E.coli RNAP-RapA elongation complex
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7m8e
Q-score: 0.455
Shi W, Zhou W, Chen M, Yang Y, Hu Y, Liu B
Nucleic Acids Res (2021) 49 pp. 10707-10716 [ Pubmed: 34428297 DOI: doi:10.1093/nar/gkab744 ]
- Rna polymerase-associated protein rapa (110 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (156 kDa, Protein from Escherichia coli)
- Template dna (39-mer) (12 kDa, DNA from Escherichia coli)
- Rnap-rapa elongation complex (530 kDa, Complex from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Rna (5'-r(p*ap*up*cp*gp*gp*cp*up*cp*a)-3') (2 kDa, RNA from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Nontemplate dna (39-mer) (11 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 6xh7
Q-score: 0.344
Shi W, Zhang B, Jiang Y, Liu C, Zhou W, Chen M, Yang Y, Hu Y, Liu B
iScience (2021) 24 pp. 102449-102449 [ Pubmed: 34113812 DOI: doi:10.1016/j.isci.2021.102449 ]
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli)
- Hth-type transcriptional regulator cuer (16 kDa, Protein from Escherichia coli)
- Nontemplate strand dna (54-mer) (16 kDa, DNA from Escherichia coli)
- Template strand dna (54-mer) (16 kDa, DNA from Escherichia coli)
- Copper (ii) ion (63 Da, Ligand)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Rna polymerase sigma factor rpod (72 kDa, Protein from Escherichia coli)
- Cuer-tac without rna (530 kDa, Complex from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
CueR-transcription activation complex with RNA transcript
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 6xh8
Q-score: 0.318
Shi W, Zhang B, Jiang Y, Liu C, Zhou W, Chen M, Yang Y, Hu Y, Liu B
iScience (2021) 24 pp. 102449-102449 [ DOI: doi:10.1016/j.isci.2021.102449 Pubmed: 34113812 ]
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli)
- Rna polymerase sigma factor rpod (72 kDa, Protein from Escherichia coli)
- Hth-type transcriptional regulator cuer (16 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Nontemplate strand dna (54-mer) (16 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Nascent rna (1 kDa, RNA from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Copper (ii) ion (63 Da, Ligand)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Template strand dna (54-mer) (16 kDa, DNA from Escherichia coli)
- Cuer-tac with rna (540 kDa, Complex from Escherichia coli)
Cryo-EM structure of EcmrR-RNAP-promoter open complex (EcmrR-RPo)
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 6xl5
Q-score: 0.541
Yang Y, Liu C, Zhou W, Shi W, Chen M, Zhang B, Schatz DG, Hu Y, Liu B
Nat Commun (2021) 12 pp. 2702-2702 [ Pubmed: 33976201 DOI: doi:10.1038/s41467-021-22990-8 ]
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli O157:H7)
- Water (18 Da, Ligand)
- Tetraphenylantimonium ion (430 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli O157:H7)
- Synthetic template strand dna (54-mer) (16 kDa, DNA from Escherichia coli O157:H7)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli O157:H7)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli O157:H7)
- Chapso (631 Da, Ligand)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli O157:H7)
- Synthetic non-template strand dna (54-mer) (16 kDa, DNA from Escherichia coli O157:H7)
- Ecmrr-rnap-promoter open complex (ecmrr-rpo) (Complex from Escherichia coli O157:H7)
- Zinc ion (65 Da, Ligand)
- Merr family transcriptional regulator ecmrr (31 kDa, Protein from Escherichia coli O157:H7)
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 6xl9
Q-score: 0.517
Yang Y, Liu C, Zhou W, Shi W, Chen M, Zhang B, Schatz DG, Hu Y, Liu B
Nat Commun (2021) 12 pp. 2702-2702 [ Pubmed: 33976201 DOI: doi:10.1038/s41467-021-22990-8 ]
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli O157:H7)
- Water (18 Da, Ligand)
- Tetraphenylantimonium ion (430 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Synthetic template strand dna (54-mer) (16 kDa, DNA from Escherichia coli O157:H7)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli O157:H7)
- Ecmrr-rnap-promoter initial transcribing complex with 3-nt rna transcript (ecmrr-rpitc-3nt) (Complex from Escherichia coli O157:H7)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli O157:H7)
- Rna (5'-d(*(gtp))-r(p*ap*g)-3') (1 kDa, RNA from Escherichia coli O157:H7)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli O157:H7)
- Synthetic non-template strand dna (54-mer) (16 kDa, DNA from Escherichia coli O157:H7)
- Zinc ion (65 Da, Ligand)
- Merr family transcriptional regulator ecmrr (31 kDa, Protein from Escherichia coli O157:H7)
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 6xlj
Q-score: 0.512
Yang Y, Liu C, Zhou W, Shi W, Chen M, Zhang B, Schatz DG, Hu Y, Liu B
Nat Commun (2021) 12 pp. 2702-2702 [ Pubmed: 33976201 DOI: doi:10.1038/s41467-021-22990-8 ]
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli O157:H7)
- Tetraphenylantimonium ion (430 Da, Ligand)
- Rna (5'-d(*(gtp))-r(p*cp*ap*g)-3') (1 kDa, RNA from Escherichia coli O157:H7)
- Ecmrr-rnap-promoter initial transcribing complex with 4-nt rna transcript (ecmrr-rpitc-4nt) (Complex from Escherichia coli O157:H7)
- Synthetic template strand dna (54-mer) (16 kDa, DNA from Escherichia coli O157:H7)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli O157:H7)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli O157:H7)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli O157:H7)
- Chapso (631 Da, Ligand)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli O157:H7)
- Synthetic non-template strand dna (54-mer) (16 kDa, DNA from Escherichia coli O157:H7)
- Zinc ion (65 Da, Ligand)
- Merr family transcriptional regulator ecmrr (31 kDa, Protein from Escherichia coli O157:H7)
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 6xll
Q-score: 0.519
Yang Y, Liu C, Zhou W, Shi W, Chen M, Zhang B, Schatz DG, Hu Y, Liu B
Nat Commun (2021) 12 pp. 2702-2702 [ Pubmed: 33976201 DOI: doi:10.1038/s41467-021-22990-8 ]
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli O157:H7)
- Synthetic template strand dna (54-mer) (16 kDa, DNA from Escherichia coli O157:H7)
- Rnap-promoter initial transcribing complex with 5-nt rna transcript (rpitc-5nt) (Complex from Escherichia coli O157:H7)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli O157:H7)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli O157:H7)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli O157:H7)
- Chapso (631 Da, Ligand)
- Rna transcript (5-mer) (1 kDa, RNA from Escherichia coli O157:H7)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli O157:H7)
- Synthetic non-template strand dna (54-mer) (16 kDa, DNA from Escherichia coli O157:H7)
- Zinc ion (65 Da, Ligand)
Cryo-EM structure of E.coli RNAP-DNA elongation complex 1 (RDe1) in EcmrR-dependent transcription
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 6xlm
Q-score: 0.462
Yang Y, Liu C, Zhou W, Shi W, Chen M, Zhang B, Schatz DG, Hu Y, Liu B
Nat Commun (2021) 12 pp. 2702-2702 [ Pubmed: 33976201 DOI: doi:10.1038/s41467-021-22990-8 ]
- 9-nt rna transcript (2 kDa, RNA from Escherichia coli O157:H7)
- E. coli rnap-dna elongation complex 1 (rde1) (Complex from Escherichia coli O157:H7)
- Zinc ion (65 Da, Ligand)
- Synthetic template strand dna (54-mer) (16 kDa, DNA from Escherichia coli O157:H7)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli O157:H7)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli O157:H7)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli O157:H7)
- Chapso (631 Da, Ligand)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli O157:H7)
- Synthetic non-template strand dna (54-mer) (16 kDa, DNA from Escherichia coli O157:H7)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli O157:H7)
Cryo-EM structure of E. coli RNAP-DNA elongation complex 2 (RDe2) in EcmrR-dependent transcription
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 6xln
Q-score: 0.528
Yang Y, Liu C, Zhou W, Shi W, Chen M, Zhang B, Schatz DG, Hu Y, Liu B
Nat Commun (2021) 12 pp. 2702-2702 [ DOI: doi:10.1038/s41467-021-22990-8 Pubmed: 33976201 ]
- Chapso (631 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli O157:H7)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli O157:H7)
- E. coli rnap-dna elongation complex 2 (rde2) (Complex from Escherichia coli O157:H7)
- Synthetic non-template strand dna (54-mer) (16 kDa, DNA from Escherichia coli O157:H7)
- Synthetic template strand dna (54-mer) (16 kDa, DNA from Escherichia coli O157:H7)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli O157:H7)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli O157:H7)
- 9-nt rna transcript (2 kDa, RNA from Escherichia coli O157:H7)
Cryo-EM structure of cat ACE2 and SARS-CoV-2 RBD
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7c8d
Q-score: 0.529
Wu L, Chen Q, Liu K, Wang J, Han P, Zhang Y, Hu Y, Meng Y, Pan X, Qiao C, Tian S, Du P, Song H, Shi W, Qi J, Wang HW, Yan J, Gao GF, Wang Q
Cell Discov (2020) 6 pp. 68-68 [ DOI: doi:10.1038/s41421-020-00210-9 Pubmed: 33020722 ]
- Cryo-em structure of cat ace2 and sars-cov-2 rbd (Complex from Felis catus)
- Zinc ion (65 Da, Ligand)
- Spike protein s1 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 rbd (Complex)
- Angiotensin-converting enzyme 2 (85 kDa, Protein from Felis catus)
- Cat ace2 (Complex)