Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 9bct
Q-score: 0.554
You L, Wang C, Molodtsov V, Kuznedelov K, Miao X, Wenck BR, Ulisse P, Sanders TJ, Marshall CJ, Firlar E, Kaelber JT, Santangelo TJ, Ebright RH
Nature (2024) 635 pp. 229-236 [ DOI: doi:10.1038/s41586-024-07979-9 Pubmed: 39322680 ]
- Dna-directed rna polymerase subunit l (11 kDa, Protein from Thermococcus kodakarensis)
- Template strand dna (11 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit p (5 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit f (14 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit a' (103 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit n (7 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit k (6 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit e (21 kDa, Protein from Thermococcus kodakarensis)
- Ftta-dependent transcription termination complex (556 kDa, Complex from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit h (9 kDa, Protein from Thermococcus kodakarensis)
- Transcription termination factor ftta (73 kDa, Protein from Thermococcus kodakarensis)
- Non-template strand dna (11 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Rna (13 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase subunit a" (43 kDa, Protein from Thermococcus kodakarensis)
- Zinc ion (65 Da, Ligand)
- Transcription elongation factor spt4 (8 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit b (127 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit d (29 kDa, Protein from Thermococcus kodakarensis)
- Transcription elongation factor spt5 (16 kDa, Protein from Thermococcus kodakarensis)
Resolution: 2.2 Å
EM Method: Single-particle
Fitted PDBs: 9bcu
Q-score: 0.613
You L, Wang C, Molodtsov V, Kuznedelov K, Miao X, Wenck BR, Ulisse P, Sanders TJ, Marshall CJ, Firlar E, Kaelber JT, Santangelo TJ, Ebright RH
Nature (2024) 635 pp. 229-236 [ DOI: doi:10.1038/s41586-024-07979-9 Pubmed: 39322680 ]
- Dna-directed rna polymerase subunit l (11 kDa, Protein from Thermococcus kodakarensis)
- Template strand dna (11 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit p (5 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit f (14 kDa, Protein from Thermococcus kodakarensis)
- Ftta-dependent transcription termination complex containing 52 nt rna (556 kDa, Complex from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit a' (103 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit n (7 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit k (6 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit e (21 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit h (9 kDa, Protein from Thermococcus kodakarensis)
- Rna (29-mer) (16 kDa, RNA from synthetic construct)
- Transcription termination factor ftta (73 kDa, Protein from Thermococcus kodakarensis)
- Non-template strand dna (11 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit a" (43 kDa, Protein from Thermococcus kodakarensis)
- Zinc ion (65 Da, Ligand)
- Transcription elongation factor spt4 (8 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit b (127 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit d (29 kDa, Protein from Thermococcus kodakarensis)
- Transcription elongation factor spt5 (16 kDa, Protein from Thermococcus kodakarensis)
Zophobas morio black wasting virus strain NJ2-molitor virion structure
Resolution: 2.0 Å
EM Method: Single-particle
Fitted PDBs: 8t9x
Q-score: 0.736
Penzes JJ, Holm M, Firlar E, Kaelber JT
To Be Published
- Dna (5'-d(p*tp*cp*gp*ap*a)-3') (1 kDa, DNA from Zophobas morio black wasting virus)
- Dna (5'-d(p*cp*ap*gp*gp*cp*cp*ap*ap*a)-3') (2 kDa, DNA from Zophobas morio black wasting virus)
- Major capsid protein (48 kDa, Protein from Zophobas morio black wasting virus)
- Zophobas morio densovirus (Virus from Zophobas morio densovirus)
- Dna (5'-d(p*cp*gp*a)-3') (886 Da, DNA from Zophobas morio black wasting virus)
- Water (18 Da, Ligand)
Zophobas morio black wasting virus strain UT-morio virion structure
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8t9c
Q-score: 0.641
Penzes JJ, Holm M, Firlar E, Kaelber JT
To Be Published
- Dna (5'-d(p*cp*gp*a)-3') (886 Da, DNA from Zophobas morio)
- Dna (5'-d(p*cp*ap*gp*gp*cp*cp*ap*a)-3') (2 kDa, DNA from Zophobas morio)
- Dna (5'-d(p*cp*g)-3') (573 Da, DNA from Zophobas morio)
- Major capsid protein (65 kDa, Protein from Zophobas morio)
- Zophobas morio densovirus (Virus from Zophobas morio densovirus)
Zophobas morio black wasting virus strain OR-molitor virion structure
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8tje
Q-score: 0.529
Penzes JJ, Holm M, Firlar E, Kaelber JT
To Be Published
- Dna (5'-d(p*tp*cp*gp*ap*a)-3') (1 kDa, DNA from Tenebrio molitor)
- Dna (5'-d(p*cp*ap*gp*gp*cp*cp*ap*ap*a)-3') (2 kDa, DNA from Tenebrio molitor)
- Zophobas morio densovirus (Virus from Zophobas morio densovirus)
- Dna (5'-d(p*cp*g)-3') (573 Da, DNA from Tenebrio molitor)
- Major capsid protein (48 kDa, Protein from Tenebrio molitor)
Resolution: 6.5 Å
EM Method: Single-particle
Fitted PDBs: 8e3f
Q-score: 0.158
Molodtsov V, Wang C, Firlar E, Kaelber JT, Ebright RH
Nature (2023) 614 pp. 367-374 [ DOI: doi:10.1038/s41586-022-05658-1 Pubmed: 36697824 ]
- T dna (18 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Escherichia coli rho-dependent transcription pre-termination complex containing 18 nt long rna spacer, mg-adp-bef3, and nusg, tec part (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli)
- Nt dna (18 kDa, DNA from synthetic construct)
- Transcription termination/antitermination protein nusg (20 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Rna with 18 nt long spacer (11 kDa, RNA from synthetic construct)
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 8e5k
Q-score: 0.228
Molodtsov V, Wang C, Firlar E, Kaelber JT, Ebright RH
Nature (2023) 614 pp. 367-374 [ DOI: doi:10.1038/s41586-022-05658-1 Pubmed: 36697824 ]
- T dna (18 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli)
- Nt dna (18 kDa, DNA from synthetic construct)
- Transcription termination/antitermination protein nusg (20 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Rna with 21 nt long spacer (11 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Escherichia coli rho-dependent transcription pre-termination complex containing 21 nt long rna spacer, mg-adp-bef3, and nusg, tec part (Complex from Escherichia coli)
Resolution: 4.4 Å
EM Method: Single-particle
Fitted PDBs: 8e5o
Q-score: 0.151
Molodtsov V, Wang C, Firlar E, Kaelber JT, Ebright RH
Nature (2023) 614 pp. 367-374 [ DOI: doi:10.1038/s41586-022-05658-1 Pubmed: 36697824 ]
- T dna (18 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli)
- Nt dna (18 kDa, DNA from synthetic construct)
- Escherichia coli rho-dependent transcription pre-termination complex containing 24 nt long rna spacer, mg-adp-bef3, and nusg; tec part (Complex from Escherichia coli)
- Transcription termination/antitermination protein nusg (20 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Rna with 24 nt long spacer (12 kDa, RNA from synthetic construct)
Resolution: 4.27 Å
EM Method: Single-particle
Fitted PDBs: 8e6x
Q-score: 0.264
Molodtsov V, Wang C, Firlar E, Kaelber JT, Ebright RH
Nature (2023) 614 pp. 367-374 [ DOI: doi:10.1038/s41586-022-05658-1 Pubmed: 36697824 ]
- T dna (18 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli)
- Nt dna (18 kDa, DNA from synthetic construct)
- Transcription termination/antitermination protein nusg (20 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Escherichia coli rho-dependent transcription pre-termination complex containing 18 nt long rna spacer, lambda-tr1 rut rna, mg-adp-bef3, and nusg; tec part (Complex from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Rna with 18 nt long spacer (11 kDa, RNA from synthetic construct)
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 8e6z
Q-score: 0.273
Molodtsov V, Wang C, Firlar E, Kaelber JT, Ebright RH
Nature (2023) 614 pp. 367-374 [ DOI: doi:10.1038/s41586-022-05658-1 Pubmed: 36697824 ]
- T dna (18 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Escherichia coli rho-dependent transcription pre-termination complex containing 18 nt long rna spacer, dc75 rut mimic rna, mg-adp-bef3, and nusg; tec part (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli)
- Nt dna (18 kDa, DNA from synthetic construct)
- Transcription termination/antitermination protein nusg (20 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Rna with 18 nt long spacer (11 kDa, RNA from synthetic construct)