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- EMDB-10073: Ribosome nascent chain in complex with SecA -

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Basic information

Entry
Database: EMDB / ID: EMD-10073
TitleRibosome nascent chain in complex with SecA
Map data
Sampleribosome nascent chain in complex with SecA:
ribosome / SecA / nascent chain / (nucleic-acidNucleic acid) x 3 / (50S ribosomal protein ...) x 30 / Protein translocase subunit SecA / Cytoskeleton protein RodZ / (ligand) x 2
Function / homology
Function and homology information


protein import / intracellular protein transmembrane transport / stringent response / positive regulation of ribosome biogenesis / endoribonuclease inhibitor activity / negative regulation of endoribonuclease activity / translation repressor activity / mature ribosome assembly / protein targeting / ribosome assembly ...protein import / intracellular protein transmembrane transport / stringent response / positive regulation of ribosome biogenesis / endoribonuclease inhibitor activity / negative regulation of endoribonuclease activity / translation repressor activity / mature ribosome assembly / protein targeting / ribosome assembly / polysomal ribosome / translational termination / assembly of large subunit precursor of preribosome / DNA-templated transcription, termination / helicase activity / translation repressor activity, mRNA regulatory element binding / DNA-binding transcription repressor activity / regulation of cell growth / response to reactive oxygen species / large ribosomal subunit rRNA binding / ribosome biogenesis / cytosolic large ribosomal subunit / large ribosomal subunit / ribosome binding / ribosomal large subunit assembly / 5S rRNA binding / protein-DNA complex / response to radiation / negative regulation of translation / tRNA binding / transferase activity / ribosome / rRNA binding / structural constituent of ribosome / translation / mRNA binding / response to antibiotic / negative regulation of transcription, DNA-templated / zinc ion binding / ATP binding / plasma membrane / metal ion binding / cytosol / cytoplasm
Ribosomal protein L2, conserved site / Ribosomal protein L36 superfamily / Ribosomal protein L4 domain superfamily / Ribosomal protein L28/L24 / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein L21-like / Ribosomal protein L25 / Ribosomal protein L15 / Ribosomal protein L5, C-terminal / Ribosomal protein L5, N-terminal ...Ribosomal protein L2, conserved site / Ribosomal protein L36 superfamily / Ribosomal protein L4 domain superfamily / Ribosomal protein L28/L24 / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein L21-like / Ribosomal protein L25 / Ribosomal protein L15 / Ribosomal protein L5, C-terminal / Ribosomal protein L5, N-terminal / L28p-like / Ribosomal protein L20, C-terminal / Ribosomal protein L29/L35 superfamily / Ribosomal protein L10 / L21-like superfamily / Ribosomal L18e/L15P superfamily / SecA, Wing/Scaffold superfamily / Ribosomal protein L17 superfamily / Ribosomal protein L22/L17 superfamily / SecA, preprotein cross-linking domain superfamily / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L14 superfamily / Ribosomal protein L13, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L35, conserved site / Ribosomal protein L6, bacterial-type / 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 L9, N-terminal / Ribosomal protein L11, C-terminal / Ribosomal protein L29 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L11, conserved site / Ribosomal protein L16, conserved site / Ribosomal protein L5, conserved site / Ribosomal protein L5, bacterial-type / SecA conserved site / Ribosomal protein L34, conserved site / Ribosomal protein L18e/L15P / Ribosomal protein L35 / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2, C-terminal / Ribosomal protein L13 superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L27, conserved site / Ribosomal protein L11, N-terminal domain / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal L27 protein / SecA preprotein cross-linking domain / Ribosomal protein L17 / Ribosomal protein L19 / Ribosomal protein L9, N-terminal domain / Ribosomal L25p family / Ribosomal protein L35 / Ribosomal L32p protein family / SEC-C motif / Ribosomal Proteins L2, C-terminal domain / Ribosomal L28 family / Ribosomal protein L9, C-terminal domain / SecA Wing and Scaffold domain / SecA DEAD-like domain / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L14 signature. / Ribosomal protein L23 signature. / Ribosomal protein L5 signature. / Ribosomal protein L11 signature. / Ribosomal protein L22 signature. / Ribosomal protein L2 signature. / Ribosomal protein L3 signature. / Ribosomal L29 protein / Ribosomal prokaryotic L21 protein / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L3 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L35 superfamily / Ribosomal protein L33 superfamily / Ribosomal protein L19 superfamily / Ribosomal Protein L26/L24, KOW domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L22p/L17e / Ribosomal protein L14p/L23e / Ribosomal protein L16p/L10e / Ribosomal protein L23 / Ribosomal protein L5 / Ribosomal protein L11, RNA binding domain / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal protein L30p/L7e / Ribosomal protein L6 / Ribosomal protein L36 / Ribosomal protein L20
50S ribosomal protein L23 / 50S ribosomal protein L17 / 50S ribosomal protein L21 / 50S ribosomal protein L30 / 50S ribosomal protein L6 / 50S ribosomal protein L18 / 50S ribosomal protein L2 / 50S ribosomal protein L14 / 50S ribosomal protein L3 / 50S ribosomal protein L24 ...50S ribosomal protein L23 / 50S ribosomal protein L17 / 50S ribosomal protein L21 / 50S ribosomal protein L30 / 50S ribosomal protein L6 / 50S ribosomal protein L18 / 50S ribosomal protein L2 / 50S ribosomal protein L14 / 50S ribosomal protein L3 / 50S ribosomal protein L24 / 50S ribosomal protein L4 / 50S ribosomal protein L22 / 50S ribosomal protein L5 / 50S ribosomal protein L16 / 50S ribosomal protein L27 / 50S ribosomal protein L13 / 50S ribosomal protein L9 / 50S ribosomal protein L36 / 50S ribosomal protein L35 / 50S ribosomal protein L34 / 50S ribosomal protein L33 / 50S ribosomal protein L32 / 50S ribosomal protein L29 / 50S ribosomal protein L28 / 50S ribosomal protein L20 / 50S ribosomal protein L19 / 50S ribosomal protein L11 / 50S ribosomal protein L15 / 50S ribosomal protein L10 / Protein translocase subunit SecA / 50S ribosomal protein L25
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsJomaa A / Wang S / Shan S / Ban N
Funding support Switzerland, United States, 2 items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
National Institutes of Health/National Center for Research Resources United States
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2019
Title: The molecular mechanism of cotranslational membrane protein recognition and targeting by SecA.
Authors: Shuai Wang / Ahmad Jomaa / Mateusz Jaskolowski / Chien-I Yang / Nenad Ban / Shu-Ou Shan /
Abstract: Cotranslational protein targeting is a conserved process for membrane protein biogenesis. In Escherichia coli, the essential ATPase SecA was found to cotranslationally target a subset of nascent ...Cotranslational protein targeting is a conserved process for membrane protein biogenesis. In Escherichia coli, the essential ATPase SecA was found to cotranslationally target a subset of nascent membrane proteins to the SecYEG translocase at the plasma membrane. The molecular mechanism of this pathway remains unclear. Here we use biochemical and cryoelectron microscopy analyses to show that the amino-terminal amphipathic helix of SecA and the ribosomal protein uL23 form a composite binding site for the transmembrane domain (TMD) on the nascent protein. This binding mode further enables recognition of charged residues flanking the nascent TMD and thus explains the specificity of SecA recognition. Finally, we show that membrane-embedded SecYEG promotes handover of the translating ribosome from SecA to the translocase via a concerted mechanism. Our work provides a molecular description of the SecA-mediated cotranslational targeting pathway and demonstrates an unprecedented role of the ribosome in shielding nascent TMDs.
Validation ReportPDB-ID: 6s0k

SummaryFull reportAbout validation report
History
DepositionJun 17, 2019-
Header (metadata) releaseOct 9, 2019-
Map releaseOct 9, 2019-
UpdateOct 9, 2019-
Current statusOct 9, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.82
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.82
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6s0k
  • Surface level: 0.82
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6s0k
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_10073.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 320 pix.
= 444.8 Å
1.39 Å/pix.
x 320 pix.
= 444.8 Å
1.39 Å/pix.
x 320 pix.
= 444.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.39 Å
Density
Contour LevelBy AUTHOR: 0.82 / Movie #1: 0.82
Minimum - Maximum-2.5681784 - 6.125954
Average (Standard dev.)0.014772073 (±0.4107664)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 444.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z444.800444.800444.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-2.5686.1260.015

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Supplemental data

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Sample components

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Entire ribosome nascent chain in complex with SecA

EntireName: ribosome nascent chain in complex with SecA / Number of components: 41

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Component #1: protein, ribosome nascent chain in complex with SecA

ProteinName: ribosome nascent chain in complex with SecA / Recombinant expression: No
MassTheoretical: 2.6 MDa

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Component #2: protein, ribosome

ProteinName: ribosome / Recombinant expression: No
SourceSpecies: Escherichia coli (E. coli)

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Component #3: protein, SecA

ProteinName: SecA / Recombinant expression: No
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: protein, nascent chain

ProteinName: nascent chain / Recombinant expression: No
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #5: nucleic-acid, tRNA-CCA

nucleic acidName: tRNA-CCA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
CCA
MassTheoretical: 0.894612 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #6: 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 ACGCUGGCGU GUGACUGCGU ACCUUUUGUA UAAUGGGUCA GCGACUUAUA UUCUGUAGCA AGGUUAACCG AAUAGGGGAG CCGAAGGGAA ACCGAGUCUU AACUGGGCGU UAAGUUGCAG GGUAUAGACC CGAAACCCGG UGAUCUAGCC AUGGGCAGGU UGAAGGUUGG GUAACACUAA CUGGAGGACC GAACCGACUA AUGUUGAAAA AUUAGCGGAU GACUUGUGGC UGGGGGUGAA AGGCCAAUCA AACCGGGAGA UAGCUGGUUC UCCCCGAAAG CUAUUUAGGU AGCGCCUCGU GAAUUCAUCU CCGGGGGUAG AGCACUGUUU CGGCAAGGGG UUACCAACCC GAUGCAAACU GCGAAUACCG GAGAAUGUUA UCACGGGAGA CACACGGCGG GUGCUAACGU CCGUCGUGAA GAGGGAAACA ACCCAGACCG CCAGCUAAGG UCCCAAAGUC AUGGUUAAGU GGGAAACGAU GUGGGAAGGC CCAGACAGCC AGGAUGUUGG CUUAGAAGCA GCCAUCAUUU AAAGAAAGCG UAAUAGCUCA CUGGUCGAGU CGGCCUGCGC GGAAGAUGUA ACGGGGCUAA ACCAUGCACC GAAGCUGCGG CAGCGACGCU GCGUUGUUGG GUAGGGGAGC GUUCUGUAAG CCUGCGAAGG UGUGCUGUGA GGCAUGCUGG AGGUAUCAGA AGUGCGAAUG CUGACAUAAG UAACGAUAAA GCGGGUGAAA AGCCCGCUCG CCGGAAGACC AAGGGUUCCU GUCCAACGUU AAUCGGGGCA GGGUGAGUCG ACCCCUAAGG CGAGGCCGAA AGGCGUAGUC GAUGGGAAAC AGGUUAAUAU UCCUGUACUU GGUGUUACUG CGAAGGGGGG ACGGAGAAGG CUAUGUUGGC CGGGCGACGG UUGUCCCGGU UUAAGCGUGU AGGCUGGUUU UCCAGGCAAA UCCGGAAAAU CAAGGCUGAG GCGUGAUGAC GAGGCACUAC GGUGCUGAAG CAACAAAUGC CCUGCUUCCA GGAAAAGCCU CUAAGCAUCA GGUAACAUCA AAUCGUACCC CAAACCGACA CAGGUGGUCA GGUAGAGAAU ACCAAGGCGC UUGAGAGAAC UCGGGUGAAG GAACUAGGCA AAAUGGUGCC GUAACUUCGG GAGAAGGCAC GCUGAUAUGU AGGUGAGGUC CCUCGCGGAU GGAGCUGAAA UCAGUCGAAG AUACCAGCUG GCUGCAACUG UUUAUUAAAA ACACAGCACU GUGCAAACAC GAAAGUGGAC GUAUACGGUG UGACGCCUGC CCGGUGCCGG AAGGUUAAUU GAUGGGGUUA GCGCAAGCGA AGCUCUUGAU CGAAGCCCCG GUAAACGGCG GCCGUAUAAC 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 CCU
MassTheoretical: 934.972188 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #7: 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 UGCCAGGCAU
MassTheoretical: 38.79009 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #8: protein, 50S ribosomal protein L2

ProteinName: 50S ribosomal protein L2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.923619 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #9: protein, 50S ribosomal protein L3

ProteinName: 50S ribosomal protein L3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.277535 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #10: protein, 50S ribosomal protein L4

ProteinName: 50S ribosomal protein L4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.121566 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #11: protein, 50S ribosomal protein L5

ProteinName: 50S ribosomal protein L5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.333611 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #12: protein, 50S ribosomal protein L6

ProteinName: 50S ribosomal protein L6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.932791 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #13: protein, 50S ribosomal protein L9

ProteinName: 50S ribosomal protein L9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.78902 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #14: protein, 50S ribosomal protein L10

ProteinName: 50S ribosomal protein L10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.736596 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #15: protein, 50S ribosomal protein L11

ProteinName: 50S ribosomal protein L11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.894362 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #16: protein, 50S ribosomal protein L13

ProteinName: 50S ribosomal protein L13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.050606 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #17: protein, 50S ribosomal protein L14

ProteinName: 50S ribosomal protein L14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.565067 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #18: protein, 50S ribosomal protein L15

ProteinName: 50S ribosomal protein L15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.008471 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #19: protein, 50S ribosomal protein L16

ProteinName: 50S ribosomal protein L16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.312269 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #20: protein, 50S ribosomal protein L17

ProteinName: 50S ribosomal protein L17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.393657 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #21: protein, 50S ribosomal protein L18

ProteinName: 50S ribosomal protein L18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.794668 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #22: protein, 50S ribosomal protein L19

ProteinName: 50S ribosomal protein L19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.159278 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #23: protein, 50S ribosomal protein L20

ProteinName: 50S ribosomal protein L20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.528024 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #24: protein, 50S ribosomal protein L21

ProteinName: 50S ribosomal protein L21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.586374 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #25: protein, 50S ribosomal protein L22

ProteinName: 50S ribosomal protein L22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.253359 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #26: protein, 50S ribosomal protein L23

ProteinName: 50S ribosomal protein L23 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.22216 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #27: protein, 50S ribosomal protein L24

ProteinName: 50S ribosomal protein L24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.33925 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #28: protein, 50S ribosomal protein L25

ProteinName: 50S ribosomal protein L25 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.713465 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #29: protein, 50S ribosomal protein L27

ProteinName: 50S ribosomal protein L27 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.14654 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #30: protein, 50S ribosomal protein L28

ProteinName: 50S ribosomal protein L28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.027551 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #31: protein, 50S ribosomal protein L29

ProteinName: 50S ribosomal protein L29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.286464 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #32: protein, 50S ribosomal protein L30

ProteinName: 50S ribosomal protein L30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.55482 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #33: protein, 50S ribosomal protein L32

ProteinName: 50S ribosomal protein L32 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.463445 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #34: protein, 50S ribosomal protein L33

ProteinName: 50S ribosomal protein L33 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.388631 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #35: protein, 50S ribosomal protein L34

ProteinName: 50S ribosomal protein L34 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.397463 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #36: protein, 50S ribosomal protein L35

ProteinName: 50S ribosomal protein L35 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.313032 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #37: protein, 50S ribosomal protein L36

ProteinName: 50S ribosomal protein L36 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 4.37739 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #38: protein, Protein translocase subunit SecA

ProteinName: Protein translocase subunit SecA / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 95.155359 kDa
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #39: protein, Cytoskeleton protein RodZ

ProteinName: Cytoskeleton protein RodZ / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.82383 kDa
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #40: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 68 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #41: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: OTHER / Temperature: 277 K / Humidity: 95 %

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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: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 37334
3D reconstructionSoftware: RELION / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: rigid body
Input PDB model: 5GAG
Output model

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Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

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Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

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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