Cryo-EM structure of the I923V MDA5-dsRNA filament without nucleotide
Resolution: 3.35 Å
EM Method: Helical reconstruction
Fitted PDBs: 9f0j
Q-score: 0.446
Singh R, Herrero del Valle A, Joiner JD, Zwaagstra M, Ferguson BJ, van Kuppeveld FJM, Modis Y
bioRxiv (2024) [ DOI: doi:10.1101/2024.10.03.616466 ]
- Rna (5'-uccaugcgcaugacg-3') (4 kDa, RNA from Mus musculus)
- Double stranded rna (Complex from Mus musculus)
- Rna (5'-cgucaugcgcaugga-3') (4 kDa, RNA from Mus musculus)
- Zinc ion (65 Da, Ligand)
- Interferon-induced helicase c domain-containing protein 1 (116 kDa, Protein from Mus musculus)
- Mouse mda5 i923v (Complex from Mus musculus)
- Mouse mda5 i923v in complex with double stranded rna (28 MDa, Complex)
Cryo-EM structure of the I923V MDA5-dsRNA filament with ADP-AlF4 bound and 81-degree helical twist
Resolution: 3.67 Å
EM Method: Helical reconstruction
Fitted PDBs: 9f1u
Q-score: 0.335
Singh R, Herrero del Valle A, Joiner JD, Zwaagstra M, Ferguson BJ, van Kuppeveld FJM, Modis Y
bioRxiv (2024) [ DOI: doi:10.1101/2024.10.03.616466 ]
- Rna (5'-r(p*ap*up*cp*up*cp*cp*up*cp*gp*gp*cp*up*up*g)-3') (4 kDa, RNA from Mus musculus)
- Tetrafluoroaluminate ion (102 Da, Ligand)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Double stranded rna (Complex from Mus musculus)
- Rna (5'-r(p*cp*ap*ap*gp*cp*cp*gp*ap*gp*gp*ap*gp*ap*u)-3') (4 kDa, RNA from Mus musculus)
- Zinc ion (65 Da, Ligand)
- Interferon-induced helicase c domain-containing protein 1 (116 kDa, Protein from Mus musculus)
- Mouse mda5 i923v (Complex from Mus musculus)
- Mouse mda5 i923v in complex with double stranded rna (28 MDa, Complex)
Cryo-EM structure of the I923V MDA5-dsRNA filament with ADP-AlF4 bound and 88-degree helical twist
Resolution: 4.13 Å
EM Method: Helical reconstruction
Fitted PDBs: 9f20
Q-score: 0.297
Singh R, Herrero del Valle A, Joiner JD, Zwaagstra M, Ferguson BJ, van Kuppeveld FJM, Modis Y
bioRxiv (2024) [ DOI: doi:10.1101/2024.10.03.616466 ]
- Rna (5'-r(p*gp*up*cp*ap*ap*gp*cp*cp*gp*ap*gp*gp*ap*gp*a)-3') (4 kDa, RNA from Mus musculus)
- Tetrafluoroaluminate ion (102 Da, Ligand)
- Rna (5'-r(p*up*cp*up*cp*cp*up*cp*gp*gp*cp*up*up*gp*ap*c)-3') (4 kDa, RNA from Mus musculus)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Double stranded rna (Complex from Mus musculus)
- Zinc ion (65 Da, Ligand)
- Interferon-induced helicase c domain-containing protein 1 (116 kDa, Protein from Mus musculus)
- Mouse mda5 i923v (Complex from Mus musculus)
- Mouse mda5 i923v in complex with double stranded rna (28 MDa, Complex)
Cryo-EM structure of the I923V MDA5-dsRNA filament with ADP-AlF4 bound and 73-degree helical twist
Resolution: 3.86 Å
EM Method: Helical reconstruction
Fitted PDBs: 9f2l
Q-score: 0.385
Singh R, Herrero del Valle A, Joiner JD, Zwaagstra M, Ferguson BJ, van Kuppeveld FJM, Modis Y
bioRxiv (2024) [ DOI: doi:10.1101/2024.10.03.616466 ]
- Tetrafluoroaluminate ion (102 Da, Ligand)
- Rna (5'-r(p*cp*ap*ap*gp*cp*cp*gp*ap*gp*gp*ap*gp*ap*g)-3') (4 kDa, RNA from Mus musculus)
- Rna (5'-r(p*cp*up*cp*up*cp*cp*up*cp*gp*gp*cp*up*up*g)-3') (4 kDa, RNA from Mus musculus)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Double stranded rna (Complex from Mus musculus)
- Zinc ion (65 Da, Ligand)
- Interferon-induced helicase c domain-containing protein 1 (116 kDa, Protein from Mus musculus)
- Mouse mda5 i923v (Complex from Mus musculus)
- Mouse mda5 i923v in complex with double stranded rna (28 MDa, Complex)
Cryo-EM structure of the I923V MDA5-dsRNA filament in complex with ATP
Resolution: 4.21 Å
EM Method: Helical reconstruction
Fitted PDBs: 9f2w
Q-score: 0.32
Singh R, Herrero del Valle A, Joiner JD, Zwaagstra M, Ferguson BJ, van Kuppeveld FJM, Modis Y
bioRxiv (2024) [ DOI: doi:10.1101/2024.10.03.616466 ]
- Rna (5'-r(p*ap*up*cp*up*cp*cp*up*cp*gp*gp*cp*up*up*g)-3') (4 kDa, RNA from Mus musculus)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Double stranded rna (Complex from Mus musculus)
- Rna (5'-r(p*cp*ap*ap*gp*cp*cp*gp*ap*gp*gp*ap*gp*ap*u)-3') (4 kDa, RNA from Mus musculus)
- Zinc ion (65 Da, Ligand)
- Interferon-induced helicase c domain-containing protein 1 (116 kDa, Protein from Mus musculus)
- Mouse mda5 i923v (Complex from Mus musculus)
- Mouse mda5 i923v in complex with double stranded rna (28 MDa, Complex)
Cryo-EM structure of the A946T MDA5-dsRNA filament
Resolution: 3.97 Å
EM Method: Helical reconstruction
Fitted PDBs: 9f3p
Q-score: 0.348
Singh R, Herrero del Valle A, Joiner JD, Zwaagstra M, Ferguson BJ, van Kuppeveld FJM, Modis Y
bioRxiv (2024) [ DOI: doi:10.1101/2024.10.03.616466 ]
- Rna (5'-r(p*gp*up*cp*ap*ap*gp*cp*cp*gp*ap*gp*gp*ap*gp*a)-3') (4 kDa, RNA from Mus musculus)
- Rna (5'-r(p*up*cp*up*cp*cp*up*cp*gp*gp*cp*up*up*gp*ap*c)-3') (4 kDa, RNA from Mus musculus)
- Mouse mda5 a946t (Complex from Mus musculus)
- Double stranded rna (Complex from Mus musculus)
- Zinc ion (65 Da, Ligand)
- Mouse mda5 a946t in complex with double stranded rna (28 MDa, Complex)
- Interferon-induced helicase c domain-containing protein 1 (116 kDa, Protein from Mus musculus)
Resolution: 3.2 Å
EM Method: Helical reconstruction
Fitted PDBs: 9fvd
Q-score: 0.45
Zinzula L, Beck F, Camasta M, Bohn S, Liu C, Morado D, Bracher A, Plitzko JM, Baumeister W
Nat Commun (2024) 15 pp. 10307-10307 [ Pubmed: 39604358 DOI: doi:10.1038/s41467-024-54431-7 ]
- Helical assembly of nucleoprotein-rna complex from marburg virus (Complex from Marburg virus - Musoke, Kenya, 1980)
- Rna (5'-r(p*ap*gp*ap*cp*ap*cp*ap*cp*ap*ap*ap*ap*ap*cp*ap*ap*gp*a)-3') (5 kDa, RNA from Marburg virus - Musoke, Kenya, 1980)
- Nucleoprotein (49 kDa, Protein from Marburg virus - Musoke, Kenya, 1980)
Resolution: 3.09 Å
EM Method: Helical reconstruction
Fitted PDBs: 8ope
Q-score: 0.527
Kavcic L, Kezar A, Koritnik N, Znidaric MT, Klobucar T, Vicic Z, Merzel F, Holden E, Benesch JLP, Podobnik M
Commun Chem (2024) 7 pp. 14-14 [ DOI: doi:10.1038/s42004-024-01100-x Pubmed: 38233506 ]
Resolution: 2.41 Å
EM Method: Helical reconstruction
Fitted PDBs: 8opl
Q-score: 0.667
Kavcic L, Kezar A, Koritnik N, Znidaric MT, Klobucar T, Vicic Z, Merzel F, Holden E, Benesch JLP, Podobnik M
Commun Chem (2024) 7 pp. 14-14 [ DOI: doi:10.1038/s42004-024-01100-x Pubmed: 38233506 ]
beta-2-microglobulin DeltaN6 amyloid fibril form 2PFa
Resolution: 3.0 Å
EM Method: Helical reconstruction
Fitted PDBs: 8a7o
Q-score: 0.579
Wilkinson M, Gallardo RU, Martinez RM, Guthertz N, So M, Aubrey LD, Radford SE, Ranson NA
Nat Commun (2023) 14 pp. 1190-1190 [ Pubmed: 36864041 DOI: doi:10.1038/s41467-023-36791-8 ]