Exploring molecular mechanisms of RNA-mediated gene regulation
Doudna Lab Structures
Ai5G Group II Intron | CRISPR systems | Dicer | HCV IRES | HDV Ribozyme | P4-P6 Ribozyme | SRP
Ai5G Group II Intron Structures
Zhang, L. and Doudna, J.A. Structural insights into group II intron catalysis and branch-site selection. Science 295, 2084-2088 (2002).
| Structure | Title | PDB ID |
|---|---|---|
| Ai5G Group II Self-Splicing Intron: Domains 5 and 6 | 1KXK |
CRISPR-related structures
Rachel E. Haurwitz, Samuel H. Sternberg and Jennifer A. Doudna. Csy4 relies on an unusual catalytic dyad to position and cleave CRISPR RNA. EMBO J. 31, 2824 (2012).
| Structure | Title | PDB ID |
|---|---|---|
| Crystal structure of the Csy4-crRNA product complex | 4AL5 | |
| Crystal structure of the S148ACsy4-crRNA complex | 4AL6 | |
| Crystal structure of the Csy4-minimal crRNA complex | 4AL7 |
Dipali G. Sashital, Blake Wiedenheft, and Jennifer A. Doudna. Mechanism of Foreign DNA Selection in a Bacterial Adaptive Immune System. Mol. Cell 46, 606 (2012).
| Structure | Title | PDB ID |
|---|---|---|
| Structure of Thermus thermophilus CasA (Cse1) | 4AN8 |
Wiedenheft B, Lander GC, Zhou K, Jore MM, Brouns SJ, van der Oost J, Doudna JA, Nogales E. Structures of the RNA-guided surveillance complex from a bacterial immune system. Nature. 477, 486 (2011).
| Structure | Title | EMDB ID |
|---|---|---|
 |
8.8 Å EM Reconstruction of E. coli Cascade complex | 5314 |
 |
9.2 Å EM Reconstruction of E. coli Cascade complex bound to complementary RNA target | 5315 |
Dipali G. Sashital, Martin Jinek, and Jennifer A. Doudna. An RNA-induced conformational change required for CRISPR RNA cleavage by the endoribonuclease Cse3. Nat. Struct. Mol. Biol. 18, 680 (2011).
| Structure | Title | PDB ID |
|---|---|---|
| Structure of CRISPR endoribonuclease Cse3 bound to 20 nt RNA | 2Y8W | |
| Structure A of CRISPR endoribonuclease Cse3 bound to 19 nt RNA | 2Y9H | |
| Structure B of CRISPR endoribonuclease Cse3 bound to 19 nt RNA | 2Y8Y |
Rachel E. Haurwitz, Martin Jinek, Blake Wiedenheft, Kaihong Zhou, and Jennifer A. Doudna. Sequence- and Structure-Specific RNA Processing by a CRISPR Endonuclease. Science 329, 1355 (2010).
| Structure | Title | PDB ID |
|---|---|---|
| Crystal Structure of the Csy4-crRNA Complex, Monoclinic Form | 2XLI | |
| Crystal Structure of the Csy4-crRNA Complex, Hexagonal Form | 2XLJ | |
| Crystal Structure of the Csy4-crRNA Complex, Orthorhombic Form | 2XLK |
Wiedenheft, B., Zhou, K., Jinek, M., Coyle, S.M., Ma, W. and Doudna, J.A. Structural basis for DNase activity of a conserved protein implicated in CRISPR-mediated genome defense. Structure 17, 904-12 (2009).
| Structure | Title | PDB ID |
|---|---|---|
| Structural basis for DNase activity of a conserved protein implicated in CRISPR-mediated antiviral defense | 3GOD |
Dicer Structures
MacRae, I.J., Zhou, K., Li, F., Repic, A., Brooks, A.N., Cande, W.Z., Adams, P.D., and Doudna, J.A. Structural basis for double-stranded RNA processing by Dicer. Science 311, 195-198 (2006).
| Structure | Title | PDB ID |
|---|---|---|
| Crystal Structure of Dicer from Giardia intestinalis | 2FFL |
Hepatitis C Virus IRES Structures
Siridechadilok, B., Fraser, C.S., Hall, R.J., Doudna, J.A. and Nogales, E. Structural roles for human translation factor eIF3 in initiation of protein synthesis. Science 310, 1513-1515 (2005).
| Structure | Title | EMDB ID |
|---|---|---|
 |
EM Reconstruction of Human eIF3 | 1170 |
 |
EM Reconstruction of Human eIF3 bound to the HCV IRES | 1171 |
Kieft, J.S., Zhou, K., Grech, A., Jubin. R. and Doudna, J.A. Crystal structure of an RNA tertiary domain essential to HCV IRES-mediated translation initiation. Nature Struct. Biol. 9, 370-374 (2002).
| Structure | Title | PDB ID |
|---|---|---|
| Crystal Structure of an RNA Tertiary Domain Essential to HCV IRES-mediated Translation Initiation. | 1KH6 |
Hepatitis Delta Virus Ribozyme Structures
Ke, A., Zhou, K., Ding, F., Cate, J.H.D. and Doudna, J.A. A conformational switch controls hepatitis delta virus ribozyme catalysis. Nature 429, 201-205 (2004).
| Structure | Title | PDB ID |
|---|---|---|
| HDV Ribozyme Precursor with Mg2+ Bound + U1A: RNA Binding Domain complex | 1SJ3 | |
| HDV Ribozyme Precursor: C75U Mutant in Cu2+ Solution + U1A: RNA Binding Domain complex | 1SJ4 | |
| HDV Ribozyme Precursor: C75U Mutant in Cobalt Hexammine Solution + U1A: RNA Binding Domain complex | 1SJF | |
| HDV Ribozyme Precursor: C75U Mutant in EDTA Solution + U1A: RNA Binding Domain complex | 1VBX | |
| HDV Ribozyme Precursor: C75U Mutant with Mn2+ Bound + U1A: RNA Binding Domain complex | 1VBY | |
| HDV Ribozyme Precursor: C75U Mutant in Ba2+ Solution + U1A: RNA Binding Domain complex | 1VBZ | |
| HDV Ribozyme Precursor: C75U Mutant in Imidazole and Sr2+ Solution + U1A: RNA Binding Domain complex | 1VC0 | |
| HDV Ribozyme Precursor in EDTA Solution + U1A: RNA Binding Domain complex | 1VC5 | |
| HDV Ribozyme Precursor: C75U Mutant Cleaved in Imidazole and Mg2+ Solution + U1A: RNA Binding Domain complex | 1VC6 | |
| HDV Ribozyme Precursor: C75U Mutant in Sr2+ Solution + U1A: RNA Binding Domain complex | 1VC7 |
Ferré-D'Amaré, A.R., Zhou, K. and Doudna J.A. Crystal structure of a hepatitis delta virus ribozyme. Nature 395, 567-574 (1998).
| Structure | Title | PDB ID |
|---|---|---|
| HDV Ribozyme + U1A: RNA Binding Domain complex | 1CX0 | |
| HDV Ribozyme + U1A: RNA Binding Domain complex | 1DRZ |
P4-P6 Ribozyme Structures
Battle, D.J. and Doudna, J.A. Specificity of RNA-RNA helix recognition. Proc. Natl. Acad. Sci. 99, 11676-11681 (2002).
| Structure | Title | PDB ID |
|---|---|---|
| P4-P6 RNA Ribozyme Domain: Mutant (C109G/G212C) | 1L8V |
Cate, J.H., Gooding, A., Podell, E., Zhou, K., Golden, B., Kundrot, C., Cech, T.R. and Doudna, J.A. Crystal structure of a group I ribozyme domain: Principles of RNA packing. Science 273, 1678-85 (1996).
| Structure | Title | PDB ID |
|---|---|---|
| P4-P6 RNA Ribozyme Domain | 1GID |
Signal Recognition Particle Structures
Ataide SF, Schmitz N, Shen K, Ke A, Shan SO, Doudna JA, Ban N. The crystal structure of the signal recognition particle in complex with its receptor. Science. 331, 881-886 (2011).
| Structure | Title | PDB ID |
|---|---|---|
| The Crystal Structure Of The Signal Recognition Particle (SRP) In Complex With Its Receptor (SR) | 2XXA |
Batey, R.T., Sagar, M.B. and Doudna, J.A. Structural and energetic analysis of nucleic acid recognition by a universally conserved protein from the signal recognition particle. J. Mol. Biol. 307, 229-246 (2001).
| Structure | Title | PDB ID |
|---|---|---|
| 4.5S RNA Domain IV Fragment + SRP Protein: C Terminal Domain complex, 1.52Å | 1HQ1 |
Batey, R.T., Rambo, R.P., Lucast, L., Rha, B. and Doudna, J.A. Crystal structure of the ribonucleoprotein core of the signal recognition particle. Science 287, 1232-1239 (2000).
| Structure | Title | PDB ID |
|---|---|---|
| 4.5S RNA Domain IV Fragment + SRP Protein: C Terminal Domain complex, 1.80Å | 1DUL |