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)
Chromosome Passenger Complex (CPC) localization module in complex with H3.T3p-nucleosome
Resolution: 2.42 Å
EM Method: Single-particle
Fitted PDBs: 8rup
Q-score: 0.551
Ruza RR, Chung CW, Gold DB, Serena M, Roberts E, Gruneberg U, Barr FA
bioRxiv (2025) [ DOI: doi:10.1101/2025.01.22.634029 ]
- Human cpc localisation module in complex with xenopus h3.t3p-nucleosome (202 kDa, Complex from Homo sapiens)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Baculoviral iap repeat-containing protein 5 (16 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Inner centromere protein (9 kDa, Protein from Homo sapiens)
- Chromosome passenger complex localisation module (Complex from Homo sapiens)
- Borealin (9 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna (147-mer) (46 kDa, DNA from synthetic construct)
- Dna (Complex from synthetic construct)
- H3.t3p-nucleosome (Complex from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (147-mer) (47 kDa, DNA from synthetic construct)
Human Vault Cage in complex with PARP4 and NAD+
Lodwick JE, Shen R, Erramilli S, Xie Y, Roganowicz K, Kossiakoff AA, Zhao M
bioRxiv (2024) [ DOI: doi:10.1101/2024.06.27.601040 Pubmed: 38979142 ]
- Major vault protein (99 kDa, Protein from Homo sapiens)
- Ternary complex of nad+ and human parp4 bound to oligomerized human mvp (12 MDa, Complex from Homo sapiens)
- Protein mono-adp-ribosyltransferase parp4 (192 kDa, Protein from Homo sapiens)
- Nicotinamide-adenine-dinucleotide (663 Da, Ligand)
Cryo-EM structure of the Rail RNA motif
Haack DB, Rudolfs B, Jin S, Weeks KM, Toor N
bioRxiv (2024) [ Pubmed: 38915706 DOI: doi:10.1101/2024.06.10.598011 ]
- Rna (200-mer) (192 kDa, RNA from Clostridium acetobutylicum)
- Bacterial raia rna motif (Cellular component from Clostridium acetobutylicum)
- Magnesium ion (24 Da, Ligand)
Autoinhibited full-length LRRK2(I2020T) on microtubules with MLi-2
Resolution: 7.8 Å
EM Method: Subtomogram averaging
Fitted PDBs: 9cho
Q-score: 0.159
Chen S, Basiashvili T, Hutchings J, Murillo MS, Suarez AV, Louro JA, Leschziner AE, Villa E
bioRxiv (2024) [ DOI: doi:10.1101/2024.06.18.599606 Pubmed: 38948781 ]
- Full-length autoinhibited lrrk2 i2020t on microtubules (286 kDa, Complex from Homo sapiens)
- (2~{r},6~{s})-2,6-dimethyl-4-[6-[5-(1-methylcyclopropyl)oxy-1~{h}-indazol-3-yl]pyrimidin-4-yl]morpholine (379 Da, Ligand)
- Leucine-rich repeat serine/threonine-protein kinase 2 (224 kDa, Protein from Homo sapiens)
- Guanosine-5'-diphosphate (443 Da, Ligand)