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- EMDB-3640: 2.9S structure of the 70S ribosome composing the S. aureus 100S c... -

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Basic information

Entry
Database: EMDB / ID: 3640
Title2.9S structure of the 70S ribosome composing the S. aureus 100S complex
Sample70S ribosome of the S. aureus 100S complex
SourceStaphylococcus aureus / bacteria / スタフィロコッカス・アウレウス, 黄色ブドウ球菌
Map data2.9A cryo-EM map of one of the 70S ribosomes composing the S. aureus 100S complex
Methodsingle particle reconstruction, at 2.9 Å resolution
AuthorsMatzov D / Aibara S
CitationNat Commun, 2017, 8, 723-723

Nat Commun, 2017, 8, 723-723 Yorodumi Papers
The cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus.
Donna Matzov / Shintaro Aibara / Arnab Basu / Ella Zimmerman / Anat Bashan / Mee-Ngan F Yap / Alexey Amunts / Ada E Yonath

Validation ReportPDB-ID: 5ngm

SummaryFull reportAbout validation report
DateDeposition: Mar 18, 2017 / Header (metadata) release: Oct 4, 2017 / Map release: Oct 4, 2017 / Last update: Oct 11, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.08
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 0.08
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5ngm
  • Surface level: 0.08
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_3640.map.gz (map file in CCP4 format, 256001 KB)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
400 pix
1.07 Å/pix.
= 428. Å
400 pix
1.07 Å/pix.
= 428. Å
400 pix
1.07 Å/pix.
= 428. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.07 Å
Density
Contour Level:0.08 (by author), 0.08 (movie #1):
Minimum - Maximum-0.64437616 - 1.0560213
Average (Standard dev.)0.0015266285 (0.026998984)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions400400400
Origin000
Limit399399399
Spacing400400400
CellA=B=C: 428.00003 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z428.000428.000428.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.6441.0560.002

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Supplemental data

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Sample components

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Entire 70S ribosome of the S. aureus 100S complex

EntireName: 70S ribosome of the S. aureus 100S complex / Number of components: 60

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Component #1: protein, 70S ribosome of the S. aureus 100S complex

ProteinName: 70S ribosome of the S. aureus 100S complex / 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
Strain: USA300_FPR3757

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Component #2: protein, 30S subunit

ProteinName: 30S subunit / 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
Strain: USA300_FPR3757

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Component #3: protein, 16S rRNA

ProteinName: 16S rRNA / 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
Strain: USA300_FPR3757

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Component #4: protein, 30S ribosomal proteins

ProteinName: 30S ribosomal proteins / 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
Strain: USA300_FPR3757

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Component #5: protein, 50S subunit

ProteinName: 50S subunit / 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
Strain: USA300_FPR3757

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Component #6: protein, 23S and 5S rRNA

ProteinName: 23S and 5S rRNA / 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
Strain: USA300_FPR3757

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Component #7: protein, 50S ribosomal proteins

ProteinName: 50S ribosomal proteins / 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
Strain: USA300_FPR3757

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Component #8: nucleic-acid, 16S ribosomal RNA

Nucleic-acidName: 16S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UUUUAUGGAG AGUUUGAUCC UGGCUCAGGA UGAACGCUGG CGGCGUGCCU AAUACAUGCA AGUCGAGCGA ACGGACGAGA AGCUUGCUUC UCUGAUGUUA GCGGCGGACG GGUGAGUAAC ACGUGGAUAA CCUACCUAUA AGACUGGGAU AACUUCGGGA AACCGGAGCU AAUACCGGAU AAUAUUUUGA ACCGCAUGGU UCAAAAGUGA AAGACGGUCU UGCUGUCACU UAUAGAUGGA UCCGCGCUGC AUUAGCUAGU UGGUAAGGUA ACGGCUUACC AAGGCAACGA UGCAUAGCCG ACCUGAGAGG GUGAUCGGCC ACACUGGAAC UGAGACACGG UCCAGACUCC UACGGGAGGC AGCAGUAGGG AAUCUUCCGC AAUGGGCGAA AGCCUGACGG AGCAACGCCG CGUGAGUGAU GAAGGUCUUC GGAUCGUAAA ACUCUGUUAU UAGGGAAGAA CAUAUGUGUA AGUAACUGUG CACAUCUUGA CGGUACCUAA UCAGAAAGCC ACGGCUAACU ACGUGCCAGC AGCCGCGGUA AUACGUAGGU GGCAAGCGUU AUCCGGAAUU AUUGGGCGUA AAGCGCGCGU AGGCGGUUUU UUAAGUCUGA UGUGAAAGCC CACGGCUCAA CCGUGGAGGG UCAUUGGAAA CUGGAAAACU UGAGUGCAGA AGAGGAAAGU GGAAUUCCAU GUGUAGCGGU GAAAUGCGCA GAGAUAUGGA GGAACACCAG UGGCGAAGGC GACUUUCUGG UCUGUAACUG ACGCUGAUGU GCGAAAGCGU GGGGAUCAAA CAGGAUUAGA UACCCUGGUA GUCCACGCCG UAAACGAUGA GUGCUAAGUG UUAGGGGGUU UCCGCCCCUU AGUGCUGCAG CUAACGCAUU AAGCACUCCG CCUGGGGAGU ACGACCGCAA GGUUGAAACU CAAAGGAAUU GACGGGGACC CGCACAAGCG GUGGAGCAUG UGGUUUAAUU CGAAGCAACG CGAAGAACCU UACCAAAUCU UGACAUCCUU UGACAACUCU AGAGAUAGAG CCUUCCCCUU CGGGGGACAA AGUGACAGGU GGUGCAUGGU UGUCGUCAGC UCGUGUCGUG AGAUGUUGGG UUAAGUCCCG CAACGAGCGC AACCCUUAAG CUUAGUUGCC AUCAUUAAGU UGGGCACUCU AAGUUGACUG CCGGUGACAA ACCGGAGGAA GGUGGGGAUG ACGUCAAAUC AUCAUGCCCC UUAUGAUUUG GGCUACACAC GUGCUACAAU GGACAAUACA AAGGGCAGCG AAACCGCGAG GUCAAGCAAA UCCCAUAAAG UUGUUCUCAG UUCGGAUUGU AGUCUGCAAC UCGACUACAU GAAGCUGGAA UCGCUAGUAA UCGUAGAUCA GCAUGCUACG GUGAAUACGU UCCCGGGUCU UGUACACACC GCCCGUCACA CCACGAGAGU UUGUAACACC CGAAGCCGGU GGAGUAACCU UUUAGGAGCU AGCCGUCGAA GGUGGGACAA AUGAUUGGGG UGAAGUCGUA ACAAGGUAGC CGUAUCGGAA GGUGCGGCUG GAUCACCUCC UUUCU
MassTheoretical: 502.975906 kDa
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

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Component #9: protein, 30S ribosomal protein S2

ProteinName: 30S ribosomal protein S2 / Recombinant expression: No
MassTheoretical: 29.136369 kDa
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

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Component #10: protein, 30S ribosomal protein S3

ProteinName: 30S ribosomal protein S3 / Recombinant expression: No
MassTheoretical: 24.143867 kDa
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

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Component #11: protein, 30S ribosomal protein S4

ProteinName: 30S ribosomal protein S4 / Recombinant expression: No
MassTheoretical: 23.051416 kDa
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

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Component #12: protein, 30S ribosomal protein S5

ProteinName: 30S ribosomal protein S5 / Recombinant expression: No
MassTheoretical: 17.770512 kDa
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

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Component #13: protein, 30S ribosomal protein S6

ProteinName: 30S ribosomal protein S6 / Recombinant expression: No
MassTheoretical: 11.613146 kDa
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

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Component #14: protein, 30S ribosomal protein S7

ProteinName: 30S ribosomal protein S7 / Recombinant expression: No
MassTheoretical: 17.826555 kDa
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

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Component #15: protein, 30S ribosomal protein S8

ProteinName: 30S ribosomal protein S8 / Recombinant expression: No
MassTheoretical: 14.854315 kDa
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

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Component #16: protein, 30S ribosomal protein S9

ProteinName: 30S ribosomal protein S9 / Recombinant expression: No
MassTheoretical: 14.856987 kDa
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

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Component #17: protein, 30S ribosomal protein S10

ProteinName: 30S ribosomal protein S10 / Recombinant expression: No
MassTheoretical: 11.598503 kDa
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

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Component #18: protein, 30S ribosomal protein S11

ProteinName: 30S ribosomal protein S11 / Recombinant expression: No
MassTheoretical: 13.907978 kDa
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

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Component #19: protein, 30S ribosomal protein S12

ProteinName: 30S ribosomal protein S12 / Recombinant expression: No
MassTheoretical: 15.32087 kDa
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

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Component #20: protein, 30S ribosomal protein S13

ProteinName: 30S ribosomal protein S13 / Recombinant expression: No
MassTheoretical: 13.747919 kDa
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

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Component #21: protein, 30S ribosomal protein S14 type Z

ProteinName: 30S ribosomal protein S14 type Z / Recombinant expression: No
MassTheoretical: 7.317769 kDa
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

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Component #22: protein, 30S ribosomal protein S15

ProteinName: 30S ribosomal protein S15 / Recombinant expression: No
MassTheoretical: 10.63433 kDa
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

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Component #23: protein, 30S ribosomal protein S16

ProteinName: 30S ribosomal protein S16 / Recombinant expression: No
MassTheoretical: 10.253886 kDa
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

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Component #24: protein, 30S ribosomal protein S17

ProteinName: 30S ribosomal protein S17 / Recombinant expression: No
MassTheoretical: 10.196888 kDa
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

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Component #25: protein, 30S ribosomal protein S18

ProteinName: 30S ribosomal protein S18 / Recombinant expression: No
MassTheoretical: 9.332018 kDa
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

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Component #26: protein, 30S ribosomal protein S19

ProteinName: 30S ribosomal protein S19 / Recombinant expression: No
MassTheoretical: 10.639309 kDa
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

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Component #27: protein, 30S ribosomal protein S20

ProteinName: 30S ribosomal protein S20 / Recombinant expression: No
MassTheoretical: 9.039472 kDa
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

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Component #28: protein, 30S ribosomal protein S21

ProteinName: 30S ribosomal protein S21 / Recombinant expression: No
MassTheoretical: 6.994267 kDa
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

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Component #29: protein, Ribosome hibernation promoting factor

ProteinName: Ribosome hibernation promoting factor / Recombinant expression: No
MassTheoretical: 22.244914 kDa
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

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Component #30: nucleic-acid, 23S Ribosomal RNA

Nucleic-acidName: 23S Ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GAUUAAGUUA UUAAGGGCGC ACGGUGGAUG CCUUGGCACU AGAAGCCGAU GAAGGACGUU ACUAACGACG AUAUGCUUUG GGGAGCUGUA AGUAAGCUUU GAUCCAGAGA UUUCCGAAUG GGGAAACCCA GCAUGAGUUA UGUCAUGUUA UCGAUAUGUG AAUACAUAGC AUAUCAGAAG GCACACCCGG AGAACUGAAA CAUCUUAGUA CCCGGAGGAA GAGAAAGAAA AUUCGAUUCC CUUAGUAGCG GCGAGCGAAA UGGGAAGAGC CCAAACCAAC AAGCUUGCUU GUUGGGGUUG UAGGACACUC UAUACGGAGU UACAAAGGAC GACAUUAGAC GAAUCAUCUG GAAAGAUGAA UCAAAGAAGG UAAUAAUCCU GUAGUCGAAA AUGUUGUCUC UCUUGAGUGG AUCCUGAGUA CGACGGAGCA CGUGAAAUUC CGUCGGAAUC UGGGAGGACC AUCUCCUAAG GCUAAAUACU CUCUAGUGAC CGAUAGUGAA CCAGUACCGU GAGGGAAAGG UGAAAAGCAC CCCGGAAGGG GAGUGAAAUA GAACCUGAAA CCGUGUGCUU ACAAGUAGUC AGAGCCCGUU AAUGGGUGAU GGCGUGCCUU UUGUAGAAUG AACCGGCGAG UUACGAUUUG AUGCAAGGUU AAGCAGUAAA UGUGGAGCCG UAGCGAAAGC GAGUCUGAAU AGGGCGUUUA GUAUUUGGUC GUAGACCCGA AACCAGGUGA UCUACCCUUG GUCAGGUUGA AGUUCAGGUA ACACUGAAUG GAGGACCGAA CCGACUUACG UUGAAAAGUG AGCGGAUGAA CUGAGGGUAG CGGAGAAAUU CCAAUCGAAC CUGGAGAUAG CUGGUUCUCU CCGAAAUAGC UUUAGGGCUA GCCUCAAGUG AUGAUUAUUG GAGGUAGAGC ACUGUUUGGA CGAGGGGCCC CUCUCGGGUU ACCGAAUUCA GACAAACUCC GAAUGCCAAU UAAUUUAACU UGGGAGUCAG AACAUGGGUG AUAAGGUCCG UGUUCGAAAG GGAAACAGCC CAGACCACCA GCUAAGGUCC CAAAAUAUAU GUUAAGUGGA AAAGGAUGUG GCGUUGCCCA GACAACUAGG AUGUUGGCUU AGAAGCAGCC AUCAUUUAAA GAGUGCGUAA UAGCUCACUA GUCGAGUGAC ACUGCGCCGA AAAUGUACCG GGGCUAAACA UAUUACCGAA GCUGUGGAUU GUCCUUUGGA CAAUGGUAGG AGAGCGUUCU AAGGGCGUUG AAGCAUGAUC GUAAGGACAU GUGGAGCGCU UAGAAGUGAG AAUGCCGGUG UGAGUAGCGA AAGACGGGUG AGAAUCCCGU CCACCGAUUG ACUAAGGUUU CCAGAGGAAG GCUCGUCCGC UCUGGGUUAG UCGGGUCCUA AGCUGAGGCC GACAGGCGUA GGCGAUGGAU AACAGGUUGA UAUUCCUGUA CCACCUAUAA UCGUUUUAAU CGAUGGGGGG ACGCAGUAGG AUAGGCGAAG CGUGCGAUUG GAUUGCACGU CUAAGCAGUA AGGCUGAGUA UUAGGCAAAU CCGGUACUCG UUAAGGCUGA GCUGUGAUGG GGAGAAGACA UUGUGUCUUC GAGUCGUUGA UUUCACACUG CCGAGAAAAG CCUCUAGAUA GAAAAUAGGU GCCCGUACCG CAAACCGACA CAGGUAGUCA AGAUGAGAAU UCUAAGGUGA GCGAGCGAAC UCUCGUUAAG GAACUCGGCA AAAUGACCCC GUAACUUCGG GAGAAGGGGU GCUCUUUAGG GUUAACGCCC AGAAGAGCCG CAGUGAAUAG GCCCAAGCGA CUGUUUAUCA AAAACACAGG UCUCUGCUAA ACCGUAAGGU GAUGUAUAGG GGCUGACGCC UGCCCGGUGC UGGAAGGUUA AGAGGAGUGG UUAGCUUCUG CGAAGCUACG AAUCGAAGCC CCAGUAAACG GCGGCCGUAA CUAUAACGGU CCUAAGGUAG CGAAAUUCCU UGUCGGGUAA GUUCCGACCC GCACGAAAGG CGUAACGAUU UGGGCACUGU CUCAACGAGA GACUCGGUGA AAUCAUAGUA CCUGUGAAGA UGCAGGUUAC CCGCGACAGG ACGGAAAGAC CCCGUGGAGC UUUACUGUAG CCUGAUAUUG AAAUUCGGCA CAGCUUGUAC AGGAUAGGUA GGAGCCUUUG AAACGUGAGC GCUAGCUUAC GUGGAGGCGC UGGUGGGAUA CUACCCUAGC UGUGUUGGCU UUCUAACCCG CACCACUUAU CGUGGUGGGA GACAGUGUCA GGCGGGCAGU UUGACUGGGG CGGUCGCCUC CUAAAAGGUA ACGGAGGCGC UCAAAGGUUC CCUCAGAAUG GUUGGAAAUC AUUCAUAGAG UGUAAAGGCA UAAGGGAGCU UGACUGCGAG ACCUACAAGU CGAGCAGGGU CGAAAGACGG ACUUAGUGAU CCGGUGGUUC CGCAUGGAAG GGCCAUCGCU CAACGGAUAA AAGCUACCCC GGGGAUAACA GGCUUAUCUC CCCCAAGAGU UCACAUCGAC GGGGAGGUUU GGCACCUCGA UGUCGGCUCA UCGCAUCCUG GGGCUGUAGU CGGUCCCAAG GGUUGGGCUG UUCGCCCAUU AAAGCGGUAC GCGAGCUGGG UUCAGAACGU CGUGAGACAG UUCGGUCCCU AUCCGUCGUG GGCGUAGGAA AUUUGAGAGG AGCUGUCCUU AGUACGAGAG GACCGGGAUG GACAUACCUC UGGUGUACCA GUUGUCGUGC CAACGGCAUA GCUGGGUAGC UAUGUGUGGA CGGGAUAAGU GCUGAAAGCA UCUAAGCAUG AAGCCCCCCU CAAGAUGAGA UUUCCCAACU UCGGUUAUAA GAUCCCUCAA AGAUGAUGAG GUUAAUAGGU UCGAGGUGGA AGCAUGGUGA CAUGUGGAGC UGACGAAUAC UAAUCGAUCG AAGACUUAAU CAA
MassTheoretical: 946.697625 kDa
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

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Component #31: nucleic-acid, 5S Ribosomal RNA

Nucleic-acidName: 5S Ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UCUGGUGACU AUAGCAAGGA GGUCACACCU GUUCCCAUGC CGAACACAGA AGUUAAGCUC CUUAGCGUCG AUGGUAGUCG AACUUACGUU CCGCUAGAGU AGAACGUUGC CAGGC
MassTheoretical: 36.974945 kDa
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

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Component #32: protein, 50S ribosomal protein L2

ProteinName: 50S ribosomal protein L2 / Recombinant expression: No
MassTheoretical: 30.217164 kDa
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

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Component #33: protein, 50S ribosomal protein L3

ProteinName: 50S ribosomal protein L3 / Recombinant expression: No
MassTheoretical: 23.760256 kDa
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

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Component #34: protein, 50S ribosomal protein L4

ProteinName: 50S ribosomal protein L4 / Recombinant expression: No
MassTheoretical: 22.495697 kDa
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

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Component #35: protein, 50S ribosomal protein L5

ProteinName: 50S ribosomal protein L5 / Recombinant expression: No
MassTheoretical: 20.296637 kDa
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

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Component #36: protein, 50S ribosomal protein L6

ProteinName: 50S ribosomal protein L6 / Recombinant expression: No
MassTheoretical: 19.81858 kDa
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

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Component #37: protein, 50S ribosomal protein L13

ProteinName: 50S ribosomal protein L13 / Recombinant expression: No
MassTheoretical: 16.359427 kDa
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

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Component #38: protein, 50S ribosomal protein L14

ProteinName: 50S ribosomal protein L14 / Recombinant expression: No
MassTheoretical: 13.157342 kDa
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

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Component #39: protein, 50S ribosomal protein L15

ProteinName: 50S ribosomal protein L15 / Recombinant expression: No
MassTheoretical: 15.62889 kDa
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

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Component #40: protein, 50S ribosomal protein L16

ProteinName: 50S ribosomal protein L16 / Recombinant expression: No
MassTheoretical: 16.274049 kDa
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

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Component #41: protein, 50S ribosomal protein L17

ProteinName: 50S ribosomal protein L17 / Recombinant expression: No
MassTheoretical: 13.771773 kDa
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

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Component #42: protein, 50S ribosomal protein L18

ProteinName: 50S ribosomal protein L18 / Recombinant expression: No
MassTheoretical: 13.124093 kDa
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

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Component #43: protein, 50S ribosomal protein L19

ProteinName: 50S ribosomal protein L19 / Recombinant expression: No
MassTheoretical: 13.392771 kDa
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

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Component #44: protein, 50S ribosomal protein L20

ProteinName: 50S ribosomal protein L20 / Recombinant expression: No
MassTheoretical: 13.720295 kDa
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

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Component #45: protein, 50S ribosomal protein L21

ProteinName: 50S ribosomal protein L21 / Recombinant expression: No
MassTheoretical: 11.354081 kDa
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

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Component #46: protein, 50S ribosomal protein L22

ProteinName: 50S ribosomal protein L22 / Recombinant expression: No
MassTheoretical: 12.857922 kDa
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

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Component #47: protein, 50S ribosomal protein L23

ProteinName: 50S ribosomal protein L23 / Recombinant expression: No
MassTheoretical: 10.625398 kDa
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

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Component #48: protein, 50S ribosomal protein L24

ProteinName: 50S ribosomal protein L24 / Recombinant expression: No
MassTheoretical: 11.561504 kDa
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

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Component #49: protein, 50S ribosomal protein L25

ProteinName: 50S ribosomal protein L25 / Recombinant expression: No
MassTheoretical: 23.810609 kDa
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

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Component #50: protein, 50S ribosomal protein L27

ProteinName: 50S ribosomal protein L27 / Recombinant expression: No
MassTheoretical: 10.334798 kDa
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

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Component #51: protein, 50S ribosomal protein L28

ProteinName: 50S ribosomal protein L28 / Recombinant expression: No
MassTheoretical: 6.995289 kDa
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

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Component #52: protein, 50S ribosomal protein L29

ProteinName: 50S ribosomal protein L29 / Recombinant expression: No
MassTheoretical: 8.5929 kDa
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

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Component #53: protein, 50S ribosomal protein L30

ProteinName: 50S ribosomal protein L30 / Recombinant expression: No
MassTheoretical: 6.565683 kDa
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

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Component #54: protein, 50S ribosomal protein L31 type B

ProteinName: 50S ribosomal protein L31 type B / Recombinant expression: No
MassTheoretical: 9.737912 kDa
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

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Component #55: protein, 50S ribosomal protein L32

ProteinName: 50S ribosomal protein L32 / Recombinant expression: No
MassTheoretical: 6.500609 kDa
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

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Component #56: protein, 50S ribosomal protein L33

ProteinName: 50S ribosomal protein L33 / Recombinant expression: No
MassTheoretical: 5.944937 kDa
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

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Component #57: protein, 50S ribosomal protein L34

ProteinName: 50S ribosomal protein L34 / Recombinant expression: No
MassTheoretical: 5.454642 kDa
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

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Component #58: protein, 50S ribosomal protein L35

ProteinName: 50S ribosomal protein L35 / Recombinant expression: No
MassTheoretical: 7.722368 kDa
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

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Component #59: protein, 50S ribosomal protein L36

ProteinName: 50S ribosomal protein L36 / Recombinant expression: No
MassTheoretical: 4.318422 kDa
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

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Component #60: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 205 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 7.5
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: 2.3 e/Å2 / Illumination mode: FLOOD BEAM
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: 224554
3D reconstructionResolution: 2.9 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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