Solved Molecular Structures
CRISPRs
Wiedenheft, B., Zhou, K., Jinek, M., Coyle, S.M., Ma, W. and Doudna, J.A. (2009) Structural basis for DNase activity of a conserved protein implicated in CRISPR-mediated genome defense. Structure 17, 904-12.
| Structure | PDB File |
Ai5G Group II Self-Splicing Intron
Zhang, L. and Doudna, J.A. (2002) Structural insights into group II intron catalysis and branch-site selection. Science 295, 2084-2088. (352KB PDF)
| Structure | PDB File | mmCIF File |
|---|---|---|
| Ai5G Group II Self-Splicing Intron: Domains 5 and 6 (PDB entry) (PDB beta site entry) | 1KXK.pdb (144KB) | 1KXK.cif (180KB) |
Dicer
MacRae, I.J., Zhou, K., Li, F., Repic, A., Brooks, A.N., Cande, W.Z., Adams, P.D., and Doudna, J.A. (2006) Structural basis for double-stranded RNA processing by Dicer. Science 311, 195-198. (288KB .pdf) (Figure)
Structure |
PDB File | mmCIF File |
| Crystal Structure of Dicer from Giardia intestinalis (PDB entry) (PDB beta site entry) | 2FFL.pdb (1.9MB) | 2FFL.cif (2.5MB) |
HCV IRES
Siridechadilok, B., Fraser, C.S., Hall, R.J., Doudna, J.A. and Nogales, E. (2005) Structural roles for human translation factor eIF3 in initiation of protein synthesis. Science 310, 1513-1515. (216KB .pdf)
(Supplemental material: 712KB .pdf)
| Structure | Cryo-EM Volume |
|---|---|
| eIF3 | emd-1170.ccp4.gz (1.9MB) |
| eIF3-IRES (refined conformer-1) | emd-1171.ccp4.gz (9.8MB) |
Kieft, J.S., Zhou, K., Grech, A., Jubin. R. and Doudna, J.A. (2002) Crystal structure of an RNA tertiary domain essential to HCV IRES-mediated translation initiation. Nature Struct. Biol. 9, 370-374. (1356KB PDF)
| Structure | PDB File | mmCIF File |
|---|---|---|
| Jiiiabc RNA Four-Way Junction (PDB entry) (PDB beta site entry) | 1KH6.pdb (108KB) | 1KH6.cif (132KB) |
Hepatitis Delta Virus Ribozyme
Ke, A., Zhou, K., Ding, F., Cate, J.H.D. and Doudna, J.A. (2004) A conformational switch controls hepatitis delta virus ribozyme catalysis. Nature, 429, 201-205. (348KB PDF) (Figures and QuickTime Movies)
| Structure | PDB File | mmCIF File |
|---|---|---|
| HDV Ribozyme Precursor with Mg2+ Bound + U1A: RNA Binding Domain complex (PDB entry) (PDB beta site entry) | 1SJ3.pdb (228KB) | 1SJ3.cif (284KB) |
| HDV Ribozyme Precursor: C75U Mutant in Cu2+ Solution + U1A: RNA Binding Domain complex (PDB entry) (PDB beta site entry) | 1SJ4.pdb (224KB) | 1SJ4.cif (280KB) |
| HDV Ribozyme Precursor: C75U Mutant in Cobalt Hexammine Solution + U1A: RNA Binding Domain complex (PDB entry) (PDB beta site entry) | 1SJF.pdb (228KB) | 1SJF.cif (284KB) |
| HDV Ribozyme Precursor: C75U Mutant in EDTA Solution + U1A: RNA Binding Domain complex (PDB entry) (PDB beta site entry) | 1VBX.pdb (224KB) | 1VBX.cif (280KB) |
| HDV Ribozyme Precursor: C75U Mutant with Mn2+ Bound + U1A: RNA Binding Domain complex (PDB entry) (PDB beta site entry) | 1VBY.pdb (224KB) | 1VBY.cif (280KB) |
| HDV Ribozyme Precursor: C75U Mutant in Ba2+ Solution + U1A: RNA Binding Domain complex (PDB entry) (PDB beta site entry) | 1VBZ.pdb (224KB) | 1VBZ.cif (280KB) |
| HDV Ribozyme Precursor: C75U Mutant in Imidazole and Sr2+ Solution + U1A: RNA Binding Domain complex (PDB entry) (PDB beta site entry) | 1VC0.pdb (224KB) | 1VC0.cif (284KB) |
| HDV Ribozyme Precursor in EDTA Solution + U1A: RNA Binding Domain complex (PDB entry) (PDB beta site entry) | 1VC5.pdb (396KB) | 1VC5.cif (488KB) |
| HDV Ribozyme Precursor: C75U Mutant Cleaved in Imidazole and Mg2+ Solution + U1A: RNA Binding Domain complex (PDB entry) (PDB beta site entry) | 1VC6.pdb (224KB) | 1VC6.cif (280KB) |
| HDV Ribozyme Precursor: C75U Mutant in Sr2+ Solution + U1A: RNA Binding Domain complex (PDB entry) (PDB beta site entry) | 1VC7.pdb (416KB) | 1VC7.cif (512KB) |
Ferré-D'Amaré, A.R., Zhou, K. and Doudna J.A. (1998) Crystal structure of a hepatitis delta virus ribozyme. Nature 395, 567-574. (684KB PDF) (Figures and QuickTime Movies)
| Structure | PDB File | mmCIF File |
|---|---|---|
| HDV Ribozyme + U1A: RNA Binding Domain complex (PDB entry) (PDB beta site entry) | 1CX0.pdb (228KB) | 1CX0.cif (288KB) |
| HDV Ribozyme: Ribozyme Domain + U1A: RNA Binding Domain complex (PDB entry) (PDB beta site entry) | 1DRZ.pdb (228KB) | 1DRZ.cif (296KB) |
P4-P6 Ribozyme
Battle, D.J. and Doudna, J.A. (2002) Specificity of RNA-RNA helix recognition. Proc. Natl. Acad. Sci. 99, 11676-11681. (576KB PDF)
Erratum (624KB PDF)
| Structure | PDB File | mmCIF File |
|---|---|---|
| P4-P6 RNA Ribozyme Domain: Mutant (C109G/G212C) (PDB entry) (PDB beta site entry) | 1L8V.pdb (580KB) | 1L8V.cif (796KB) |
Cate, J.H., Gooding, A., Podell, E., Zhou, K., Golden, B., Kundrot, C., Cech, T.R. and Doudna, J.A. (1996) Crystal structure of a group I ribozyme domain: Principles of RNA packing. Science 273, 1678-85. (360KB PDF) (Figure)
| P4-P6 RNA Ribozyme Domain (PDB entry) (PDB beta site entry) | 1GID.pdb (572KB) | 1GID.cif (784KB) |
Signal Recognition Particle
Batey, R.T., Sagar, M.B. and Doudna, J.A. (2001) Structural and energetic analysis of nucleic acid recognition by a universally conserved protein from the signal recognition particle. J. Mol. Biol. 307, 229-246. (840KB PDF) (Figure)
| Structure | PDB File | mmCIF File |
|---|---|---|
| 4.5S RNA Domain IV Fragment + SRP Protein: C Terminal Domain complex, 1.52Å (PDB entry) (PDB beta site entry) | 1HQ1.pdb (344KB) | 1HQ1.cif (436KB) |
Batey, R.T., Rambo, R.P., Lucast, L., Rha, B. and Doudna, J.A. (2000) Crystal structure of the ribonucleoprotein core of the signal recognition particle. Science 287, 1232-1239. (1992KB PDF) (Figure)
Comment: Science 287, 1212-1213.
| 4.5S RNA Domain IV Fragment + SRP Protein: C Terminal Domain complex, 1.80Å (PDB entry) (PDB beta site entry) | 1DUL.pdb (188KB) | 1DUL.cif (236KB) |