The Doudna Lab

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).

StructureTitlePDB 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).

StructureTitlePDB 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).

StructureTitlePDB 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).

StructureTitleEMDB 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).

StructureTitlePDB 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).

StructureTitlePDB 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).

StructureTitlePDB 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).

StructureTitlePDB 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).

StructureTitleEMDB 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).

StructureTitlePDB 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).

StructureTitlePDB 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).

StructureTitlePDB 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).

StructureTitlePDB 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).

StructureTitlePDB 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).

StructureTitlePDB 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).

StructureTitlePDB 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).

StructureTitlePDB ID
4.5S RNA Domain IV Fragment + SRP Protein: C Terminal Domain complex, 1.80Å 1DUL