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Solved Molecular Structures
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)
Crystal Structure of Dicer from Giardia intestinalis
(PDB entry)
(PDB beta site entry) |
2FFL.pdb
(1.9MB) |
2FFL.cif
(2.5MB) |
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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)
(Figure and QuickTime Movies)
| 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) |
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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) |
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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)
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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) |
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