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- EMDB-3730: Cryo-EM structure of the proline-rich antimicrobial peptide Api13... -

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Basic information

Entry
Database: EMDB / ID: 3730
TitleCryo-EM structure of the proline-rich antimicrobial peptide Api137 bound to the terminating ribosome
SampleEscherichia coli 70S ribosome
SourceEscherichia coli (strain k12) / bacteria /
Staphylococcus aureus / bacteria / スタフィロコッカス・アウレウス, 黄色ブドウ球菌
Apis mellifera / arthropod / セイヨウミツバチ, ヨウシュミツバチ /
Escherichia coli k-12 / bacteria / image: Escherichia coli
Map dataCryo-EM reconstruction of an E. coli 70S ribosome in complex with Api137 and RF1.
Methodsingle particle reconstruction, at 3.4 Å resolution
AuthorsGraf M / Berninghausen O
CitationNat. Struct. Mol. Biol., 2017, 24, 752-757

Nat. Struct. Mol. Biol., 2017, 24, 752-757 Yorodumi Papers
An antimicrobial peptide that inhibits translation by trapping release factors on the ribosome.
Tanja Florin / Cristina Maracci / Michael Graf / Prajwal Karki / Dorota Klepacki / Otto Berninghausen / Roland Beckmann / Nora Vázquez-Laslop / Daniel N Wilson / Marina V Rodnina / Alexander S Mankin

Validation ReportPDB-ID: 5o2r

SummaryFull reportAbout validation report
DateDeposition: May 22, 2017 / Header (metadata) release: May 31, 2017 / Map release: Jul 26, 2017 / Last update: Sep 20, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.407
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 0.407
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5o2r
  • Surface level: 0.407
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

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Map

Fileemd_3730.map.gz (map file in CCP4 format, 186625 KB)
Projections & slices

Image control

Size
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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 package.

Voxel sizeX=Y=Z: 1.084 Å
Density
Contour Level:0.407 (by author), 0.407 (movie #1):
Minimum - Maximum-1.4673427 - 2.1308537
Average (Standard dev.)0.0073488215 (0.08395064)
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-1.4672.1310.007

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Supplemental data

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Sample components

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Entire Escherichia coli 70S ribosome

EntireName: Escherichia coli 70S ribosome
Details: 70S ribosome complexed with Ile-tRNA, Api137 and RF1
Number of components: 62

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Component #1: protein, Escherichia coli 70S ribosome

ProteinName: Escherichia coli 70S ribosome
Details: 70S ribosome complexed with Ile-tRNA, Api137 and RF1
Recombinant expression: No

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Component #2: protein, Escherichia coli 70S ribosome

ProteinName: Escherichia coli 70S ribosome / Details: 70S ribosome complexed with Ile-tRNA / Recombinant expression: No
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #3: protein, mRNA

ProteinName: mRNA / Details: mRNA / Recombinant expression: No
SourceSpecies: Staphylococcus aureus / bacteria / スタフィロコッカス・アウレウス, 黄色ブドウ球菌
Source (engineered)Expression System: Synthetic construct

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Component #4: protein, Apidaecin

ProteinName: Apidaecin / Details: Apidaecin / Recombinant expression: No
SourceSpecies: Apis mellifera / arthropod / セイヨウミツバチ, ヨウシュミツバチ /
Source (engineered)Expression System: Synthetic construct

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Component #5: 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 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: 941.32125 kDa
SourceSpecies: Escherichia coli k-12 / bacteria / image: Escherichia coli

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Component #6: 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 k-12 / bacteria / image: Escherichia coli

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Component #7: protein, 50S ribosomal protein L2

ProteinName: 50S ribosomal protein L2 / Recombinant expression: No
MassTheoretical: 29.663244 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #8: protein, 50S ribosomal protein L3

ProteinName: 50S ribosomal protein L3 / Recombinant expression: No
MassTheoretical: 22.277535 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #9: protein, 50S ribosomal protein L4

ProteinName: 50S ribosomal protein L4 / Recombinant expression: No
MassTheoretical: 22.121566 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #10: protein, 50S ribosomal protein L5

ProteinName: 50S ribosomal protein L5 / Recombinant expression: No
MassTheoretical: 20.073234 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #11: protein, 50S ribosomal protein L6

ProteinName: 50S ribosomal protein L6 / Recombinant expression: No
MassTheoretical: 18.801598 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #12: protein, 50S ribosomal protein L9

ProteinName: 50S ribosomal protein L9 / Recombinant expression: No
MassTheoretical: 15.78902 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #13: protein, 50S ribosomal protein L11

ProteinName: 50S ribosomal protein L11 / Recombinant expression: No
MassTheoretical: 14.763165 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #14: protein, 50S ribosomal protein L13

ProteinName: 50S ribosomal protein L13 / Recombinant expression: No
MassTheoretical: 16.050606 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #15: protein, 50S ribosomal protein L14

ProteinName: 50S ribosomal protein L14 / Recombinant expression: No
MassTheoretical: 13.45191 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #16: protein, 50S ribosomal protein L15

ProteinName: 50S ribosomal protein L15 / Recombinant expression: No
MassTheoretical: 14.877273 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #17: protein, 50S ribosomal protein L16

ProteinName: 50S ribosomal protein L16 / Recombinant expression: No
MassTheoretical: 15.312269 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #18: protein, 50S ribosomal protein L17

ProteinName: 50S ribosomal protein L17 / Recombinant expression: No
MassTheoretical: 13.721938 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #19: protein, 50S ribosomal protein L18

ProteinName: 50S ribosomal protein L18 / Recombinant expression: No
MassTheoretical: 12.663471 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #20: protein, 50S ribosomal protein L19

ProteinName: 50S ribosomal protein L19 / Recombinant expression: No
MassTheoretical: 13.028082 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #21: protein, 50S ribosomal protein L20

ProteinName: 50S ribosomal protein L20 / Recombinant expression: No
MassTheoretical: 13.396828 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #22: protein, 50S ribosomal protein L21

ProteinName: 50S ribosomal protein L21 / Recombinant expression: No
MassTheoretical: 11.586374 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #23: protein, 50S ribosomal protein L22

ProteinName: 50S ribosomal protein L22 / Recombinant expression: No
MassTheoretical: 12.253359 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #24: protein, 50S ribosomal protein L23

ProteinName: 50S ribosomal protein L23 / Recombinant expression: No
MassTheoretical: 10.546472 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #25: protein, 50S ribosomal protein L24

ProteinName: 50S ribosomal protein L24 / Recombinant expression: No
MassTheoretical: 11.078874 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #26: protein, 50S ribosomal protein L25

ProteinName: 50S ribosomal protein L25 / Recombinant expression: No
MassTheoretical: 10.713465 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #27: protein, 50S ribosomal protein L27

ProteinName: 50S ribosomal protein L27 / Recombinant expression: No
MassTheoretical: 8.174394 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #28: protein, 50S ribosomal protein L28

ProteinName: 50S ribosomal protein L28 / Recombinant expression: No
MassTheoretical: 8.896354 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #29: protein, 50S ribosomal protein L29

ProteinName: 50S ribosomal protein L29 / Recombinant expression: No
MassTheoretical: 7.286464 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #30: protein, 50S ribosomal protein L30

ProteinName: 50S ribosomal protein L30 / Recombinant expression: No
MassTheoretical: 6.423625 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #31: protein, 50S ribosomal protein L32

ProteinName: 50S ribosomal protein L32 / Recombinant expression: No
MassTheoretical: 6.332249 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #32: protein, 50S ribosomal protein L33

ProteinName: 50S ribosomal protein L33 / Recombinant expression: No
MassTheoretical: 5.814842 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #33: protein, 50S ribosomal protein L34

ProteinName: 50S ribosomal protein L34 / Recombinant expression: No
MassTheoretical: 5.397463 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #34: protein, 50S ribosomal protein L35

ProteinName: 50S ribosomal protein L35 / Recombinant expression: No
MassTheoretical: 7.181835 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #35: protein, 50S ribosomal protein L36

ProteinName: 50S ribosomal protein L36 / Recombinant expression: No
MassTheoretical: 4.37739 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #36: protein, 50S ribosomal protein L10

ProteinName: 50S ribosomal protein L10 / Recombinant expression: No
MassTheoretical: 14.112345 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #37: protein, 50S ribosomal protein L31

ProteinName: 50S ribosomal protein L31 / Recombinant expression: No
MassTheoretical: 7.516693 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #38: nucleic-acid, mRNA

Nucleic-acidName: mRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AUCUAGA
MassTheoretical: 2.205379 kDa

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Component #39: 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 k-12 / bacteria / image: Escherichia coli

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Component #40: protein, 30S ribosomal protein S2

ProteinName: 30S ribosomal protein S2 / Recombinant expression: No
MassTheoretical: 24.253943 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #41: protein, 30S ribosomal protein S3

ProteinName: 30S ribosomal protein S3 / Recombinant expression: No
MassTheoretical: 23.078785 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #42: protein, 30S ribosomal protein S4

ProteinName: 30S ribosomal protein S4 / Recombinant expression: No
MassTheoretical: 23.383002 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #43: protein, 30S ribosomal protein S5

ProteinName: 30S ribosomal protein S5 / Recombinant expression: No
MassTheoretical: 16.532088 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #44: protein, 30S ribosomal protein S6

ProteinName: 30S ribosomal protein S6 / Recombinant expression: No
MassTheoretical: 11.669371 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #45: protein, 30S ribosomal protein S7

ProteinName: 30S ribosomal protein S7 / Recombinant expression: No
MassTheoretical: 16.861523 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #46: protein, 30S ribosomal protein S8

ProteinName: 30S ribosomal protein S8 / Recombinant expression: No
MassTheoretical: 14.015361 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #47: protein, 30S ribosomal protein S9

ProteinName: 30S ribosomal protein S9 / Recombinant expression: No
MassTheoretical: 14.554882 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #48: protein, 30S ribosomal protein S10

ProteinName: 30S ribosomal protein S10 / Recombinant expression: No
MassTheoretical: 11.196988 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #49: protein, 30S ribosomal protein S11

ProteinName: 30S ribosomal protein S11 / Recombinant expression: No
MassTheoretical: 12.388068 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #50: protein, 30S ribosomal protein S12

ProteinName: 30S ribosomal protein S12 / Recombinant expression: No
MassTheoretical: 13.636961 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #51: protein, 30S ribosomal protein S13

ProteinName: 30S ribosomal protein S13 / Recombinant expression: No
MassTheoretical: 12.625753 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #52: protein, 30S ribosomal protein S14

ProteinName: 30S ribosomal protein S14 / Recombinant expression: No
MassTheoretical: 11.546442 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #53: protein, 30S ribosomal protein S15

ProteinName: 30S ribosomal protein S15 / Recombinant expression: No
MassTheoretical: 10.159621 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #54: protein, 30S ribosomal protein S16

ProteinName: 30S ribosomal protein S16 / Recombinant expression: No
MassTheoretical: 9.207572 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #55: protein, 30S ribosomal protein S17

ProteinName: 30S ribosomal protein S17 / Recombinant expression: No
MassTheoretical: 9.263946 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #56: protein, 30S ribosomal protein S18

ProteinName: 30S ribosomal protein S18 / Recombinant expression: No
MassTheoretical: 7.606768 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #57: protein, 30S ribosomal protein S19

ProteinName: 30S ribosomal protein S19 / Recombinant expression: No
MassTheoretical: 9.057626 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #58: protein, 30S ribosomal protein S20

ProteinName: 30S ribosomal protein S20 / Recombinant expression: No
MassTheoretical: 9.50619 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #59: protein, 30S ribosomal protein S21

ProteinName: 30S ribosomal protein S21 / Recombinant expression: No
MassTheoretical: 7.763073 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #60: protein, Peptide chain release factor RF1

ProteinName: Peptide chain release factor RF1 / Recombinant expression: No
MassTheoretical: 26.822072 kDa
SourceSpecies: Escherichia coli (strain k12) / bacteria /

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Component #61: nucleic-acid, P-site Ile-tRNA

Nucleic-acidName: P-site Ile-tRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AGGCUUGUAG CUCAGGUGGU UAGAGCGCAC CCCUGAUAAG GGUGAGGUCG GUGGUUCAAG UCCACUCAGG CCUACCA
MassTheoretical: 24.855754 kDa
SourceSpecies: Escherichia coli k-12 / bacteria / image: Escherichia coli

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Component #62: protein, Apidaecin

ProteinName: Apidaecin / Recombinant expression: No
MassTheoretical: 1.699052 kDa

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen 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
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 5132

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 36826
3D reconstructionSoftware: FREALIGN / Resolution: 3.4 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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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

  • Result of Omokage search can be filtered by keywords and the database types

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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