Cryo-EM Structure of T. kodakarensis 70S ribosome in TkNat10 deleted strain
Resolution: 2.65 Å
EM Method: Single-particle
Fitted PDBs: 6skg
Q-score: 0.614
Sas-Chen A, Thomas JM, Matzov D, Taoka M, Nance KD, Nir R, Bryson KM, Shachar R, Liman GLS, Burkhart BW, Gamage ST, Nobe Y, Briney CA, Levy MJ, Fuchs RT, Robb GB, Hartmann J, Sharma S, Lin Q, Florens L, Washburn MP, Isobe T, Santangelo TJ, Shalev-Benami M, Meier JL, Schwartz S
Nature (2020) 583 pp. 638-643 [ DOI: doi:10.1038/s41586-020-2418-2 Pubmed: 32555463 ]
- 50s ribosomal protein l21e (11 kDa, Protein from Thermococcus kodakarensis)
- 30s ribosomal protein s17 (13 kDa, Protein from Thermococcus kodakarensis)
- Unknown ribosomal protein (2 kDa, Protein from Thermococcus kodakarensis)
- 30s ribosomal protein s8e (14 kDa, Protein from Thermococcus kodakarensis)
- 30s ribosomal protein s9 (15 kDa, Protein from Thermococcus kodakarensis)
- 30s ribosomal protein s17e (8 kDa, Protein from Thermococcus kodakarensis)
- 30s ribosomal protein s14 type z (6 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l14e (8 kDa, Protein from Thermococcus kodakarensis)
- 30s ribosomal protein s28e (7 kDa, Protein from Thermococcus kodakarensis)
- 30s ribosomal protein s8 (14 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l6 (20 kDa, Protein from Thermococcus kodakarensis)
- 30s ribosomal protein s2 (23 kDa, Protein from Thermococcus kodakarensis)
- 30s ribosomal protein s5 (26 kDa, Protein from Thermococcus kodakarensis)
- 30s ribosomal protein s19e (17 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l15e (22 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l29 (7 kDa, Protein from Thermococcus kodakarensis)
- Lsu ribosomal protein l41e (5 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l34e (10 kDa, Protein from Thermococcus kodakarensis)
- 30s ribosomal protein s3ae (23 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l37e (7 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l37ae (9 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l18ae (9 kDa, Protein from Thermococcus kodakarensis)
- 30s ribosomal protein s3 (23 kDa, Protein from Thermococcus kodakarensis)
- 16s ribosomal rna (487 kDa, RNA from Thermococcus kodakarensis)
- 30s ribosomal protein s7 (24 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l10e (21 kDa, Protein from Thermococcus kodakarensis)
- Ribosomal protein el35a (11 kDa, Protein from Thermococcus kodakarensis)
- Predicted exosome subunit, upf0023 family (26 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l24e (8 kDa, Protein from Thermococcus kodakarensis)
- 30s ribosomal protein s24e (11 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l3 (39 kDa, Protein from Thermococcus kodakarensis)
- 30s ribosomal protein s27e (7 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l5 (21 kDa, Protein from Thermococcus kodakarensis)
- 30s ribosomal protein s15 (17 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l24 (14 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l2 (26 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l39e (6 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l30e (10 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l14 (15 kDa, Protein from Thermococcus kodakarensis)
- 30s ribosomal protein s4 (21 kDa, Protein from Thermococcus kodakarensis)
- 30s ribosomal protein s11 (15 kDa, Protein from Thermococcus kodakarensis)
- 30s ribosomal protein s19 (15 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l4 (28 kDa, Protein from Thermococcus kodakarensis)
- Zinc ion (65 Da, Ligand)
- 50s ribosomal protein l23 (9 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l31e (10 kDa, Protein from Thermococcus kodakarensis)
- 30s ribosomal protein s4e (27 kDa, Protein from Thermococcus kodakarensis)
- 30s ribosomal protein s10 (11 kDa, Protein from Thermococcus kodakarensis)
- Predicted zinc-ribbon rna-binding protein involved in translation (7 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l7ae (13 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l18 (22 kDa, Protein from Thermococcus kodakarensis)
- 30s ribosomal protein s6e (13 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l15 (16 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l18e (13 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l22 (17 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l40e (5 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l44e (11 kDa, Protein from Thermococcus kodakarensis)
- Water (18 Da, Ligand)
- 50s ribosomal protein l13 (16 kDa, Protein from Thermococcus kodakarensis)
- 23s ribosomal rna (987 kDa, RNA from Thermococcus kodakarensis)
- 30s ribosomal protein s13 (17 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l19e (17 kDa, Protein from Thermococcus kodakarensis)
- Nucleic acid-binding protein, containing c2h2 zinc-finger (5 kDa, Protein from Thermococcus kodakarensis)
- 70s ribosome from thermococcus kodakarensis (Complex from Thermococcus kodakarensis)
- 30s ribosomal protein s12 (16 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l32e (14 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l30 (17 kDa, Protein from Thermococcus kodakarensis)
- 5s ribosomal rna (40 kDa, RNA from Thermococcus kodakarensis)
Bat Influenza A polymerase pre-initiation complex
Resolution: 2.54 Å
EM Method: Single-particle
Fitted PDBs: 6t0n
Q-score: 0.63
Wandzik JM, Kouba T, Karuppasamy M, Pflug A, Drncova P, Provaznik J, Azevedo N, Cusack S
Cell (2020) 181 pp. 877- [ DOI: doi:10.1016/j.cell.2020.03.061 Pubmed: 32304664 ]
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- Polymerase acidic protein (85 kDa, Protein from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- 5' vrna (4 kDa, RNA from Influenza B virus)
- 3' vrna (4 kDa, RNA from Influenza B virus)
- Polymerase basic protein 2 (91 kDa, Protein from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Polymerase (Complex from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Bat influenza a polymerase pre-initiation complex (Complex)
- Rna-directed rna polymerase catalytic subunit (87 kDa, Protein from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Nucleic acid (Complex from Influenza B virus)
Resolution: 2.82 Å
EM Method: Single-particle
Fitted PDBs: 6t0r
Q-score: 0.563
Wandzik JM, Kouba T, Karuppasamy M, Pflug A, Drncova P, Provaznik J, Azevedo N, Cusack S
Cell (2020) 181 pp. 877- [ DOI: doi:10.1016/j.cell.2020.03.061 Pubmed: 32304664 ]
- Nucleic acid (Complex from synthetic construct)
- Water (18 Da, Ligand)
- Polymerase acidic protein (85 kDa, Protein from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Polymerase basic protein 2 (91 kDa, Protein from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Polymerase (Complex from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Rna-directed rna polymerase catalytic subunit (87 kDa, Protein from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Bat influenza a polymerase product dissociation complex using 44-mer vrna template with mutated oligo(u) sequence (Complex)
- Vrna (14 kDa, RNA from synthetic construct)
Resolution: 3.04 Å
EM Method: Single-particle
Fitted PDBs: 6t0s
Q-score: 0.555
Wandzik JM, Kouba T, Karuppasamy M, Pflug A, Drncova P, Provaznik J, Azevedo N, Cusack S
Cell (2020) 181 pp. 877- [ DOI: doi:10.1016/j.cell.2020.03.061 Pubmed: 32304664 ]
- Bat influenza a polymerase stuttering complex using 44-mer vrna template with intact oligo(u) sequence (Complex)
- Nucleic acid (Complex from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Polymerase acidic protein (85 kDa, Protein from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Polymerase basic protein 2 (91 kDa, Protein from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Polymerase (Complex from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Rna-directed rna polymerase catalytic subunit (87 kDa, Protein from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Mrna (3 kDa, RNA from synthetic construct)
- Vrna (13 kDa, RNA from synthetic construct)
Resolution: 3.12 Å
EM Method: Single-particle
Fitted PDBs: 6t0u
Q-score: 0.544
Wandzik JM, Kouba T, Karuppasamy M, Pflug A, Drncova P, Provaznik J, Azevedo N, Cusack S
Cell (2020) 181 pp. 877- [ DOI: doi:10.1016/j.cell.2020.03.061 Pubmed: 32304664 ]
- Polymerase acidic protein (85 kDa, Protein from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Polymerase basic protein 2 (91 kDa, Protein from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Polymerase (Complex from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Rna-directed rna polymerase catalytic subunit (87 kDa, Protein from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Vrna (13 kDa, RNA from Influenza B virus)
- Bat influenza a polymerase product dissociation complex using 44-mer vrna template with intact oligo(u) sequence (Complex)
- Nucleic acid (Complex from Influenza B virus)
Human Influenza B polymerase recycling complex
Resolution: 3.18 Å
EM Method: Single-particle
Fitted PDBs: 6t0w
Q-score: 0.546
Wandzik JM, Kouba T, Karuppasamy M, Pflug A, Drncova P, Provaznik J, Azevedo N, Cusack S
Cell (2020) 181 pp. 877- [ DOI: doi:10.1016/j.cell.2020.03.061 Pubmed: 32304664 ]
- Human influenza b polymerase recycling complex (Complex)
- Polymerase (Complex from Influenza B virus)
- Polymerase pb2 (90 kDa, Protein from Influenza B virus)
- Polymerase acidic protein (85 kDa, Protein from Influenza B virus)
- Vrna (10 kDa, RNA from Influenza B virus)
- Rna-directed rna polymerase catalytic subunit (86 kDa, Protein from Influenza B virus)
- Nucleic acid (Complex from Influenza B virus)
Cryo-EM structure of E. coli RNA polymerase elongation complex bound to GreB transcription factor
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 6ri7
Q-score: 0.369
Abdelkareem M, Saint-Andre C, Takacs M, Papai G, Crucifix C, Guo X, Ortiz J, Weixlbaumer A
Mol Cell (2019) 75 pp. 298-309.e4 [ Pubmed: 31103420 DOI: doi:10.1016/j.molcel.2019.04.029 ]
- Nucleic acid (Complex from Escherichia coli)
- Rna (4 kDa, RNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Template dna (11 kDa, DNA from Escherichia coli)
- Non-template dna (12 kDa, DNA from Escherichia coli)
- Cryo-em structure of e. coli rna polymerase elongation complex bound to greb transcription factor (Complex)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
- Rna polymerase elongation complex (Complex from Escherichia coli K-12)
- Greb (Complex from Escherichia coli)
- Transcription elongation factor greb (18 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli (strain K12))
STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH
Resolution: 4.7 Å
EM Method: Single-particle
Fitted PDBs: 5oqj
Q-score: 0.249
Schilbach S, Hantsche M, Tegunov D, Dienemann C, Wigge C, Urlaub H, Cramer P
Nature (2017) 551 pp. 204-209 [ Pubmed: 29088706 DOI: doi:10.1038/nature24282 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna repair helicase rad25 (94 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor iie subunit alpha (57 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Initiation factors (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna repair helicase rad3 (89 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor iia large subunit (32 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor iib (38 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Tata-box-binding protein (27 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription factors (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Unknown protein (3 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rna polymerase ii transcription factor b subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rna polymerase ii transcription factor b subunit 1 (65 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-initiation complex (pic) (1 MDa, Complex)
- Polymerase (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor iie subunit beta (37 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor iif subunit beta (46 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rna polymerase ii transcription factor b subunit 4 (36 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Suppressor of stem-loop protein 1 (51 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Nontemplate dna (32 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb2 (138 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Template dna (32 kDa, DNA from synthetic construct)
- Nucleic acid (Complex from synthetic construct)
- Rna polymerase ii transcription factor b subunit 2 (48 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rna polymerase ii transcription factor b subunit 5 (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Iron/sulfur cluster (351 Da, Ligand)
- Transcription initiation factor iia subunit 2 (13 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor iif subunit alpha (82 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))