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Solved Molecular Structures

Ai5G Intron | Dicer | HCV IRES | HDV Ribozyme | P4-P6 Ribozyme | SRP

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)

P4-P6 RNA Ribozyme Domain
(PDB entry) (PDB beta site entry)
1GID.pdb
(572KB)
1GID.cif
(784KB)


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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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