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- EMDB-8175: Cryo-EM structure of an ErmBL-stalled ribosome in complex with A-... -

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Basic information

Entry
Database: EMDB / ID: 8175
TitleCryo-EM structure of an ErmBL-stalled ribosome in complex with A-, P-, and E-tRNA
SampleErmBL-stalled E.coli 70S ribosome
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Map dataNone
Methodsingle particle reconstruction, at 3.6 Å resolution
AuthorsArenz S / Bock LV
CitationNat Commun, 2016, 7, 12026-12026

Nat Commun, 2016, 7, 12026-12026 Yorodumi Papers
A combined cryo-EM and molecular dynamics approach reveals the mechanism of ErmBL-mediated translation arrest.
Stefan Arenz / Lars V Bock / Michael Graf / C Axel Innis / Roland Beckmann / Helmut Grubmüller / Andrea C Vaiana / Daniel N Wilson

Validation ReportPDB-ID: 5jte

SummaryFull reportAbout validation report
DateDeposition: May 9, 2016 / Header (metadata) release: Jul 20, 2016 / Map release: Jul 20, 2016 / Last update: Aug 30, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00164
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 0.00164
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5jte
  • Surface level: 0.00164
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5jte
  • Surface level: 0.00194
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

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Map

Fileemd_8175.map.gz (map file in CCP4 format, 199345 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
368 pix
1.11 Å/pix.
= 407.744 Å
368 pix
1.11 Å/pix.
= 407.744 Å
368 pix
1.11 Å/pix.
= 407.744 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.108 Å
Density
Contour Level:0.00194 (by author), 0.00164 (movie #1):
Minimum - Maximum-0.005907116 - 0.009535342
Average (Standard dev.)4.782961E-6 (0.0004098137)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions368368368
Origin000
Limit367367367
Spacing368368368
CellA=B=C: 407.74402 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1081.1081.108
M x/y/z368368368
origin x/y/z0.0000.0000.000
length x/y/z407.744407.744407.744
α/β/γ90.00090.00090.000
start NX/NY/NZ-190-190-190
NX/NY/NZ380380380
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS368368368
D min/max/mean-0.0060.0100.000

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Supplemental data

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Sample components

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Entire ErmBL-stalled E.coli 70S ribosome

EntireName: ErmBL-stalled E.coli 70S ribosome / Number of components: 60
MassTheoretical: 2.5 MDa

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Component #1: protein, ErmBL-stalled E.coli 70S ribosome

ProteinName: ErmBL-stalled E.coli 70S ribosome / Recombinant expression: No
MassTheoretical: 2.5 MDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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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 / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #3: protein, 30S ribosomal protein S2

ProteinName: 30S ribosomal protein S2 / Recombinant expression: No
MassTheoretical: 26.652557 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #4: protein, 30S ribosomal protein S3

ProteinName: 30S ribosomal protein S3 / Recombinant expression: No
MassTheoretical: 26.031316 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #5: protein, 30S ribosomal protein S4

ProteinName: 30S ribosomal protein S4 / Recombinant expression: No
MassTheoretical: 23.514199 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #6: protein, 30S ribosomal protein S5

ProteinName: 30S ribosomal protein S5 / Recombinant expression: No
MassTheoretical: 17.629398 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #7: protein, 30S ribosomal protein S6

ProteinName: 30S ribosomal protein S6 / Recombinant expression: No
MassTheoretical: 15.727512 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #8: protein, 30S ribosomal protein S7

ProteinName: 30S ribosomal protein S7 / Recombinant expression: No
MassTheoretical: 20.055156 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #9: protein, 30S ribosomal protein S8

ProteinName: 30S ribosomal protein S8 / Recombinant expression: No
MassTheoretical: 14.146557 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #10: protein, 30S ribosomal protein S9

ProteinName: 30S ribosomal protein S9 / Recombinant expression: No
MassTheoretical: 14.88627 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #11: protein, 30S ribosomal protein S10

ProteinName: 30S ribosomal protein S10 / Recombinant expression: No
MassTheoretical: 11.755597 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #12: protein, 30S ribosomal protein S11

ProteinName: 30S ribosomal protein S11 / Recombinant expression: No
MassTheoretical: 13.870975 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #13: protein, 30S ribosomal protein S12

ProteinName: 30S ribosomal protein S12 / Recombinant expression: No
MassTheoretical: 13.768157 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #14: protein, 30S ribosomal protein S13

ProteinName: 30S ribosomal protein S13 / Recombinant expression: No
MassTheoretical: 13.128467 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #15: protein, 30S ribosomal protein S14

ProteinName: 30S ribosomal protein S14 / Recombinant expression: No
MassTheoretical: 11.60656 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #16: protein, 30S ribosomal protein S15

ProteinName: 30S ribosomal protein S15 / Recombinant expression: No
MassTheoretical: 10.290816 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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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 / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #18: protein, 30S ribosomal protein S17

ProteinName: 30S ribosomal protein S17 / Recombinant expression: No
MassTheoretical: 9.724491 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #19: protein, 30S ribosomal protein S18

ProteinName: 30S ribosomal protein S18 / Recombinant expression: No
MassTheoretical: 9.005472 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #20: protein, 30S ribosomal protein S19

ProteinName: 30S ribosomal protein S19 / Recombinant expression: No
MassTheoretical: 10.455355 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #21: protein, 30S ribosomal protein S20

ProteinName: 30S ribosomal protein S20 / Recombinant expression: No
MassTheoretical: 9.708464 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #22: protein, 30S ribosomal protein S21

ProteinName: 30S ribosomal protein S21 / Recombinant expression: No
MassTheoretical: 8.524039 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #23: nucleic-acid, mRNA

Nucleic-acidName: mRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GUAGAUAAAA
MassTheoretical: 3.23302 kDa

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Component #24: nucleic-acid, A-site Lysine tRNA Lysine

Nucleic-acidName: A-site Lysine tRNA Lysine / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GGGUCGU(4SU)AG CUCAGGGUAG AGCAGUUGAC U(U8U)UU(T6A)A(PSU)CAA UUG(7MG)(3AU)CGCAG G(5MU)(PSU)CGAAUCC UGCACGACCC ACCA
MassTheoretical: 24.117564 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #25: nucleic-acid, P-site tRNA Aspartate

Nucleic-acidName: P-site tRNA Aspartate / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GGAGCGG(4SU)AG UUCAGUCGGU UAGAAUACCU GCCU(QUO)UC(2MA)CG CAGGGG(7MG)UCG CGGG(5MU)(PSU)CGAG UCCCG(PSU)CCGU UCCGCCA
MassTheoretical: 25.004014 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #26: nucleic-acid, E-site tRNA Valine

Nucleic-acidName: E-site tRNA Valine / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GGGUGAU(4SU)AG CUCAGGGGAG AGCACCUCCC U(CM0)AC(6MZ)AGGAG GGG(7MG)UCGGCG G(5MU)(PSU)CGAUCCC GUCAUCACCC A
MassTheoretical: 23.066852 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #27: 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 GGGUCACUUA CCAACCCGAU GCAAACUGCG AAUACCGGAG AAUGUUAUCA CGGGAGACAC ACGGCGGGUG CUAACGUCCG UCGUGAAGAG GGAAACAACC CAGACCGCCA GCUAAGGUCC CAAAGUCAUG GUUAAGUGGG AAACGAUGUG GGAAGGCCCA GACAGCCAGG AUGUUGGCUU AGAAGCAGCC AUCAUUUAAA GAAAGCGUAA UAGCUCACUG GUCGAGUCGG CCUGCGCGGA AGAUGUAACG GGGCUAAACC AUGCACCGAA GCUGCGGCAG CGACGCUUAU 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 GCCGUAACUA UAACGGUCCU AAGGUAGCGA AAUUCCUUGU CGGGUAAGUU CCGACCUGCA CGAAUGGCGU AAUGAUGGCC AGGCUGUCUC CACCCGAGAC UCAGUGAAAU UGAACUCGCU GUGAAGAUGC AGUGUACCCG CGGCAAGACG GAAAGACCCC GUGAACCUUU ACUAUAGCUU GACACUGAAC AUUGAGCCUU GAUGUGUAGG AUAGGUGGGA GGCUUUGAAG UGUGGACGCC AGUCUGCAUG GAGCCGACCU UGAAAUACCA CCCUUUAAUG UUUGAUGUUC UAACGUUGAC CCGUAAUCCG GGUUGCGGAC AGUGUCUGGU GGGUAGUUUG ACUGGGGCGG UCUCCUCCUA AAGAGUAACG GAGGAGCACG AAGGUUGGCU AAUCCUGGUC GGACAUCAGG AGGUUAGUGC AAUGGCAUAA GCCAGCUUGA CUGCGAGCGU GACGGCGCGA GCAGGUGCGA AAGCAGGUCA UAGUGAUCCG GUGGUUCUGA AUGGAAGGGC CAUCGCUCAA CGGAUAAAAG GUACUCCGGG GAUAACAGGC UGAUACCGCC CAAGAGUUCA UAUCGACGGC GGUGUUUGGC ACCUCGAUGU CGGCUCAUCA CAUCCUGGGG CUGAAGUAGG UCCCAAGGGU AUGGCUGUUC GCCAUUUAAA GUGGUACGCG AGCUGGGUUU AGAACGUCGU GAGACAGUUC GGUCCCUAUC UGCCGUGGGC GCUGGAGAAC UGAGGGGGGC UGCUCCUAGU ACGAGAGGAC CGGAGUGGAC GCAUCACUGG UGUUCGGGUU GUCAUGCCAA UGGCACUGCC CGGUAGCUAA AUGCGGAAGA GAUAAGUGCU GAAAGCAUCU AAGCACGAAA CUUGCCCCGA GAUGAGUUCU CCCUGACCCU UUAAGGGUCC UGAAGGAACG UUGAAGACGA CGACGUUGAU AGGCCGGGUG UGUAAGCGCA GCGAUGCGUU GAGCUAACCG GUACUAAUGA ACCGUGAGGC UUAACCU
MassTheoretical: 939.410062 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #28: 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 / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #29: protein, 50S ribosomal protein L2

ProteinName: 50S ribosomal protein L2 / Recombinant expression: No
MassTheoretical: 29.923619 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #30: protein, 50S ribosomal protein L3

ProteinName: 50S ribosomal protein L3 / Recombinant expression: No
MassTheoretical: 22.277535 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #31: protein, 50S ribosomal protein L4

ProteinName: 50S ribosomal protein L4 / Recombinant expression: No
MassTheoretical: 22.121566 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #32: protein, 50S ribosomal protein L5

ProteinName: 50S ribosomal protein L5 / Recombinant expression: No
MassTheoretical: 20.333611 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #33: protein, 50S ribosomal protein L6

ProteinName: 50S ribosomal protein L6 / Recombinant expression: No
MassTheoretical: 18.932791 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #34: protein, 50S ribosomal protein L9

ProteinName: 50S ribosomal protein L9 / Recombinant expression: No
MassTheoretical: 15.78902 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #35: protein, 50S ribosomal protein L11

ProteinName: 50S ribosomal protein L11 / Recombinant expression: No
MassTheoretical: 14.894362 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #36: protein, 50S ribosomal protein L13

ProteinName: 50S ribosomal protein L13 / Recombinant expression: No
MassTheoretical: 16.050606 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #37: protein, 50S ribosomal protein L14

ProteinName: 50S ribosomal protein L14 / Recombinant expression: No
MassTheoretical: 13.565067 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #38: protein, 50S ribosomal protein L15

ProteinName: 50S ribosomal protein L15 / Recombinant expression: No
MassTheoretical: 15.008471 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #39: protein, 50S ribosomal protein L16

ProteinName: 50S ribosomal protein L16 / Recombinant expression: No
MassTheoretical: 15.312269 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #40: protein, 50S ribosomal protein L17

ProteinName: 50S ribosomal protein L17 / Recombinant expression: No
MassTheoretical: 14.393657 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #41: protein, 50S ribosomal protein L18

ProteinName: 50S ribosomal protein L18 / Recombinant expression: No
MassTheoretical: 12.794668 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #42: protein, 50S ribosomal protein L19

ProteinName: 50S ribosomal protein L19 / Recombinant expression: No
MassTheoretical: 13.159278 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #43: protein, 50S ribosomal protein L20

ProteinName: 50S ribosomal protein L20 / Recombinant expression: No
MassTheoretical: 13.528024 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #44: protein, 50S ribosomal protein L21

ProteinName: 50S ribosomal protein L21 / Recombinant expression: No
MassTheoretical: 11.586374 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #45: protein, 50S ribosomal protein L22

ProteinName: 50S ribosomal protein L22 / Recombinant expression: No
MassTheoretical: 12.253359 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #46: protein, 50S ribosomal protein L23

ProteinName: 50S ribosomal protein L23 / Recombinant expression: No
MassTheoretical: 11.22216 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #47: protein, 50S ribosomal protein L24

ProteinName: 50S ribosomal protein L24 / Recombinant expression: No
MassTheoretical: 11.33925 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #48: protein, 50S ribosomal protein L25

ProteinName: 50S ribosomal protein L25 / Recombinant expression: No
MassTheoretical: 10.713465 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #49: protein, 50S ribosomal protein L27

ProteinName: 50S ribosomal protein L27 / Recombinant expression: No
MassTheoretical: 9.14654 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #50: protein, 50S ribosomal protein L28

ProteinName: 50S ribosomal protein L28 / Recombinant expression: No
MassTheoretical: 9.027551 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #51: protein, 50S ribosomal protein L29

ProteinName: 50S ribosomal protein L29 / Recombinant expression: No
MassTheoretical: 7.286464 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #52: protein, 50S ribosomal protein L30

ProteinName: 50S ribosomal protein L30 / Recombinant expression: No
MassTheoretical: 6.55482 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #53: protein, 50S ribosomal protein L32

ProteinName: 50S ribosomal protein L32 / Recombinant expression: No
MassTheoretical: 6.463445 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #54: protein, 50S ribosomal protein L33

ProteinName: 50S ribosomal protein L33 / Recombinant expression: No
MassTheoretical: 6.388631 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #55: protein, 50S ribosomal protein L34

ProteinName: 50S ribosomal protein L34 / Recombinant expression: No
MassTheoretical: 5.397463 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #56: protein, 50S ribosomal protein L35

ProteinName: 50S ribosomal protein L35 / Recombinant expression: No
MassTheoretical: 7.313032 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #57: protein, 50S ribosomal protein L36

ProteinName: 50S ribosomal protein L36 / Recombinant expression: No
MassTheoretical: 4.37739 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #58: protein, ErmBL

ProteinName: ErmBL / Recombinant expression: No
MassTheoretical: 1.080237 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #59: ligand, LYSINE

LigandName: LYSINE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.147195 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #60: ligand, ERYTHROMYCIN A

LigandName: ERYTHROMYCIN A / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.733927 kDa

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Experimental details

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Sample preparation

Specimen stateparticle
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: 4 e/Å2 / Illumination mode: SPOT SCAN
LensImaging mode: BRIGHT FIELD / Defocus: 700 - 1200 nm
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 85393
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF
Details: Due to image processing in the absence of spatial frequencies higher than 8 angstroms, the FSC value of 0.143 was used for average resolution determination.

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL
Input PDB model: 5AFI
Output model

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About Yorodumi

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News

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Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Jun 16, 2017. Omokage search with filter

Omokage search with filter

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Related info.: Omokage search

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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 / EM Navigator (legacy version) / Yorodumi (legacy version)

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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 / EM Navigator (legacy version) / Yorodumi (legacy version)

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Yorodumi

Thousand views of thousand structures

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

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

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