Helical reconstruction of CHIKV nsP3 helical scaffolds
Kril V, Hons M, Amadori C, Zimberger C, Couture L, Bouery Y, Burlaud-Gaillard J, Karpov A, Ptchelkine D, Thienel AL, Kummerer BM, Desfosses A, Jones R, Roingeard P, Meertens L, Amara A, Reguera J
Nat Commun (2024) 15 pp. 8106-8106 [ Pubmed: 39285216 DOI: doi:10.1038/s41467-024-51952-z ]
Helical reconstruction of CHIKV nsP3 helical scaffolds
Kril V, Hons M, Amadori C, Zimberger C, Couture L, Bouery Y, Burlaud-Gaillard J, Karpov A, Ptchelkine D, Thienel AL, Kummerer BM, Desfosses A, Jones R, Roingeard P, Meertens L, Amara A, Reguera J
Nat Commun (2024) 15 pp. 8106-8106 [ Pubmed: 39285216 DOI: doi:10.1038/s41467-024-51952-z ]
Kril V, Hons M, Amadori C, Zimberger C, Couture L, Bouery Y, Burlaud-Gaillard J, Karpov A, Ptchelkine D, Thienel AL, Kummerer BM, Desfosses A, Jones R, Roingeard P, Meertens L, Amara A, Reguera J
Nat Commun (2024) 15 pp. 8106-8106 [ Pubmed: 39285216 DOI: doi:10.1038/s41467-024-51952-z ]
Cryo-EM Structure of Chikungunya Virus Nonstructural Protein 1 with m7GpppAmU
Resolution: 2.41 Å
EM Method: Single-particle
Fitted PDBs: 8jce
Q-score: 0.643
Law MCY, Zhang K, Tan YB, Nguyen TM, Luo D
J Biol Chem (2023) 299 pp. 105415-105415 [ Pubmed: 37918803 DOI: doi:10.1016/j.jbc.2023.105415 ]
- Water (18 Da, Ligand)
- Nonstructural protein 1 (Complex from Chikungunya virus strain S27-African prototype)
- [(2~{r},3~{r},4~{r},5~{r})-5-(6-azanyl-7,8-dihydropurin-9-yl)-2-[[[[[(2~{r},3~{s},4~{r},5~{r})-5-(2-azanyl-7-methyl-6-oxidanylidene-1,8-dihydropurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-4-methoxy-oxolan-3-yl] [(2~{r},3~{s},4~{r},5~{s})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate (1 kDa, Ligand)
- Mrna-capping enzyme nsp1 (61 kDa, Protein from Chikungunya virus strain S27-African prototype)
- Magnesium ion (24 Da, Ligand)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Zinc ion (65 Da, Ligand)
CryoEM structure of the Chikungunya virus nsP1 capping pores in complex with GTP
Resolution: 2.48 Å
EM Method: Single-particle
Fitted PDBs: 8aov
Q-score: 0.616
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 ]
- Water (18 Da, Ligand)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Dodecameric complex of chikungunya virus nsp1 in complex with gtp (1 MDa, Complex from Baculovirus expression vector pFastBac1-HM)
- Mrna-capping enzyme nsp1 (60 kDa, Protein from Chikungunya virus strain S27-African prototype)
- Zinc ion (65 Da, Ligand)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8apx
Q-score: 0.391
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 ]
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Polyprotein p1234 (53 kDa, Protein from Chikungunya virus strain S27-African prototype)
- Chikv nsp1 capping pores covalently linked to m7gmp cap via h37 (720 kDa, Complex from Chikungunya virus strain S27-African prototype)
- Zinc ion (65 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 ]
- Chikv nsp1 capping pores in complex with m7gtp and sah ligand with magnesium cofactor. (720 kDa, Complex from Chikungunya virus strain S27-African prototype)
- Water (18 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- 7-methyl-guanosine-5'-triphosphate (538 Da, Ligand)
- Mrna-capping enzyme nsp1 (60 kDa, Protein from Chikungunya virus strain S27-African prototype)
- Zinc ion (65 Da, Ligand)
CryoEM structure of the Chikungunya virus nsP1 capping pores in complex with SAM
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8aox
Q-score: 0.574
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 ]
- Water (18 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Chikv nsp1 capping pores in complex with s-adenosyl methionine (sam) ligand. (1 MDa, Complex from Chikungunya virus strain S27-African prototype)
- S-adenosylmethionine (398 Da, Ligand)
- Mrna-capping enzyme nsp1 (59 kDa, Protein from Chikungunya virus strain S27-African prototype)
Structure of an open form of CHIKV nsP1 capping pores
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8axv
Q-score: 0.47
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 ]
- 2-amino-7-methyl-1,7-dihydro-6h-purin-6-one (165 Da, Ligand)
- Chikungunya nsp1 in an open form (720 kDa, Complex from Chikungunya virus strain S27-African prototype)
- Zinc ion (65 Da, Ligand)
- Mrna-capping enzyme nsp1 (59 kDa, Protein from Chikungunya virus strain S27-African prototype)
Molecular architecture of the chikungunya virus replication complex
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7y38
Q-score: 0.539
Tan YB, Chmielewski D, Law MCY, Zhang K, He Y, Chen M, Jin J, Luo D
Sci Adv (2022) 8 pp. eadd2536-eadd2536 [ Pubmed: 36449616 DOI: doi:10.1126/sciadv.add2536 ]
- Rna-directed rna polymerase nsp4 (68 kDa, Protein from Onyong-nyong virus)
- Mrna-capping enzyme nsp1,affinity-tag (strepii-3xflag) (64 kDa, Protein from Chikungunya virus strain S27-African prototype)
- Nsp2 helicase-protease; docked on top of viral complex with synthetic rna bound (Complex from Chikungunya virus strain S27-African prototype)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Protease nsp2 (89 kDa, Protein from Chikungunya virus strain S27-African prototype)
- Nsp1 dodecameric ring (Complex from Chikungunya virus strain S27-African prototype)
- Alphavirus replication complex (100 kDa, Complex)
- Nsp4 rdrp; docked within nsp1 central cavity (Complex from Onyong-nyong virus)
- Zinc ion (65 Da, Ligand)
- Rna (5'-r(p*cp*cp*a)-3') (894 Da, RNA from in vitro transcription vector pT7-TP(deltai))