Cryo-EM structure of Thogoto virus polymerase in a transcription elongation conformation
Resolution: 2.65 Å
EM Method: Single-particle
Fitted PDBs: 8z97
Q-score: 0.566
Xue L, Chang T, Li Z, Wang C, Zhao H, Li M, Tang P, Wen X, Yu M, Wu J, Bao X, Wang X, Gong P, He J, Chen X, Xiong X
Nat Commun (2024) 15 pp. 4620-4620 [ Pubmed: 38816392 DOI: doi:10.1038/s41467-024-48848-3 ]
- 7-methyl-guanosine-5'-triphosphate-5'-(2'-o-methyl)-adenosine (801 Da, Ligand)
- Rna (5'-r(*gp*ap*cp*up*gp*cp*cp*up*gp*up*up*up*up*up*gp*cp*u)-3') (5 kDa, RNA from Thogoto virus (isolate SiAr 126))
- Rna (5'-r(p*gp*cp*ap*ap*ap*ap*ap*cp*a)-3') (2 kDa, RNA from Thogoto virus (isolate SiAr 126))
- Rna-directed rna polymerase catalytic subunit (81 kDa, Protein from Thogoto virus (isolate SiAr 126))
- Polymerase acidic protein (71 kDa, Protein from Thogoto virus (isolate SiAr 126))
- Rna (5'-r(*ap*gp*ap*gp*ap*ap*ap*up*cp*ap*ap*gp*gp*cp*ap*gp*up*u)-3') (5 kDa, RNA from Thogoto virus (isolate SiAr 126))
- Cryo-em structure of thogoto virus polymerase in a transcription elongation conformation (Complex from Thogoto virus (isolate SiAr 126))
- Polymerase basic protein 2 (94 kDa, Protein from Thogoto virus (isolate SiAr 126))
Cryo-EM structure of Thogoto virus polymerase in a transcription reception conformation
Resolution: 2.52 Å
EM Method: Single-particle
Fitted PDBs: 8z98
Q-score: 0.569
Xue L, Chang T, Li Z, Wang C, Zhao H, Li M, Tang P, Wen X, Yu M, Wu J, Bao X, Wang X, Gong P, He J, Chen X, Xiong X
Nat Commun (2024) 15 pp. 4620-4620 [ Pubmed: 38816392 DOI: doi:10.1038/s41467-024-48848-3 ]
- 7-methyl-guanosine-5'-triphosphate-5'-(2'-o-methyl)-adenosine (801 Da, Ligand)
- Rna (5'-r(p*gp*cp*ap*ap*ap*ap*ap*cp*a)-3') (2 kDa, RNA from Thogoto virus (isolate SiAr 126))
- Cryo-em structure of thogoto virus polymerase in a transcription reception conformation (Complex from Thogoto virus (isolate SiAr 126))
- Rna-directed rna polymerase catalytic subunit (81 kDa, Protein from Thogoto virus (isolate SiAr 126))
- Polymerase acidic protein (71 kDa, Protein from Thogoto virus (isolate SiAr 126))
- Polymerase basic protein 2 (94 kDa, Protein from Thogoto virus (isolate SiAr 126))
Cryo-EM structure of Thogoto virus polymerase in a transcription elongation-reception conformation
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8z9h
Q-score: 0.514
Xue L, Chang T, Li Z, Wang C, Zhao H, Li M, Tang P, Wen X, Yu M, Wu J, Bao X, Wang X, Gong P, He J, Chen X, Xiong X
Nat Commun (2024) 15 pp. 4620-4620 [ Pubmed: 38816392 DOI: doi:10.1038/s41467-024-48848-3 ]
- Cryo-em structure of thogoto virus polymerase in a transcription elongation-reception conformation (Complex from Thogoto virus (isolate SiAr 126))
- Rna (5'-r(*ap*gp*ap*gp*ap*ap*ap*up*cp*ap*ap*gp*gp*cp*ap*gp*up*u)-3') (5 kDa, RNA from Thogoto virus (isolate SiAr 126))
- Polymerase acidic protein (71 kDa, Protein from Thogoto virus (isolate SiAr 126))
- Rna (5'-r(*gp*ap*cp*up*gp*cp*cp*up*gp*up*up*up*up*up*gp*cp*u)-3') (5 kDa, RNA from Thogoto virus (isolate SiAr 126))
- 7-methyl-guanosine-5'-triphosphate-5'-(2'-o-methyl)-adenosine (801 Da, Ligand)
- Polymerase basic protein 2 (94 kDa, Protein from Thogoto virus (isolate SiAr 126))
- Rna (5'-r(p*gp*cp*ap*ap*ap*ap*ap*cp*a)-3') (2 kDa, RNA from Thogoto virus (isolate SiAr 126))
- Rna-directed rna polymerase catalytic subunit (81 kDa, Protein from Thogoto virus (isolate SiAr 126))
Structure of the human nuclear cap-binding complex bound to NCBP3(560-620) and cap-analogue m7GpppG
Resolution: 3.19 Å
EM Method: Single-particle
Fitted PDBs: 8by6
Q-score: 0.483
Dubiez E, Pellegrini E, Finderup Brask M, Garland W, Foucher AE, Huard K, Heick Jensen T, Cusack S, Kadlec J
Cell Rep (2024) 43 pp. 113639-113639 [ DOI: doi:10.1016/j.celrep.2023.113639 Pubmed: 38175753 ]
- Nuclear cap-binding protein subunit 3 (6 kDa, Protein from Homo sapiens)
- Nuclear cap-binding protein subunit 2 (18 kDa, Protein from Homo sapiens)
- Nuclear cap-binding protein subunit 1 (89 kDa, Protein from Homo sapiens)
- Ternary complex of cbp80, cbp20 and ncbp3 with bound m7gpppg (Complex from Homo sapiens)
- 7-methyl-guanosine-5'-triphosphate-5'-guanosine (803 Da, Ligand)
CryoEM structure of the Chikungunya virus nsP1 capping pores in complex with m7GTP and SAH ligands
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8aow
Q-score: 0.584
Jones R, Hons M, Rabah N, Zamarreno N, Arranz R, Reguera J
PNAS (2023) 120 pp. e2213934120-e2213934120 [ DOI: doi:10.1073/pnas.2213934120 Pubmed: 36913573 ]
- 7-methyl-guanosine-5'-triphosphate (538 Da, Ligand)
- Water (18 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Chikv nsp1 capping pores in complex with m7gtp and sah ligand with magnesium cofactor. (720 kDa, Complex from Chikungunya virus strain S27-African prototype)
- Magnesium ion (24 Da, Ligand)
- Mrna-capping enzyme nsp1 (60 kDa, Protein from Chikungunya virus strain S27-African prototype)
Cryo-EM Structure of Chikungunya Virus Nonstructural Protein 1 with m7GTP
Resolution: 2.19 Å
EM Method: Single-particle
Fitted PDBs: 7fgg
Q-score: 0.698
Zhang K, Law MCY, Nguyen TM, Tan YB, Wirawan M, Law YS, Jeong LS, Luo D
Cell Rep (2022) 40 pp. 111133-111133 [ Pubmed: 35905713 DOI: doi:10.1016/j.celrep.2022.111133 ]
- Water (18 Da, Ligand)
- Nonstructural protein 1 (Complex from Chikungunya virus strain S27-African prototype)
- Magnesium ion (24 Da, Ligand)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Mrna-capping enzyme nsp1 (62 kDa, Protein from Chikungunya virus strain S27-African prototype)
- 7-methyl-guanosine-5'-triphosphate (538 Da, Ligand)
- Zinc ion (65 Da, Ligand)
La Crosse virus polymerase at transcription initiation stage
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 7orl
Q-score: 0.474
Arragain B, Durieux Trouilleton Q, Baudin F, Provaznik J, Azevedo N, Cusack S, Schoehn G, Malet H
Nat Commun (2022) 13 pp. 902-902 [ Pubmed: 35173159 DOI: doi:10.1038/s41467-022-28428-z ]
- Rna (5'-r(p*ap*cp*gp*ap*gp*up*gp*up*cp*gp*up*ap*cp*cp*ap*ap*g)-3') (5 kDa, RNA from La Crosse virus)
- Magnesium ion (24 Da, Ligand)
- 7-methyl-guanosine-5'-triphosphate-5'-guanosine (803 Da, Ligand)
- Rna (5'-r(p*cp*up*up*gp*gp*up*ap*gp*up*ap*cp*ap*cp*up*ap*cp*u)-3') (7 kDa, RNA from La Crosse virus)
- La crosse virus polymerase at transcription initiation (284 kDa, Complex from La Crosse virus)
- Rna-directed rna polymerase l (264 kDa, Protein from La Crosse virus)
- Pyrophosphate 2- (175 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Rna (5'-d(*(gtg))-r(p*ap*ap*up*ap*cp*up*ap*up*ap*gp*up*a)-3') (4 kDa, RNA from La Crosse virus)
Resolution: 7.8 Å
EM Method: Single-particle
Fitted PDBs: 7abg
Q-score: 0.147
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 ]
- U6 snrna-associated sm-like protein lsm8 (10 kDa, Protein from Homo sapiens)
- Splicing factor 3a subunit 1 (88 kDa, Protein from Homo sapiens)
- Pre-mrna-processing-splicing factor 8 (273 kDa, Protein from Homo sapiens)
- Pre-bact-1 spliceosomal complex (Complex from Homo sapiens)
- Ubiquitin-like protein 5 (8 kDa, Protein from Homo sapiens)
- Inositol hexakisphosphate (660 Da, Ligand)
- Cell division cycle 5-like protein (92 kDa, Protein from Homo sapiens)
- U6 snrna-associated sm-like protein lsm5 (9 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Homo sapiens)
- Transcription elongation regulator 1 (124 kDa, Protein from Homo sapiens)
- Pre-mrna-splicing factor rbm22 (46 kDa, Protein from Homo sapiens)
- Pre-mrna-splicing factor 38a (37 kDa, Protein from Homo sapiens)
- U6 snrna-associated sm-like protein lsm6 (9 kDa, Protein from Homo sapiens)
- Splicing factor 3b subunit 1 (146 kDa, Protein from Homo sapiens)
- Pre-bact-1 spliceosomal complex (Complex)
- U2 snrna (60 kDa, RNA from Homo sapiens)
- U6 snrna-associated sm-like protein lsm7 (11 kDa, Protein from Homo sapiens)
- Splicing factor 3a subunit 3 (58 kDa, Protein from Homo sapiens)
- U2 small nuclear ribonucleoprotein b'' (25 kDa, Protein from Homo sapiens)
- Ww domain-binding protein 11 (70 kDa, Protein from Homo sapiens)
- U2 small nuclear ribonucleoprotein a' (28 kDa, Protein from Homo sapiens)
- Minx m3 pre-mrna (73 kDa, RNA from synthetic construct)
- Protein bud31 homolog (17 kDa, Protein from Homo sapiens)
- Microfibrillar-associated protein 1 (52 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein-associated proteins b and b' (24 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein sm d3 (13 kDa, Protein from Homo sapiens)
- Splicing factor 3b subunit 4 (44 kDa, Protein from Homo sapiens)
- U5 small nuclear ribonucleoprotein 200 kda helicase (244 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein sm d2 (13 kDa, Protein from Homo sapiens)
- Spliceosome-associated protein cwc15 homolog (26 kDa, Protein from Homo sapiens)
- Splicing factor 3b subunit 5 (10 kDa, Protein from Homo sapiens)
- Nuclear cap-binding protein subunit 1 (91 kDa, Protein from Homo sapiens)
- Serine/arginine-rich splicing factor 1 (27 kDa, Protein from Homo sapiens)
- Splicing factor 3b subunit 3 (135 kDa, Protein from Homo sapiens)
- Pleiotropic regulator 1 (57 kDa, Protein from Homo sapiens)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- U6 snrna-associated sm-like protein lsm2 (10 kDa, Protein from Homo sapiens)
- 116 kda u5 small nuclear ribonucleoprotein component (109 kDa, Protein from Homo sapiens)
- Smad nuclear-interacting protein 1 (45 kDa, Protein from Homo sapiens)
- U6 snrna-associated sm-like protein lsm4 (15 kDa, Protein from Homo sapiens)
- Splicing factor 3a subunit 2 (49 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein sm d1 (13 kDa, Protein from Homo sapiens)
- Snw domain-containing protein 1 (61 kDa, Protein from Homo sapiens)
- Phd finger-like domain-containing protein 5a (12 kDa, Protein from Homo sapiens)
- U5 snrna (36 kDa, RNA from Homo sapiens)
- U6 snrna-associated sm-like protein lsm3 (11 kDa, Protein from Homo sapiens)
- Splicing factor 3b subunit 2 (100 kDa, Protein from Homo sapiens)
- Zinc finger matrin-type protein 2 (23 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Homo sapiens)
- U6 snrna (34 kDa, RNA from Homo sapiens)
- 7-methyl-guanosine-5'-triphosphate-5'-guanosine (803 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- U5 small nuclear ribonucleoprotein 40 kda protein (39 kDa, Protein from Homo sapiens)
- Serine/arginine repetitive matrix protein 1 (102 kDa, Protein from Homo sapiens)
- Splicing factor 3b subunit 6 (14 kDa, Protein from Homo sapiens)
- Nuclear cap-binding protein subunit 2 (18 kDa, Protein from Homo sapiens)