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- EMDB-3581: Structure of 70S ribosome from Lactococcus lactis -

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Basic information

Entry
Database: EMDB / ID: 3581
TitleStructure of 70S ribosome from Lactococcus lactis
Sample70S ribosome
SourceLactococcus lactis / bacteria / lactic acid bacteria / ラクトコッカス・ラクティス
Lactococcus lactis subsp. cremoris mg1363 / bacteria / lactic acid bacteria
Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Map data
Methodsingle particle reconstruction, at 5.6 Å resolution
AuthorsFranken LE / Oostergetel GT
CitationNat Commun, 2017, 8, 722-722

Nat Commun, 2017, 8, 722-722 Yorodumi Papers
A general mechanism of ribosome dimerization revealed by single-particle cryo-electron microscopy.
Linda E Franken / Gert T Oostergetel / Tjaard Pijning / Pranav Puri / Valentina Arkhipova / Egbert J Boekema / Bert Poolman / Albert Guskov

Validation ReportPDB-ID: 5myj

SummaryFull reportAbout validation report
DateDeposition: Jan 26, 2017 / Header (metadata) release: Feb 15, 2017 / Map release: Oct 11, 2017 / Last update: Oct 11, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.035
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5myj
  • Surface level: 0.035
  • Imaged by UCSF CHIMERA
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5myj
  • Imaged by Jmol
  • Download
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Supplemental images

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Map

Fileemd_3581.map.gz (map file in CCP4 format, 864001 KB)
Projections & slices

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Size
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AxesZ (Sec.)Y (Row.)X (Col.)
600 pix
1.11 Å/pix.
= 663. Å
600 pix
1.11 Å/pix.
= 663. Å
600 pix
1.11 Å/pix.
= 663. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.105 Å
Density
Contour Level:0.035 (by author), 0.035 (movie #1):
Minimum - Maximum-0.0636561 - 0.16130547
Average (Standard dev.)0.00072141824 (0.006043833)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions600600600
Origin000
Limit599599599
Spacing600600600
CellA=B=C: 663 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1051.1051.105
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z663.000663.000663.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS600600600
D min/max/mean-0.0640.1610.001

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Supplemental data

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Sample components

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Entire 70S ribosome

EntireName: 70S ribosome / Number of components: 52

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Component #1: protein, 70S ribosome

ProteinName: 70S ribosome / Recombinant expression: No
SourceSpecies: Lactococcus lactis / bacteria / lactic acid bacteria / ラクトコッカス・ラクティス

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

Nucleic-acidName: 16S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UUGAGAGUUU GAUCCUGGCU CAGGACGAAC GCUGGCGGCG UGCCUAAUAC AUGCAAGUUG AGCGAUGAAG AUUGGUGCUU GCACCAAUUU GAAGAGCAGC GAACGGGUGA GUAACGCGUG GGGAAUCUGC CUUUGAGCGG GGGACAACAU UUGGAAACGA AUGCUAAUAC CGCAUAAUAA CUUUAAACAU AAGUUUUAAG UUUGAAAGAU GCAAUUGCAU CACUCAAAGA UGAUCCCGCG UUGUAUUAGC UAGUUGGUGA GGUAAAGGCU CACCAAGGCG AUGAUACAUA GCCGACCUGA GAGGGUGAUC GGCCACAUUG GGACUGAGAC ACGGCCCAAA CUCCUACGGG AGGCAGCAGU AGGGAAUCUU CGGCAAUGGA CGAAAGUCUG ACCGAGCAAC GCCGCGUGAG UGAAGAAGGU UUUCGGAUCG UAAAACUCUG UUGGUAGAGA AGAACGUUGG UGAGAGUGGA AAGCUCAUCA AGUGACGGUA ACUACCCAGA AAGGGACGGC UAACUACGUG CCAGCAGCCG CGGUAAUACG UAGGUCCCGA GCGUUGUCCG GAUUUAUUGG GCGUAAAGCG AGCGCAGGUG GUUUAUUAAG UCUGGUGUAA AAGGCAGUGG CUCAACCAUU GUAUGCAUUG GAAACUGGUA GACUUGAGUG CAGGAGAGGA GAGUGGAAUU CCAUGUGUAG CGGUGAAAUG CGUAGAUAUA UGGAGGAACA CCGGUGGCGA AAGCGGCUCU CUGGCCUGUA ACUGACACUG AGGCUCGAAA GCGUGGGGAG CAAACAGGAU UAGAUACCCU GGUAGUCCAC GCCGUAAACG AUGAGUGCUA GAUGUAGGGA GCUAUAAGUU CUCUGUAUCG CAGCUAACGC AAUAAGCACU CCGCCUGGGG AGUACGACCG CAAGGUUGAA ACUCAAAGGA AUUGACGGGG GCCCGCACAA GCGGUGGAGC AUGUGGUUUA AUUCGAAGCA ACGCGAAGAA CCUUACCAGG UCUUGACAUA CUCGUGCUAU UCCUAGAGAU AGGAAGUUCC UUCGGGACAC GGGAUACAGG UGGUGCAUGG UUGUCGUCAG CUCGUGUCGU GAGAUGUUGG GUUAAGUCCC GCAACGAGCG CAACCCCUAU UGUUAGUUGC CAUCAUUAAG UUGGGCACUC UAACGAGACU GCCGGUGAUA AACCGGAGGA AGGUGGGGAU GACGUCAAAU CAUCAUGCCC CUUAUGACCU GGGCUACACA CGUGCUACAA UGGAUGGUAC AACGAGUCGC GAGACAGUGA UGUUUAGCUA AUCUCUUAAA ACCAUUCUCA GUUCGGAUUG UAGGCUGCAA CUCGCCUACA UGAAGUCGGA AUCGCUAGUA AUCGCGGAUC AGCACGCCGC GGUGAAUACG UUCCCGGGCC UUGUACACAC CGCCCGUCAC ACCACGGGAG UUGGGAGUAC CCGAAGUAGG UUGCCUAACC GCAAGGAGGG CGCUUCCUAA GGUAAGACCG AUGACUGGGG UGAAGUCGUA ACAAGGUAGC CGUAUCGGAA GGUGCGGCUG GAUCA
MassTheoretical: 497.142344 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris mg1363 / bacteria / lactic acid bacteria

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Component #3: protein, 30S ribosomal protein S2

ProteinName: 30S ribosomal protein S2 / Recombinant expression: No
MassTheoretical: 28.58976 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #4: protein, 30S ribosomal protein S3

ProteinName: 30S ribosomal protein S3 / Recombinant expression: No
MassTheoretical: 24.058795 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #5: protein, 30S ribosomal protein S4

ProteinName: 30S ribosomal protein S4 / Recombinant expression: No
MassTheoretical: 23.232605 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #6: protein, 30S ribosomal protein S5

ProteinName: 30S ribosomal protein S5 / Recombinant expression: No
MassTheoretical: 17.609285 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #7: protein, 30S ribosomal protein S6

ProteinName: 30S ribosomal protein S6 / Recombinant expression: No
MassTheoretical: 11.321831 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #8: protein, 30S ribosomal protein S7

ProteinName: 30S ribosomal protein S7 / Recombinant expression: No
MassTheoretical: 17.713443 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #9: protein, 30S ribosomal protein S8

ProteinName: 30S ribosomal protein S8 / Recombinant expression: No
MassTheoretical: 14.692106 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #10: protein, 30S ribosomal protein S9

ProteinName: 30S ribosomal protein S9 / Recombinant expression: No
MassTheoretical: 14.124289 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #11: protein, 30S ribosomal protein S10

ProteinName: 30S ribosomal protein S10 / Recombinant expression: No
MassTheoretical: 11.764765 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #12: protein, 30S ribosomal protein S11

ProteinName: 30S ribosomal protein S11 / Recombinant expression: No
MassTheoretical: 13.310352 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #13: protein, 30S ribosomal protein S12

ProteinName: 30S ribosomal protein S12 / Recombinant expression: No
MassTheoretical: 15.157884 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #14: protein, 30S ribosomal protein S13

ProteinName: 30S ribosomal protein S13 / Recombinant expression: No
MassTheoretical: 13.519672 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #15: protein, 30S ribosomal protein S14 type Z

ProteinName: 30S ribosomal protein S14 type Z / Recombinant expression: No
MassTheoretical: 7.151611 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #16: protein, 30S ribosomal protein S15

ProteinName: 30S ribosomal protein S15 / Recombinant expression: No
MassTheoretical: 10.367041 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #17: protein, 30S ribosomal protein S16

ProteinName: 30S ribosomal protein S16 / Recombinant expression: No
MassTheoretical: 10.270938 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #18: protein, 30S ribosomal protein S17

ProteinName: 30S ribosomal protein S17 / Recombinant expression: No
MassTheoretical: 10.166831 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #19: protein, 30S ribosomal protein S18

ProteinName: 30S ribosomal protein S18 / Recombinant expression: No
MassTheoretical: 9.392087 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #20: protein, 30S ribosomal protein S19

ProteinName: 30S ribosomal protein S19 / Recombinant expression: No
MassTheoretical: 10.595238 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #21: protein, 30S ribosomal protein S20

ProteinName: 30S ribosomal protein S20 / Recombinant expression: No
MassTheoretical: 8.38474 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #22: protein, 30S ribosomal protein S21

ProteinName: 30S ribosomal protein S21 / Recombinant expression: No
MassTheoretical: 7.041308 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #23: protein, 50S ribosomal protein L28

ProteinName: 50S ribosomal protein L28 / Recombinant expression: No
MassTheoretical: 7.187417 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #24: protein, 50S ribosomal protein L29

ProteinName: 50S ribosomal protein L29 / Recombinant expression: No
MassTheoretical: 7.874178 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #25: protein, 50S ribosomal protein L30

ProteinName: 50S ribosomal protein L30 / Recombinant expression: No
MassTheoretical: 6.202401 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #26: protein, 50S ribosomal protein L31 type B

ProteinName: 50S ribosomal protein L31 type B / Recombinant expression: No
MassTheoretical: 9.366479 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #27: protein, 50S ribosomal protein L32

ProteinName: 50S ribosomal protein L32 / Recombinant expression: No
MassTheoretical: 6.681631 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #28: protein, 50S ribosomal protein L33 3

ProteinName: 50S ribosomal protein L33 3 / Recombinant expression: No
MassTheoretical: 5.567652 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #29: protein, 50S ribosomal protein L34

ProteinName: 50S ribosomal protein L34 / Recombinant expression: No
MassTheoretical: 5.200206 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #30: protein, 50S ribosomal protein L35

ProteinName: 50S ribosomal protein L35 / Recombinant expression: No
MassTheoretical: 7.844419 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #31: protein, 50S ribosomal protein L36

ProteinName: 50S ribosomal protein L36 / Recombinant expression: No
MassTheoretical: 4.432446 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #32: nucleic-acid, 23S ribosomal RNA

Nucleic-acidName: 23S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
CAAAGUUAAU AAGGGCGCAC GGUGGAUGCC UUGGCACUAA GAGCCGAUGA AGGACGUGAC UAACGACGAU AUUCUAGGGG GAGCAGUAAG UACGCAUUGA UCCCUAGGUC UCCGAAUGGG GAAACCCAGC UGUUACUAGC AGUUAUUCAU GAGUGAAUAC AUAGCUCAUG UAAAGGUAAC GCAGAGAACU GAAACAUCUA AGUACCUGCA GGAAGAGAAA GUAAAAACGA UUUCGUAAGU AGCGGCGAGC GAACGCGAAG AAGGGCAAAC CAAGAAGCUU GCUUCUUGGG GUUGUAGGAC UGCAACGUGG ACUUAAGCAU UAUAGUCGAA UAACCUGGGA AGGUUAAUCA AAGAGGGUAA UAAUCCCGUA GACAAAAUAG CGCUUAUACC UAGCAGUAUC CUGAGUAGGG CUGGACACGC GAAAUCCAGU UUGAAUCCGG GAGGACCAUC UCCCAACCCU AAAUACUCCU UAGUGACCGA UAGUGAACCA GUACCGUGAG GGAAAGGUGA AAAGAACCCC GAGAGGGGAG UGAAAUAGCA CCUGAAACCG UGUGCCUACA AGAAGUUCGA GCCCGUUAAU GGGUGAGAGC GUGCCUUUUG UAGAAUGAAC CGGCGAGUUA CGUUAUGAUG CGAGGUUAAG UUGAAGAGAC GGAGCCGUAG GGAAACCGAG UCUGAAUAGG GCGACUUAGU AUCAUGAUGU AGACCCGAAA CCUAGUGACC UAUCCAUGAG CAGGGUGAAG GUGUGGUAAG ACGCACUGGA GGCCCGAACC AGGACACGUU GAAAAGUGUU UGGAUGACUU GUGGAUAGCG GAGAAAUUCC AAACGAACUG GGAGAUAGCU GGUUCUCUCC GAAAUAGCUU UAGGGCUAGC GUCGAAAUGU AAGUGUAUUG GAGGUAGAGC ACUGUUUGGG UGAGGGGUCC GUCUAGGAUU ACCAAUCUCA GAUAAACUCC GAAUGCUAAU ACACAUGUUC GGCAGUCAGA CUGCGAGUGC UAAGAUCCGU AGUCGAAAGG GAAACAGCCC AGACCAACAG CUAAGGUCCC AAAAUAUAUG UUAAGUGGAA AAGGAUGUGG GGUUGCACAG ACAACUAGGA UGUUAGCUCA GAAGCAGCUA UCAUUCAAAG AGUGCGUAAU AGCUCACUAG UCGAGUGACC CUGCGCCGAA AAUGUACCGG GGCUAAACAU AUUACCGAAG CUUUGGAUUG AUAUUUUAUC AAUGGUAGGA GAGCGUUCUU AACCGCAAUG AAGGUAUACC GUGAGGAGUG CUGGAGCGUU AAGAAGUGAG AAUGCCGGUA UGAGUAGCGC AAGAUAAGUG AGAAUCUUAU CCACCGUAAG ACUAAGGUUU CCAGGGGAAG GCUCGUCCGC CCUGGGUUAG UCGGGACCUA AGGCGAGGCC GAAAGGCGUA GUCGAUGGAC AACUGGUUGA UAUUCCAGUA CUAGAUAUGA UCGUGAUGGA GGGACGCAGU AGGCUAAGAG AUGCCAGUUA AUGGAUCCUG GUCUAAGCAG UGAGGUGUGA GAUGUGUCAA AUGCAUUUCU CUCUAACAUU GAGCUGUGAU GGGGAAGCAA CUACGGUUGC GAACUCUCUG AUGUCACACU GCCAAGAAAA GCUUCUAGCG UAAAGUCAUA UCUACCCGUA CCGCAAACCG ACACAGGUAG UCGAGGCGAG UAGCCUCAGG UGAUCGAGAG AACUCUCGUU AAGGAACUCG GCAAAAUAGC CCCGUAACUU CGGGAGAAGG GGUGCUGGUG UAAAAGCCAG CCGCAGUGAA UAGGCCCAAG CAACUGUUUA UCAAAAACAC AGCUCUCUGC UAAACCGCAA GGUGAUGUAU AGGGGGUGAC GCCUGCCCGG UGCUGGAAGG UUAAGAGGAG UGCUUAGACG UAAGUCGAAG GUAUGAAUUG AAGCCCCAGU AAACGGCGGC CGUAACUAUA ACGGUCCUAA GGUAGCGAAA UUCCUUGUCG GGUAAGUUCC GACCCGCACG AAAGGCGUAA UGAUUUGGGC ACUGUCUCAA CGAGAGACUC GGUGAAAUUU UAGUACCUGU GAAGAUGCAG GUUACCCGCG ACAGGACGGA AAGACCCCAU GGAGCUUUAC UGUAGUUUGA UAUUGAGUAC CUGUAAGUCA UGUACAGGAU AGGUAGGAGC CAUUGAAAUA GGGACGCUAG UUUCUAUUGA GGCGUUGUUG GGAUACUACC CUUGACUUAU GGUUACUCUA ACCCGCUGGC AUAAUCGGCC AGGGAGACAG UGUCUGACGG ACAGUUUGAC UGGGGCGGUC GCCUCCUAAA GAGUAACGGA GGCGCUCAAA GGUUGGCUCA GAUUGGUUGG AAAUCAAUCG UAGAGUGUAA AGGUAAAAGC CAGCUUGACU GCGAGAGCUA CAACUCGAGC AGGUAGGAAA CUAGGACUUA GUGAUCCGGU GGUACCGCAU GGAAGGGCCA UCGCUCAACG GAUAAAAGCU ACCCUGGGGA UAACAGGCUU AUCUCCCCCA AGAGUUCACA UCGACGGGGA GGUUUGGCAC CUCGAUGUCG GCUCGUCGCA UCCUGGGGCU GUAGUCGGUC CCAAGGGUUG GGCUGUUCGC CCAUUAAAGC GGCACGCGAG CUGGGUUCAG AACGUCGUGA GACAGUUCGG UCCCUAUCCG UCGCGGGCGU AGGUAAUUUG AGAGGAUCUG UCCUUAGUAC GAGAGGACCG GGAUGGACUU ACCGCUGGUG UACCAGUUGU UCCGCCAGGA GCACGGCUGG AUAGCUAUGU AGGGAAGGGA UAAGCGCUGA AAGCAUCUAA GUGCGAAGCC CACCUCAAGA UGAGAUUACC CAUUCGUAAG AAUUAAGAGC CCAGAGAGAU GAUCUGGUAG AUAGGCUGGA AGUGGAAGAG UUGCGAGACU UGGAGCGGAC CAGUACUAAU CGCUCGAGGA CUUUACC
MassTheoretical: 938.591125 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris mg1363 / bacteria / lactic acid bacteria

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Component #33: nucleic-acid, 5S ribosomal RNA

Nucleic-acidName: 5S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UUGGUAUUAA UUGCAUAGGA GAUAUACCUG UUCCCAUGUC GAACACAGAA GUCAAGUCCU AUUGCGCUGG AAGUACUUGG GGGUUGCCCC CUGGGAGAUA AAGACGAUGC CAAGU
MassTheoretical: 37.065969 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris mg1363 / bacteria / lactic acid bacteria

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Component #34: protein, 50S ribosomal protein L2

ProteinName: 50S ribosomal protein L2 / Recombinant expression: No
MassTheoretical: 29.641348 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #35: protein, 50S ribosomal protein L3

ProteinName: 50S ribosomal protein L3 / Recombinant expression: No
MassTheoretical: 21.956568 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #36: protein, 50S ribosomal protein L4

ProteinName: 50S ribosomal protein L4 / Recombinant expression: No
MassTheoretical: 22.393461 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #37: protein, 50S ribosomal protein L5

ProteinName: 50S ribosomal protein L5 / Recombinant expression: No
MassTheoretical: 20.03427 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #38: protein, 50S ribosomal protein L6

ProteinName: 50S ribosomal protein L6 / Recombinant expression: No
MassTheoretical: 19.313266 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #39: protein, 50S ribosomal protein L13

ProteinName: 50S ribosomal protein L13 / Recombinant expression: No
MassTheoretical: 16.192855 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #40: protein, 50S ribosomal protein L14

ProteinName: 50S ribosomal protein L14 / Recombinant expression: No
MassTheoretical: 12.944098 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #41: protein, 50S ribosomal protein L15

ProteinName: 50S ribosomal protein L15 / Recombinant expression: No
MassTheoretical: 15.376553 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #42: protein, 50S ribosomal protein L16

ProteinName: 50S ribosomal protein L16 / Recombinant expression: No
MassTheoretical: 15.375058 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #43: protein, 50S ribosomal protein L17

ProteinName: 50S ribosomal protein L17 / Recombinant expression: No
MassTheoretical: 14.280492 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #44: protein, 50S ribosomal protein L18

ProteinName: 50S ribosomal protein L18 / Recombinant expression: No
MassTheoretical: 12.426203 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #45: protein, 50S ribosomal protein L19

ProteinName: 50S ribosomal protein L19 / Recombinant expression: No
MassTheoretical: 13.129329 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #46: protein, 50S ribosomal protein L20

ProteinName: 50S ribosomal protein L20 / Recombinant expression: No
MassTheoretical: 13.726362 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #47: protein, 50S ribosomal protein L21

ProteinName: 50S ribosomal protein L21 / Recombinant expression: No
MassTheoretical: 11.444199 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #48: protein, 50S ribosomal protein L22

ProteinName: 50S ribosomal protein L22 / Recombinant expression: No
MassTheoretical: 12.49054 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #49: protein, 50S ribosomal protein L23

ProteinName: 50S ribosomal protein L23 / Recombinant expression: No
MassTheoretical: 10.819567 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #50: protein, 50S ribosomal protein L24

ProteinName: 50S ribosomal protein L24 / Recombinant expression: No
MassTheoretical: 10.897782 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #51: protein, 50S ribosomal protein L27

ProteinName: 50S ribosomal protein L27 / Recombinant expression: No
MassTheoretical: 10.053518 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Component #52: protein, Ribosome hibernation promotion factor

ProteinName: Ribosome hibernation promotion factor / Recombinant expression: No
MassTheoretical: 21.345988 kDa
SourceSpecies: Lactococcus lactis subsp. cremoris (strain mg1363) / bacteria / lactic acid bacteria
Strain: MG1363

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 7.6
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 291.15 K / Humidity: 80 %

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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: 25 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 / Applied symmetry: C1 (asymmetric) / Number of projections: 43530
3D reconstructionSoftware: RELION / Resolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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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)

Read more

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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

Read more