12.388068 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #13: protein, 30S ribosomal protein S12

ProteinName: 30S ribosomal protein S12 / Recombinant expression: No
MassTheoretical: 13.636961 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #14: protein, 30S ribosomal protein S13

ProteinName: 30S ribosomal protein S13 / Recombinant expression: No
MassTheoretical: 12.625753 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #15: protein, 30S ribosomal protein S14

ProteinName: 30S ribosomal protein S14 / Recombinant expression: No
MassTheoretical: 11.546442 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #16: protein, 30S ribosomal protein S15

ProteinName: 30S ribosomal protein S15 / Recombinant expression: No
MassTheoretical: 10.159621 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #17: protein, 30S ribosomal protein S16

ProteinName: 30S ribosomal protein S16 / Recombinant expression: No
MassTheoretical: 9.207572 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #18: protein, 30S ribosomal protein S17

ProteinName: 30S ribosomal protein S17 / Recombinant expression: No
MassTheoretical: 9.263946 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #19: protein, 30S ribosomal protein S18

ProteinName: 30S ribosomal protein S18 / Recombinant expression: No
MassTheoretical: 7.606768 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #20: protein, 30S ribosomal protein S19

ProteinName: 30S ribosomal protein S19 / Recombinant expression: No
MassTheoretical: 9.057626 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #21: protein, 30S ribosomal protein S20

ProteinName: 30S ribosomal protein S20 / Recombinant expression: No
MassTheoretical: 9.50619 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #22: protein, 30S ribosomal protein S21

ProteinName: 30S ribosomal protein S21 / Recombinant expression: No
MassTheoretical: 7.763073 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #23: nucleic-acid, mRNA

Nucleic-acidName: mRNAMessenger RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
CCGCCG
MassTheoretical: 1.866181 kDa

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Component #24: 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 UAAUGUCGAA 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 UGCCGGGAGG UUAAUUGAUG GGGUUAGCGC AAGCGAAGCU CUUGAUCGAA GCCCCGGUAA ACGGCGGCCG UAACUAUAAC GGUCCUAAGG UAGCGAAAUU CCUUGUCGGG UAAGUUCCGA CCUGCACGAA UGGCGUAAUG AUGGCCAGGC UGUCUCCACC CGAGACUCAG UGAAAUUGAA CUCGCUGUGA AGAUGCAGUG UACCCGCGGC AAGACGGAAA GACCCCGUAA ACCUUUACUA UAGCUUGACA CUGAACAUUG AGCUUUGAUG 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 CCU
MassTheoretical: 941.30625 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #25: 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 UGCCAGGCAA
MassTheoretical: 38.813133 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #26: protein, 50S ribosomal protein L2

ProteinName: 50S ribosomal protein L2 / Recombinant expression: No
MassTheoretical: 29.663244 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #27: protein, 50S ribosomal protein L3

ProteinName: 50S ribosomal protein L3 / Recombinant expression: No
MassTheoretical: 22.277535 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #28: protein, 50S ribosomal protein L4

ProteinName: 50S ribosomal protein L4 / Recombinant expression: No
MassTheoretical: 22.121566 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #29: protein, 50S ribosomal protein L5

ProteinName: 50S ribosomal protein L5 / Recombinant expression: No
MassTheoretical: 20.073234 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #30: protein, 50S ribosomal protein L6

ProteinName: 50S ribosomal protein L6 / Recombinant expression: No
MassTheoretical: 18.801598 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #31: protein, 50S ribosomal protein L9

ProteinName: 50S ribosomal protein L9 / Recombinant expression: No
MassTheoretical: 15.78902 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #32: protein, 50S ribosomal protein L13

ProteinName: 50S ribosomal protein L13 / Recombinant expression: No
MassTheoretical: 16.050606 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #33: protein, 50S ribosomal protein L14

ProteinName: 50S ribosomal protein L14 / Recombinant expression: No
MassTheoretical: 13.45191 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #34: protein, 50S ribosomal protein L15

ProteinName: 50S ribosomal protein L15 / Recombinant expression: No
MassTheoretical: 14.877273 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #35: protein, 50S ribosomal protein L16

ProteinName: 50S ribosomal protein L16 / Recombinant expression: No
MassTheoretical: 15.312269 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #36: protein, 50S ribosomal protein L17

ProteinName: 50S ribosomal protein L17 / Recombinant expression: No
MassTheoretical: 13.721938 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #37: protein, 50S ribosomal protein L18

ProteinName: 50S ribosomal protein L18 / Recombinant expression: No
MassTheoretical: 12.663471 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #38: protein, 50S ribosomal protein L19

ProteinName: 50S ribosomal protein L19 / Recombinant expression: No
MassTheoretical: 13.028082 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #39: protein, 50S ribosomal protein L20

ProteinName: 50S ribosomal protein L20 / Recombinant expression: No
MassTheoretical: 13.396828 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #40: protein, 50S ribosomal protein L21

ProteinName: 50S ribosomal protein L21 / Recombinant expression: No
MassTheoretical: 11.586374 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #41: protein, 50S ribosomal protein L22

ProteinName: 50S ribosomal protein L22 / Recombinant expression: No
MassTheoretical: 12.253359 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #42: protein, 50S ribosomal protein L23

ProteinName: 50S ribosomal protein L23 / Recombinant expression: No
MassTheoretical: 10.546472 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #43: protein, 50S ribosomal protein L24

ProteinName: 50S ribosomal protein L24 / Recombinant expression: No
MassTheoretical: 11.078874 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #44: protein, 50S ribosomal protein L25

ProteinName: 50S ribosomal protein L25 / Recombinant expression: No
MassTheoretical: 10.713465 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #45: protein, 50S ribosomal protein L27

ProteinName: 50S ribosomal protein L27 / Recombinant expression: No
MassTheoretical: 8.419629 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #46: protein, 50S ribosomal protein L28

ProteinName: 50S ribosomal protein L28 / Recombinant expression: No
MassTheoretical: 8.896354 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #47: protein, 50S ribosomal protein L29

ProteinName: 50S ribosomal protein L29 / Recombinant expression: No
MassTheoretical: 7.286464 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #48: protein, 50S ribosomal protein L30

ProteinName: 50S ribosomal protein L30 / Recombinant expression: No
MassTheoretical: 6.423625 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #49: protein, 50S ribosomal protein L32

ProteinName: 50S ribosomal protein L32 / Recombinant expression: No
MassTheoretical: 6.332249 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #50: protein, 50S ribosomal protein L33

ProteinName: 50S ribosomal protein L33 / Details: ribosomal protein L33 / Recombinant expression: No
MassTheoretical: 5.814842 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #51: protein, 50S ribosomal protein L34

ProteinName: 50S ribosomal protein L34 / Recombinant expression: No
MassTheoretical: 5.397463 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #52: protein, 50S ribosomal protein L35

ProteinName: 50S ribosomal protein L35 / Recombinant expression: No
MassTheoretical: 7.181835 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #53: protein, 50S ribosomal protein L36

ProteinName: 50S ribosomal protein L36 / Recombinant expression: No
MassTheoretical: 4.37739 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #54: protein, 50S ribosomal protein L31

ProteinName: 50S ribosomal protein L31 / Recombinant expression: No
MassTheoretical: 7.516693 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #55: nucleic-acid, Proline tRNA

Nucleic-acidName: Proline tRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
CGGUGAUUGG CGCAGCCUGG UAGCGCACUU CGUUCGGGAC GAAGGGGUCG GAGGUUCGAA UCCUCUAUCA CCGACCA
MassTheoretical: 24.846746 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #56: protein, 50S ribosomal protein L1

ProteinName: 50S ribosomal protein L1 / Recombinant expression: No
MassTheoretical: 23.761477 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #57: protein, Elongation factor P

ProteinName: Elongation factor P / Recombinant expression: No
MassTheoretical: 20.755414 kDa
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #58: ligand, PROLINE

LigandName: PROLINE / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.11513 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 28 e/Å2 / Illumination mode: SPOT SCAN
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 63665
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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About Yorodumi

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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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