Cryo-EM structure of Dragon Grouper nervous necrosis virion at pH6.5 (3.12A)
Resolution: 3.12 Å
EM Method: Single-particle
Fitted PDBs: 8yf9
Q-score: 0.317
Sterbova P, Wang CH, Carillo KJD, Lou YC, Kato T, Namba K, Tzou DM, Chang WH
Acs Infect Dis. (2024) 10 pp. 3304-3319 [ DOI: doi:10.1021/acsinfecdis.4c00407 Pubmed: 39087906 ]
Cryo-EM structure of Pyrococcus furiosus transcription elongation complex bound to Spt4/5
Resolution: 3.45 Å
EM Method: Single-particle
Fitted PDBs: 8oki
Q-score: 0.48
Tarau D, Grunberger F, Pilsl M, Reichelt R, Heiss F, Konig S, Urlaub H, Hausner W, Engel C, Grohmann D
Nucleic Acids Res (2024) 52 pp. 6017-6035 [ Pubmed: 38709902 DOI: doi:10.1093/nar/gkae282 ]
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit rpo3 (31 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna non-template strand (7 kDa, DNA from Pyrococcus furiosus DSM 3638)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit rpo1n (103 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Transcription elongation factor spt5 (16 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Rna (2 kDa, RNA from Pyrococcus furiosus DSM 3638)
- Dna template strand (8 kDa, DNA from Pyrococcus furiosus DSM 3638)
- Spt4/5 (Complex from Pyrococcus furiosus DSM 3638)
- Pyrococcus furiosus rna polymerase (Complex from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo11 (11 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo10 (7 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo1c (44 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo7 (21 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo5 (9 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo12 (5 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo6 (6 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Transcription elongation complex with spt4/5 (Complex)
- Nucleotide strands (Complex from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo4 (14 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Transcription elongation factor spt4 (6 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit beta (127 kDa, Protein from Pyrococcus furiosus DSM 3638)
Cryo-EM structure of Pyrococcus furiosus apo form RNA polymerase open clamp conformation
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8orq
Q-score: 0.477
Tarau D, Grunberger F, Pilsl M, Reichelt R, Heiss F, Konig S, Urlaub H, Hausner W, Engel C, Grohmann D
Nucleic Acids Res (2024) 52 pp. 6017-6035 [ Pubmed: 38709902 DOI: doi:10.1093/nar/gkae282 ]
- Dna-directed rna polymerase subunit rpo5 (9 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit rpo3 (31 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo11 (11 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo10 (7 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo1n (103 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Pyrococcus furiosus apo form of rna polymerase open clamp conformation (Complex from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo1c (44 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo6 (6 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo12 (5 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit rpo4 (14 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit beta (127 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo7 (21 kDa, Protein from Pyrococcus furiosus DSM 3638)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8p2i
Q-score: 0.461
Tarau D, Grunberger F, Pilsl M, Reichelt R, Heiss F, Konig S, Urlaub H, Hausner W, Engel C, Grohmann D
Nucleic Acids Res (2024) 52 pp. 6017-6035 [ Pubmed: 38709902 DOI: doi:10.1093/nar/gkae282 ]
- Dna-directed rna polymerase subunit rpo5 (9 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit rpo3 (31 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo6 (6 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo11 (11 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo1n (103 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Pyrococcus furiosus apo form of rna polymerase open clamp conformation (Complex from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo1c (44 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo10 (7 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo12 (5 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Transcription elongation factor spt5 (16 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit rpo4 (14 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Transcription elongation factor spt4 (6 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit beta (127 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo7 (21 kDa, Protein from Pyrococcus furiosus DSM 3638)
Cryo-EM structure of Pyrococcus furiosus apo form RNA polymerase contracted clamp conformation
Resolution: 3.02 Å
EM Method: Single-particle
Fitted PDBs: 8rbo
Q-score: 0.246
Tarau D, Grunberger F, Pilsl M, Reichelt R, Heiss F, Konig S, Urlaub H, Hausner W, Engel C, Grohmann D
Nucleic Acids Res (2024) 52 pp. 6017-6035 [ Pubmed: 38709902 DOI: doi:10.1093/nar/gkae282 ]
- Dna-directed rna polymerase subunit rpo5 (9 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Magnesium ion (24 Da, Ligand)
- Pyrococcus furiosus apo form of rna polymerase contracted clamp conformation (Complex from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo3 (31 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo6 (6 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo11 (11 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo1n (103 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo10 (7 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo1c (44 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo12 (5 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit rpo4 (14 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit beta (127 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo7 (21 kDa, Protein from Pyrococcus furiosus DSM 3638)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8a5e
Q-score: 0.409
Katsyv A, Kumar A, Saura P, Poverlein MC, Freibert SA, T Stripp S, Jain S, Gamiz-Hernandez AP, Kaila VRI, Muller V, Schuller JM
J Am Chem Soc (2023) 145 pp. 5696-5709 [ DOI: doi:10.1021/jacs.2c11683 Pubmed: 36811855 ]
- Iron hydrogenase hydc (16 kDa, Protein from Acetobacterium woodii DSM 1030)
- Electron bifurcating fe-fe hydrogenase hydabc complex from thermoanaerobacter kivui (348 kDa, Complex from Thermoanaerobacter kivui)
- 2 iron/2 sulfur/5 carbonyl/2 water inorganic cluster (355 Da, Ligand)
- Flavin mononucleotide (456 Da, Ligand)
- Iron hydrogenase hydb (64 kDa, Protein from Acetobacterium woodii DSM 1030)
- 1,4-dihydronicotinamide adenine dinucleotide (665 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Iron hydrogenase hyda1 (63 kDa, Protein from Acetobacterium woodii DSM 1030)
- Zinc ion (65 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8a6t
Q-score: 0.46
Katsyv A, Kumar A, Saura P, Poverlein MC, Freibert SA, T Stripp S, Jain S, Gamiz-Hernandez AP, Kaila VRI, Muller V, Schuller JM
J Am Chem Soc (2023) 145 pp. 5696-5709 [ DOI: doi:10.1021/jacs.2c11683 Pubmed: 36811855 ]
- Zinc ion (65 Da, Ligand)
- Electron bifurcating hydrogenase subunit hydb (68 kDa, Protein from Thermoanaerobacter kivui)
- 2 iron/2 sulfur/5 carbonyl/2 water inorganic cluster (355 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Flavin mononucleotide (456 Da, Ligand)
- Nadp nicotinamide-adenine-dinucleotide phosphate (743 Da, Ligand)
- Electron bifurcating hydrogenase subunit hyda1 (63 kDa, Protein from Thermoanaerobacter kivui)
- Iron/sulfur cluster (351 Da, Ligand)
- Electron bifurcating hydrogenase subunit hydc (18 kDa, Protein from Thermoanaerobacter kivui)
- Electron bifurcating fe-fe hydrogenase hydabc complex from thermoanaerobacter kivui (348 kDa, Complex from Thermoanaerobacter kivui)
Resolution: 3.49 Å
EM Method: Single-particle
Fitted PDBs: 8bew
Q-score: 0.411
Katsyv A, Kumar A, Saura P, Poverlein MC, Freibert SA, T Stripp S, Jain S, Gamiz-Hernandez AP, Kaila VRI, Muller V, Schuller JM
J Am Chem Soc (2023) 145 pp. 5696-5709 [ DOI: doi:10.1021/jacs.2c11683 Pubmed: 36811855 ]
- Electron bifurcating hydrogenase subunit hydb (68 kDa, Protein from Thermoanaerobacter kivui)
- Electron bifurcating hydrogenase subunit hyda1 (63 kDa, Protein from Thermoanaerobacter kivui)
- Zinc ion (65 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Dimer of the trimeric hydabc complex (Complex from Thermoanaerobacter kivui)
- Flavin mononucleotide (456 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Electron bifurcating hydrogenase subunit hydc (18 kDa, Protein from Thermoanaerobacter kivui)
Enp1TAP_A population of yeast small ribosomal subunit precursors, multibody refinement
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8c01
Q-score: 0.569
Poll G, Griesenbeck J, Tschochner H, Milkereit P
PLoS One (2023) 18 pp. e0283698-e0283698 [ DOI: doi:10.1371/journal.pone.0283698 Pubmed: 36996028 ]
- 40s ribosomal protein s8-a (22 kDa, Protein from Saccharomyces cerevisiae)
- Essential nuclear protein 1 (55 kDa, Protein from Saccharomyces cerevisiae)
- Enp1-tap associated immature ribosomal particles from s. cerevisiae (Complex from Saccharomyces cerevisiae)
- 40s ribosomal protein s22-a (14 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s5 (25 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s14-a (14 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s27-a (8 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s11-a (17 kDa, Protein from Saccharomyces cerevisiae)
- Ribosome biogenesis protein tsr1 (90 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s16-a (15 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s13 (17 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s17-a (15 kDa, Protein from Saccharomyces cerevisiae)
- Pre-rrna-processing protein pno1 (30 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s25-a (12 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s18-a (17 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- 40s ribosomal protein s28-a (7 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s6-a (27 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s4-a (29 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s19-a (15 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s30-a (7 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s23-a (16 kDa, Protein from Saccharomyces cerevisiae)
- Serine/threonine-protein kinase rio2 (49 kDa, Protein from Saccharomyces cerevisiae)
- 18s rrna precursor (581 kDa, RNA from Saccharomyces cerevisiae)
- 40s ribosomal protein s24-a (15 kDa, Protein from Saccharomyces cerevisiae)
- 20s-pre-rrna d-site endonuclease nob1 (51 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s9-a (22 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s2 (27 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s21-a (9 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s0-a (28 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s1-a (28 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s7-a (21 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s15 (16 kDa, Protein from Saccharomyces cerevisiae)
Cyanobacterial PSI Monomer from T. elongatus by Single Particle CRYO-EM at 3.2 A Resolution
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 6lu1
Q-score: 0.582
Coruh O, Frank A, Tanaka H, Kawamoto A, El-Mohsnawy E, Kato T, Namba K, Gerle C, Nowaczyk MM, Kurisu G
Commun Biol (2021) 4 pp. 304-304 [ Pubmed: 33686186 DOI: doi:10.1038/s42003-021-01808-9 ]
- Cyanobacterial psi monomer from t. elongatus (350 MDa, Complex from Thermosynechococcus elongatus BP-1)
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Photosystem i reaction center subunit xi (16 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Photosystem i reaction center subunit iii (17 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Beta-carotene (536 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 (83 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Photosystem i reaction center subunit xii (3 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Chlorophyll a (893 Da, Ligand)
- Photosystem i reaction center subunit viii (4 kDa, Protein from Thermosynechococcus elongatus BP-1)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Photosystem i reaction center subunit iv (8 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Iron/sulfur cluster (351 Da, Ligand)
- Water (18 Da, Ligand)
- Photosystem i iron-sulfur center (8 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Phylloquinone (450 Da, Ligand)