Focused refined map at the interface of the transcribing Pol II-U1 snRNP complex with 145-nt RNA
Zhang S, Aibara S, Vos SM, Agafonov DE, Luhrmann R, Cramer P
Science (2021) 371 pp. 305-309 [ DOI: doi:10.1126/science.abf1870 Pubmed: 33446560 ]
Focused refined map of U1 snRNP of the transcribing Pol II-U1 snRNP complex with 145-nt RNA
Zhang S, Aibara S, Vos SM, Agafonov DE, Luhrmann R, Cramer P
Science (2021) 371 pp. 305-309 [ Pubmed: 33446560 DOI: doi:10.1126/science.abf1870 ]
Cryo-EM map of the transcribing Pol II-U1 snRNP complex with 155-nt RNA
Zhang S, Aibara S, Vos SM, Agafonov DE, Luhrmann R, Cramer P
Science (2021) 371 pp. 305-309 [ DOI: doi:10.1126/science.abf1870 Pubmed: 33446560 ]
Overall map of a transcribing RNA polymerase II-U1 snRNP complex with 145-nt RNA
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 7b0y
Q-score: 0.344
Zhang S, Aibara S, Vos SM, Agafonov DE, Luhrmann R, Cramer P
Science (2021) 371 pp. 305-309 [ DOI: doi:10.1126/science.abf1870 Pubmed: 33446560 ]
- Small nuclear ribonucleoprotein sm d2 (13 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein sm d1 (13 kDa, Protein from Homo sapiens)
- Template dna (14 kDa, DNA from synthetic construct)
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Homo sapiens)
- U1 snrnp (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa domesticus)
- Nucleic acids (Complex from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa domesticus)
- Rpb12 (7 kDa, Protein from Sus scrofa domesticus)
- Zinc ion (65 Da, Ligand)
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Homo sapiens)
- Rna polymerase ii (Complex from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa domesticus)
- The transcribing rna polymerase ii-u1 snrnp complex with 145-nt rna (Complex)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa domesticus)
- U1 small nuclear ribonucleoprotein a (31 kDa, Protein from Homo sapiens)
- U1 small nuclear ribonucleoprotein 70 kda (51 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa domesticus)
- Small nuclear ribonucleoprotein-associated protein (23 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa domesticus)
- Small nuclear ribonucleoprotein sm d3 (13 kDa, Protein from Homo sapiens)
- U1 snrna (52 kDa, RNA from Homo sapiens)
- Non-template dna (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa domesticus)
- 145-nt rna (46 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa domesticus)
Resolution: 2.41 Å
EM Method: Single-particle
Fitted PDBs: 6szu
Q-score: 0.665
Wandzik JM, Kouba T, Karuppasamy M, Pflug A, Drncova P, Provaznik J, Azevedo N, Cusack S
Cell (2020) 181 pp. 877- [ Pubmed: 32304664 DOI: doi:10.1016/j.cell.2020.03.061 ]
- Rna-directed rna polymerase catalytic subunit (87 kDa, Protein from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Magnesium ion (24 Da, Ligand)
- Polymerase basic protein 2 (91 kDa, Protein from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Vrna (14 kDa, RNA from Influenza B virus)
- Polymerase acidic protein (85 kDa, Protein from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Water (18 Da, Ligand)
- Mrna (3 kDa, RNA from Influenza B virus)
- Polymerase (Complex from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- 5-oxidanyl-4-oxidanylidene-1-[(1-pyrrolo[2,3-b]pyridin-1-ylcyclopentyl)methyl]pyridine-3-carboxylic acid (353 Da, Ligand)
- Bat influenza a polymerase pre-termination complex with pyrophosphate using 44-mer vrna template with mutated oligo(u) sequence (Complex)
- Nucleic acids (Complex from Influenza B virus)
- Pyrophosphate 2- (175 Da, Ligand)
Bat Influenza A polymerase elongation complex with incoming UTP analogue (core + endonuclease only)
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 6szv
Q-score: 0.634
Wandzik JM, Kouba T, Karuppasamy M, Pflug A, Drncova P, Provaznik J, Azevedo N, Cusack S
Cell (2020) 181 pp. 877- [ Pubmed: 32304664 DOI: doi:10.1016/j.cell.2020.03.061 ]
- Rna-directed rna polymerase catalytic subunit (87 kDa, Protein from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Nucleic acids (Complex from Influenza B virus)
- Polymerase basic protein 2 (91 kDa, Protein from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- 5'-o-[(s)-hydroxy{[(s)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine (483 Da, Ligand)
- Polymerase acidic protein (85 kDa, Protein from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Capped mrna (8 kDa, RNA from Influenza B virus)
- 3' vrna (6 kDa, RNA from Influenza B virus)
- Water (18 Da, Ligand)
- 5-oxidanyl-4-oxidanylidene-1-[(1-pyrrolo[2,3-b]pyridin-1-ylcyclopentyl)methyl]pyridine-3-carboxylic acid (353 Da, Ligand)
- Polymerase (Complex from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Magnesium ion (24 Da, Ligand)
- 5' vrna (4 kDa, RNA from Influenza B virus)
- Bat influenza a polymerase elongation complex with incoming utp analogue (core + endonuclease only) (Complex)
Bat Influenza A polymerase elongation complex with incoming UTP analogue (complete polymerase)
Resolution: 3.02 Å
EM Method: Single-particle
Fitted PDBs: 6t0v
Q-score: 0.552
Wandzik JM, Kouba T, Karuppasamy M, Pflug A, Drncova P, Provaznik J, Azevedo N, Cusack S
Cell (2020) 181 pp. 877- [ Pubmed: 32304664 DOI: doi:10.1016/j.cell.2020.03.061 ]
- Rna-directed rna polymerase catalytic subunit (87 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)))
- 3' vrna (6 kDa, RNA from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Polymerase acidic protein (85 kDa, Protein from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Bat influenza a polymerase elongation complex with incoming utp analogue (complete polymerase) (Complex)
- Capped mrna (8 kDa, RNA from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Magnesium ion (24 Da, Ligand)
- 5-oxidanyl-4-oxidanylidene-1-[(1-pyrrolo[2,3-b]pyridin-1-ylcyclopentyl)methyl]pyridine-3-carboxylic acid (353 Da, Ligand)
- Polymerase (Complex from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- 5' vrna (4 kDa, RNA from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Nucleic acids (Complex from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- 5'-o-[(s)-hydroxy{[(s)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine (483 Da, Ligand)
Bat Influenza A polymerase recycling complex
Resolution: 3.52 Å
EM Method: Single-particle
Fitted PDBs: 6t2c
Q-score: 0.508
Wandzik JM, Kouba T, Karuppasamy M, Pflug A, Drncova P, Provaznik J, Azevedo N, Cusack S
Cell (2020) 181 pp. 877- [ Pubmed: 32304664 DOI: doi:10.1016/j.cell.2020.03.061 ]
- Bat influenza a polymerase recycling complex (Complex)
- Rna-directed rna polymerase catalytic subunit (87 kDa, Protein from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Magnesium ion (24 Da, Ligand)
- Polymerase basic protein 2 (91 kDa, Protein from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Vrna (10 kDa, RNA from Influenza B virus)
- Polymerase acidic protein (85 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)))
- Nucleic acids (Complex from Influenza B virus)
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 6tw1
Q-score: 0.591
Wandzik JM, Kouba T, Karuppasamy M, Pflug A, Drncova P, Provaznik J, Azevedo N, Cusack S
Cell (2020) [ Pubmed: 32304664 DOI: doi:10.1016/j.cell.2020.03.061 ]
- Rna-directed rna polymerase catalytic subunit (87 kDa, Protein from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Magnesium ion (24 Da, Ligand)
- Polymerase basic protein 2 (91 kDa, Protein from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Vrna (14 kDa, RNA from Influenza B virus)
- Polymerase acidic protein (85 kDa, Protein from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Water (18 Da, Ligand)
- Polymerase (Complex from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Mrna (3 kDa, RNA from Influenza B virus)
- 5-oxidanyl-4-oxidanylidene-1-[(1-pyrrolo[2,3-b]pyridin-1-ylcyclopentyl)methyl]pyridine-3-carboxylic acid (353 Da, Ligand)
- Bat influenza a polymerase termination complex with pyrophosphate using 44-mer vrna template with mutated oligo(u) sequence (Complex)
- Nucleic acids (Complex from Influenza B virus)
- Pyrophosphate 2- (175 Da, Ligand)
Structure of Vaccinia Virus DNA-dependent RNA polymerase elongation complex
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 6rid
Q-score: 0.579
Hillen HS, Bartuli J, Grimm C, Dienemann C, Bedenk K, Szalay AA, Fischer U, Cramer P
Cell (2019) 179 pp. 1525- [ Pubmed: 31835031 DOI: doi:10.1016/j.cell.2019.11.023 ]
- Dna-directed rna polymerase subunit (21 kDa, Protein from Vaccinia virus GLV-1h68)
- Dna-dependent rna polymerase subunit rpo132 (Complex from Vaccinia virus GLV-1h68)
- Dna-directed rna polymerase 19 kda subunit (19 kDa, Protein from Vaccinia virus GLV-1h68)
- Non-template strand dna (14 kDa, DNA from Vaccinia virus)
- Template strand dna (14 kDa, DNA from Vaccinia virus)
- Rna (9 kDa, RNA from Vaccinia virus)
- Dna-directed rna polymerase subunits (Complex from Vaccinia virus GLV-1h68)
- Nucleic acids (Complex from Vaccinia virus GLV-1h68)
- Dna-dependent rna polymerase subunit rpo147 (146 kDa, Protein from Vaccinia virus GLV-1h68)
- Dna-directed rna polymerase 35 kda subunit (35 kDa, Protein from Vaccinia virus GLV-1h68)
- Dna-dependent rna polymerase subunit rpo18 (17 kDa, Protein from Vaccinia virus GLV-1h68)
- Dna-dependent rna polymerase subunit rpo132 (133 kDa, Protein from Vaccinia virus GLV-1h68)
- Dna-dependent rna polymerase subunit rpo7 (7 kDa, Protein from Vaccinia virus GLV-1h68)
- Vaccinia virus dna-dependent rna polymerase elongation complex (450 kDa, Complex)
- Magnesium ion (24 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase 30 kda polypeptide (29 kDa, Protein from Vaccinia virus GLV-1h68)