CryoEM structure of DNA Polymerase alpha - primase bound to SARS CoV nsp1
Kilkenny ML, Veale CE, Guppy A, Hardwick SW, Chirgadze DY, Rzechorzek NJ, Maman JD, Pellegrini L
Protein Sci (2022) 31 pp. 333-344 [ Pubmed: 34719824 DOI: doi:10.1002/pro.4220 ]
- Non-structural protein 1 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus)
- Iron/sulfur cluster (351 Da, Ligand)
- Complex of dna polymerase alpha - primase bound to sars cov-2 nsp1 (310 kDa, Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna polymerase alpha catalytic subunit (133 kDa, Protein from Homo sapiens)
- Dna primase small subunit (52 kDa, Protein from Homo sapiens)
- Dna primase large subunit (58 kDa, Protein from Homo sapiens)
- Dna polymerase alpha subunit b (49 kDa, Protein from Homo sapiens)
Structure of the p53/RNA polymerase II assembly
Liou SH, Singh SK, Singer RH, Coleman RA, Liu WL
Commun Biol (2021) 4 pp. 397-397 [ Pubmed: 33767390 DOI: doi:10.1038/s42003-021-01934-4 ]
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Human)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Human)
- Dna-directed rna polymerase ii (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Cellular tumor antigen p53 (Complex from Homo sapien)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Human)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Human)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Human)
- Dna-directed rna polymerase ii subunit rpb2 (134 kDa, Protein from Human)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Human)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Human)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Human)
- Cellular tumor antigen p53 (43 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb5 (24 kDa, Protein from Human)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Human)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Human)
- P53/rna polymerase ii assembly (Complex)
Townsend C, Leelaram MN, Agafonov DE, Dybkov O, Will CL, Bertram K, Urlaub H, Kastner B, Stark H, Luhrmann R
Science (2020) 370 [ DOI: doi:10.1126/science.abc3753 Pubmed: 33243851 ]
- Human pre-bact-2 spliceosome (Complex from Homo sapiens)
- Splicing factor 3b subunit 5 (10 kDa, Protein from Human)
- Splicing factor 3a subunit 3 (58 kDa, Protein from Human)
- Small nuclear ribonucleoprotein sm d3 (13 kDa, Protein from Human)
- Spliceosome-associated protein cwc15 homolog (26 kDa, Protein from Human)
- U2 snrna (60 kDa, RNA from Human)
- Small nuclear ribonucleoprotein-associated proteins b and b' (24 kDa, Protein from Human)
- Intron-binding protein aquarius (171 kDa, Protein from Human)
- Beta-catenin-like protein 1 (65 kDa, Protein from Human)
- Minx m3 pre-mrna (103 kDa, RNA from synthetic construct)
- Splicing factor 3b subunit 3 (135 kDa, Protein from Human)
- Serine/arginine repetitive matrix protein 1 (102 kDa, Protein from Human)
- Splicing factor 3a subunit 1 (88 kDa, Protein from Human)
- Rna-binding motif protein, x-linked 2 (37 kDa, Protein from Human)
- Minx m3 pre-mrna (Complex from synthetic construct)
- U2 small nuclear ribonucleoprotein b'' (25 kDa, Protein from Human)
- Peptidyl-prolyl cis-trans isomerase e (33 kDa, Protein from Human)
- U2 small nuclear ribonucleoprotein a' (28 kDa, Protein from Human)
- Microfibrillar-associated protein 1 (52 kDa, Protein from Human)
- Cell division cycle 5-like protein (92 kDa, Protein from Human)
- U6 snrna (34 kDa, RNA from Human)
- Snw domain-containing protein 1 (61 kDa, Protein from Human)
- Pre-mrna-processing-splicing factor 8 (273 kDa, Protein from Human)
- Splicing factor 3b subunit 4 (44 kDa, Protein from Human)
- Pleiotropic regulator 1 (57 kDa, Protein from Human)
- Splicing factor 3b subunit 6 (14 kDa, Protein from Human)
- U5 small nuclear ribonucleoprotein 40 kda protein (39 kDa, Protein from Human)
- Dna/rna-binding protein kin17 (45 kDa, Protein from Human)
- Small nuclear ribonucleoprotein sm d2 (13 kDa, Protein from Human)
- U5 small nuclear ribonucleoprotein 200 kda helicase (244 kDa, Protein from Human)
- Pre-mrna-splicing factor rbm22 (46 kDa, Protein from Human)
- Ubiquitin-like protein 5 (8 kDa, Protein from Human)
- Splicing factor 3a subunit 2 (49 kDa, Protein from Human)
- Smad nuclear-interacting protein 1 (45 kDa, Protein from Human)
- Crooked neck-like protein 1 (100 kDa, Protein from Human)
- Bud13 homolog (70 kDa, Protein from Human)
- Inositol hexakisphosphate (660 Da, Ligand)
- Human pre-bact-2 spliceosome (Complex)
- Zinc finger matrin-type protein 2 (23 kDa, Protein from Human)
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Human)
- Ring-type e3 ubiquitin-protein ligase ppil2 (58 kDa, Protein from Human)
- Pre-mrna-splicing factor 38a (37 kDa, Protein from Human)
- Small nuclear ribonucleoprotein sm d1 (13 kDa, Protein from Human)
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Human)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Pre-mrna-splicing factor syf1 (100 kDa, Protein from Human)
- Splicing factor 3b subunit 1 (146 kDa, Protein from Human)
- Protein bud31 homolog (17 kDa, Protein from Human)
- Phd finger-like domain-containing protein 5a (12 kDa, Protein from Human)
- U5 snrna (36 kDa, RNA from Human)
- Splicing factor 3b subunit 2 (100 kDa, Protein from Human)
- Magnesium ion (24 Da, Ligand)
- Pre-mrna-processing factor 17 (65 kDa, Protein from Human)
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Human)
- 116 kda u5 small nuclear ribonucleoprotein component (109 kDa, Protein from Human)
Kokic G, Hillen HS, Tegunov D, Dienemann C, Seitz F, Schmitzova J, Farnung L, Siewert A, Hobartner C, Cramer P
Nat Commun (2021) 12 pp. 279-279 [ Pubmed: 33436624 DOI: doi:10.1038/s41467-020-20542-0 ]
- Rna (5'-r(p*up*gp*cp*ap*up*cp*gp*cp*gp*up*ap*g)-3') (18 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 rna-dependent rna polymerase (nsp12) (Complex from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Sars-cov-2 nsp8 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Dna and rna (Complex from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 nsp7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 rna-dependent rna polymerase (nsp12) (107 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 nsp7 and nsp8 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Dna/rna (5'-r(p*cp*up*ap*cp*gp*cp*g)-d(p*(rmp))-r(p*up*g)-3') (4 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 rna-dependent rna polymerase complex (nsp12, nsp7, nsp8) with elongation scaffold containing remdesivir at position -3. (Complex)
Kokic G, Hillen HS, Tegunov D, Dienemann C, Seitz F, Schmitzova J, Farnung L, Siewert A, Hobartner C, Cramer P
Nat Commun (2021) 12 pp. 279-279 [ Pubmed: 33436624 DOI: doi:10.1038/s41467-020-20542-0 ]
- Rna (5'-r(p*up*cp*ap*cp*up*up*gp*cp*gp*up*ap*g)-3') (18 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 rna-dependent rna polymerase (nsp12) (Complex from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Sars-cov-2 nsp7 and 8 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 nsp8 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Dna and rna (Complex from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 rna-dependent rna polymerase complex (nsp12, nsp7, nsp8) with elongation scaffold containing remdesivir at position -4. (Complex)
- Sars-cov-2 nsp7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 rna-dependent rna polymerase (nsp12) (107 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Dna/rna (5'-r(p*cp*up*ap*cp*gp*cp*a)-d(p*(rmp))-r(p*gp*up*g)-3') (4 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
Human pre-Bact-2 spliceosome (SF3b/U2 snRNP portion)
Townsend C, Leelaram MN, Agafonov DE, Dybkov O, Will CL, Bertram K, Urlaub H, Kastner B, Stark H, Luhrmann R
Science (2020) 370 [ DOI: doi:10.1126/science.abc3753 Pubmed: 33243851 ]
- Splicing factor 3a subunit 3 (58 kDa, Protein from Human)
- Splicing factor 3b subunit 5 (10 kDa, Protein from Human)
- U2 snrna (60 kDa, RNA from Human)
- Splicing factor 3b subunit 3 (135 kDa, Protein from Human)
- Serine/arginine repetitive matrix protein 1 (102 kDa, Protein from Human)
- Rna-binding motif protein, x-linked 2 (37 kDa, Protein from Human)
- Minx m3 pre-mrna (Complex from synthetic construct)
- Cell division cycle 5-like protein (92 kDa, Protein from Human)
- Splicing factor 3b subunit 4 (44 kDa, Protein from Human)
- Splicing factor 3b subunit 6 (14 kDa, Protein from Human)
- Dna/rna-binding protein kin17 (45 kDa, Protein from Human)
- Splicing factor 3a subunit 2 (49 kDa, Protein from Human)
- Smad nuclear-interacting protein 1 (45 kDa, Protein from Human)
- Minx m3 pre-mrna (73 kDa, RNA from synthetic construct)
- Splicing factor 3b subunit 1 (146 kDa, Protein from Human)
- Human pre-bact-2 spliceosome (sf3b/u2 snrnp portion) (Complex from Homo sapiens)
- Phd finger-like domain-containing protein 5a (12 kDa, Protein from Human)
- Splicing factor 3b subunit 2 (100 kDa, Protein from Human)
- Human pre-bact-2 spliceosome (sf3b/u2 snrnp portion) (Complex)
Vos SM, Farnung L, Linden A, Urlaub H, Cramer P
Nat Struct Mol Biol (2020) 27 pp. 668-677 [ Pubmed: 32541898 DOI: doi:10.1038/s41594-020-0437-1 ]
- Human transcription factors and associated proteins (Complex from Homo sapiens)
- Complete ec* (1 MDa, Complex)
- Rna polymerase ii-associated factor 1 homolog (60 kDa, Protein from Homo sapiens)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Pig)
- Rna polymerase-associated protein rtf1 homolog (80 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Dna (37-mer) (14 kDa, DNA from synthetic construct)
- Pig dna/rna polymerase subunits (Complex from Sus scrofa)
- Uncharacterized protein (7 kDa, Protein from Pig)
- Zinc ion (65 Da, Ligand)
- Uncharacterized protein (7 kDa, Protein from Pig)
- Wd repeat-containing protein 61 (33 kDa, Protein from Homo sapiens)
- Dna/rna (Complex from synthetic construct)
- Rna polymerase-associated protein leo1 (75 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Pig)
- Rna polymerase-associated protein ctr9 homolog (134 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit f (14 kDa, Protein from Pig)
- Transcription elongation factor spt4 and spt5 (Complex from Homo sapiens)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit c (31 kDa, Protein from Pig)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Pig)
- Rna polymerase ii subunit e (24 kDa, Protein from Pig)
- Uncharacterized protein (13 kDa, Protein from Pig)
- Rna polymerase ii subunit g (19 kDa, Protein from Pig)
- Rna (5'-r(p*up*ap*ap*cp*cp*gp*gp*ap*gp*ap*gp*gp*gp*ap*ap*cp*cp*cp*ap*cp*u)-3') (14 kDa, RNA from synthetic construct)
- Template dna (14 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase ii subunit d (16 kDa, Protein from Pig)
- Dna-directed rna polymerase subunit (219 kDa, Protein from Pig)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
Shi W, Jiang Y, Deng Y, Dong Z, Liu B
PLoS Biol (2020) 18 pp. e3000706- [ DOI: doi:10.1371/journal.pbio.3000706 ]
- Synthetic nontemplate strand dna (78-mer) (23 kDa, DNA from Escherichia coli)
- Nascent rna (1 kDa, RNA from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Camp-activated global transcriptional regulator crp (23 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Synthetic template strand dna (78-mer) (24 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit alpha, dna-directed rna polymerase subunit beta, dna-directed rna polymerase subunit beta', dna-directed rna polymerase subunit omega, rna polymerase sigma factor rpod, camp-activated global transcriptional regulator crp (Complex from Escherichia coli)
- Adenosine-3',5'-cyclic-monophosphate (329 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Dna/rna (Complex)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli)
- The e. coli class-ii cap-dependent transcription activation complex with de novo rna transcript at the state 2 (550 kDa, Complex from Escherichia coli)
- Rna polymerase sigma factor rpod (72 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
In situ structure of Rotavirus RNA-dependent RNA polymerase at duplex-open state
Ding K, Celma CC, Zhang X, Chang T, Shen W, Atanasov I, Roy P, Zhou ZH
Nat Commun (2019) 10 pp. 2216-2216 [ DOI: doi:10.1038/s41467-019-10236-7 Pubmed: 31101900 ]
- Rotavirus a (Virus from Rotavirus A)
- Inner capsid protein vp2 (103 kDa, Protein from Rotavirus A)
- Rna (5'-r(p*ap*gp*cp*c)-3') (1 kDa, RNA from Rotavirus A)
- Dna/rna (5'-d(*(gtg))-r(p*gp*c)-3') (1 kDa, Macromolecule from Rotavirus A)
- Rna-dependent rna polymerase of rotavirus a (125 kDa, Protein from Rotavirus A)
S. cerevisiae CMG-Pol epsilon-DNA
Goswami P, Abid Ali F, Douglas ME, Locke J, Purkiss A, Janska A, Eickhoff P, Early A, Nans A, Cheung AMC, Diffley JFX, Costa A
Nat Commun (2018) 9 pp. 5061-5061 [ Pubmed: 30498216 DOI: doi:10.1038/s41467-018-07417-1 ]
- Cmg-pol epsilon-dna (Complex)
- Dna/rna (5'-r(*gp*cp*ap*gp*cp*cp*ap*cp*gp*c)-d(p*t)-r(p*gp*gp*cp*cp*g)-d(p*tp*tp*tp*t)-r(p*a)-3') (6 kDa, RNA from Saccharomyces cerevisiae)
- Dna replication complex gins protein sld5 (33 kDa, Protein from Saccharomyces cerevisiae)
- Minichromosome maintenance protein 5 (86 kDa, Protein from Saccharomyces cerevisiae)
- Dna polymerase epsilon catalytic subunit a (104 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf1 (24 kDa, Protein from Saccharomyces cerevisiae)
- Cmg-pol epsilon (Complex from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Dna replication complex gins protein psf2 (25 kDa, Protein from Saccharomyces cerevisiae)
- Nucleic acid (Complex from Saccharomyces cerevisiae)
- Dna/rna (5'-d(p*t)-r(p*ap*ap*ap*ap*cp*gp*gp*cp*cp*ap*gp*cp*g)-d(p*t)-r(p*gp*gp*c)-d(p*t)-r(p*gp*c)-3') (6 kDa, RNA from Saccharomyces cerevisiae)
- Dna (5'-d(p*tp*tp*tp*tp*tp*tp*t)-3') (2 kDa, DNA from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm3 (107 kDa, Protein from Saccharomyces cerevisiae)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Dna replication licensing factor mcm7 (95 kDa, Protein from Saccharomyces cerevisiae)
- Dna polymerase epsilon subunit b (78 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm6 (113 kDa, Protein from Saccharomyces cerevisiae)
- Cell division control protein 45 (74 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm2 (98 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf3 (21 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm4 (105 kDa, Protein from Saccharomyces cerevisiae)