Volta phase plate data collection facilitates image processing and cryo-EM structure determination
von Loeffelholz O, Papai G, Danev R, Myasnikov AG, Natchiar SK, Hazemann I, Menetret JF, Klaholz BP
J Struct Biol (2018) [ Pubmed: 29337113 DOI: doi:10.1016/j.jsb.2018.01.003 ]
- Ribosome (Complex from Homo sapiens)
Volta phase plate data collection facilitates image processing and cryo-EM structure determination
von Loeffelholz O, Papai G, Danev R, Myasnikov AG, Natchiar SK, Hazemann I, Menetret JF, Klaholz BP
J Struct Biol (2018) [ Pubmed: 29337113 DOI: doi:10.1016/j.jsb.2018.01.003 ]
- Ribosome (Complex from Homo sapiens)
Volta phase plate data collection facilitates image processing and cryo-EM structure determination
von Loeffelholz O, Papai G, Danev R, Myasnikov AG, Natchiar SK, Hazemann I, Menetret JF, Klaholz BP
J Struct Biol (2018) 202 pp. 191-199 [ Pubmed: 29337113 DOI: doi:10.1016/j.jsb.2018.01.003 ]
- Ribosome (Complex from Homo sapiens)
70S ribosome from Staphylococcus aureus
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 5li0
Q-score: 0.405
Khusainov I, Vicens Q, Bochler A, Grosse F, Myasnikov A, Menetret JF, Chicher J, Marzi S, Romby P, Yusupova G, Yusupov M, Hashem Y
Nucleic Acids Res (2016) 44 pp. 10491-10504 [ Pubmed: 27906650 DOI: doi:10.1093/nar/gkw933 ]
- 30s ribosomal protein s8 (14 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- 5s ribosomal rna (36 kDa, RNA from Staphylococcus aureus (strain NCTC 8325))
- 50s ribosomal protein l13 (16 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- 50s ribosomal protein l6 (18 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- 50s ribosomal protein l18 (13 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- 30s ribosomal protein s4 (22 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- 30s ribosomal protein s10 (11 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- 50s ribosomal protein l21 (11 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- 50s ribosomal protein l2 (29 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- 30s ribosomal protein s12 (15 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- 30s ribosomal protein s16 (10 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- 50s ribosomal protein l28 (5 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- 50s ribosomal protein l17 (13 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- Magnesium ion (24 Da, Ligand)
- 30s ribosomal protein s9 (14 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- 30s ribosomal protein s6 (11 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- 50s ribosomal protein l24 (10 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- 50s ribosomal protein l29 (7 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- 30s ribosomal protein s18 (8 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- Oxygen atom (15 Da, Ligand)
- 50s ribosomal protein l23 (10 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- 50s ribosomal protein l4 (21 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- 50s ribosomal protein l3 (23 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- 50s ribosomal protein l5 (18 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- 23s ribosomal rna (945 kDa, RNA from Staphylococcus aureus (strain NCTC 8325))
- 30s ribosomal protein s17 (10 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- 30s ribosomal protein s7 (17 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- 50s ribosomal protein l30 (6 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- 30s ribosomal protein s15 (10 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- 30s ribosomal protein s13 (13 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- 30s ribosomal protein s11 (12 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- 50s ribosomal protein l19 (12 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- Zinc ion (65 Da, Ligand)
- 50s ribosomal protein l20 (13 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- 50s ribosomal protein l15 (14 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- 50s ribosomal protein l32 (6 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- 30s ribosomal protein s2 (29 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- 70s ribosome from staphylococcus aureus (Complex from Staphylococcus aureus (strain NCTC 8325))
- 50s ribosomal protein l33 2 (4 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- 16s ribosomal rna (500 kDa, RNA from Staphylococcus aureus (strain NCTC 8325))
- 30s ribosomal protein s19 (9 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- 50s ribosomal protein l31 type b (9 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- 50s ribosomal protein l34 (5 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- 50s ribosomal protein l22 (12 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- Water (18 Da, Ligand)
- 30s ribosomal protein s14 type z (7 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- 50s ribosomal protein l25 (10 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- 50s ribosomal protein l36 (4 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- 30s ribosomal protein s5 (17 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- 30s ribosomal protein s20 (8 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- 50s ribosomal protein l16 (15 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- 30s ribosomal protein s3 (24 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- 50s ribosomal protein l35 (6 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- 50s ribosomal protein l14 (13 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
- 50s ribosomal protein l27 (8 kDa, Protein from Staphylococcus aureus (strain NCTC 8325))
Ribosomal 18S rRNA base pairs with mRNA during eukaryotic translation initiation
Martin F, Menetret JF, Simonetti A, Myasnikov AG, Vicens Q, Prongidi-Fix L, Natchiar SK, Klaholz BP, Eriani G
Nat Commun (2016) 7 pp. 12622-12622 [ DOI: doi:10.1038/ncomms12622 Pubmed: 27554013 ]
The molecular structure of the left-handed supra- molecular helix of eukaryotic polyribosomes
Resolution: 34.0 Å
EM Method: Subtomogram averaging
Fitted PDBs: 4v3p
Q-score: 0.016
Myasnikov AG, Afonina ZHA, Menetret J-F, Shirokov VA, Spirin AS, Klaholz BP
Nat Commun (2014) 5 pp. 5294- [ DOI: doi:10.1038/ncomms6294 Pubmed: 25376914 ]
- Wheat germ poly-ribosome (100 MDa, Complex from Triticum aestivum)
- Poly-ribosome from in vitro wheat germ system (100 MDa, Sample)
Structure of the SecY protein translocation channel in action
Resolution: 9.0 Å
EM Method: Single-particle
Fitted PDBs: 4v4n
Q-score: 0.124
Park E, Menetret JF, Gumbart JC, Ludtke SJ, Li W, Whynot A, Rapoport TA, Akey CW
Nature (2014) 506 pp. 102-106 [ Pubmed: 24153188 DOI: doi:10.1038/nature12720 ]
- Non-translating 70s ribosome (2 MDa, Complex from Methanocaldococcus jannaschii)
- Secyebeta (61 kDa, Protein from Methanocaldococcus jannaschii)
- Methanococcus jannaschii 70s ribosome-secyebeta complex (2 MDa, Sample)
- Transfer rna (25 kDa, RNA from Methanocaldococcus jannaschii)
Structure of the SecY protein translocation channel in action
Resolution: 9.5 Å
EM Method: Single-particle
Fitted PDBs: 3j45
Q-score: 0.103
Park E, Menetret JF, Gumbart JC, Ludtke SJ, Li W, Whynot A, Rapoport TA, Akey CW
Nature (2014) 506 pp. 102-106 [ DOI: doi:10.1038/nature12720 Pubmed: 24153188 ]
- Secyeg (73 kDa, Protein from Escherichia coli)
- E. coli 70s ribosome with recombinant e. coli secyeg (2 MDa, Sample)
- Non-translating 70s ribosome (2 MDa, Complex from Escherichia coli)
Structure of the SecY protein translocation channel in action
Resolution: 10.1 Å
EM Method: Single-particle
Fitted PDBs: 3j46
Q-score: 0.079
Park E, Menetret JF, Gumbart JC, Ludtke SJ, Li W, Whynot A, Rapoport TA, Akey CW
Nature (2014) 506 pp. 102-106 [ Pubmed: 24153188 DOI: doi:10.1038/nature12720 ]
- Membrane-bound 70s ribosome (2 MDa, Complex from Escherichia coli)
- Preprotein translocase (73 kDa, Protein from Escherichia coli)
- Transfer rna (25 kDa, RNA from Escherichia coli)
- S1p (61 kDa, Protein from Escherichia coli)
- Ribosome-nascent chain-secyeg complex (2 MDa, Sample)
Electron cryo-EM of full-length Thermus thermophilus DNA gyrase
Papillon J, Menetret JF, Batisse C, Helye R, Schultz P, Potier N, Lamour V
Nucleic Acids Res (2013) 41 pp. 7815-7827 [ Pubmed: 23804759 DOI: doi:10.1093/nar/gkt560 ]
- Dna gyrase (321 kDa, Protein from Thermus thermophilus)
- Holoenzyme complex of thermus thermophilus dna gyrase with adpnp (321 kDa, Sample)