3CR1
 
 | | crystal structure of a minimal, mutant, all-RNA hairpin ribozyme (A38C, A-1OMA) grown from MgCl2 | | Descriptor: | MAGNESIUM ION, RNA (5'-R(*UP*CP*CP*CP*(A2M)P*GP*UP*CP*CP*AP*CP*CP*G)-3'), RNA (5'-R(*UP*CP*GP*UP*GP*GP*UP*CP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3'), ... | | Authors: | Salter, J.D, Wedekind, J.E. | | Deposit date: | 2008-04-04 | | Release date: | 2008-08-26 | | Last modified: | 2023-08-30 | | Method: | X-RAY DIFFRACTION (2.25 Å) | | Cite: | Structural effects of nucleobase variations at key active site residue Ade38 in the hairpin ribozyme.
Rna, 14, 2008
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6VUH
 | | APO PreQ1 riboswitch aptamer grown in Mn2+ | | Descriptor: | MANGANESE (II) ION, PREQ1 RIBOSWITCH | | Authors: | Jenkins, J.L, Wedekind, J.E. | | Deposit date: | 2020-02-15 | | Release date: | 2020-06-24 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (1.999 Å) | | Cite: | Analysis of a preQ1-I riboswitch in effector-free and bound states reveals a metabolite-programmed nucleobase-stacking spine that controls gene regulation.
Nucleic Acids Res., 48, 2020
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6VUI
 | | Metabolite-bound PreQ1 riboswitch with Mn2+ | | Descriptor: | 7-DEAZA-7-AMINOMETHYL-GUANINE, MANGANESE (II) ION, PREQ1 RIBOSWITCH | | Authors: | Jenkins, J.L, Wedekind, J.E. | | Deposit date: | 2020-02-15 | | Release date: | 2020-06-24 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (2.681 Å) | | Cite: | Analysis of a preQ1-I riboswitch in effector-free and bound states reveals a metabolite-programmed nucleobase-stacking spine that controls gene regulation.
Nucleic Acids Res., 48, 2020
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4G6P
 | | Minimal Hairpin Ribozyme in the Precatalytic State with A38P Variation | | Descriptor: | COBALT HEXAMMINE(III), Loop A Substrate strand, Loop A and Loop B Ribozyme strand, ... | | Authors: | Liberman, J.A, Jenkins, J.L, Krucinska, J, Wedekind, J.E. | | Deposit date: | 2012-07-19 | | Release date: | 2012-08-15 | | Last modified: | 2024-02-28 | | Method: | X-RAY DIFFRACTION (2.641 Å) | | Cite: | A Transition-State Interaction Shifts Nucleobase Ionization toward Neutrality To Facilitate Small Ribozyme Catalysis.
J.Am.Chem.Soc., 134, 2012
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4G6S
 | | Minimal Hairpin Ribozyme in the Transition State with A38P Variation | | Descriptor: | COBALT HEXAMMINE(III), Loop A Substrate strand, Loop A and Loop B Ribozyme strand, ... | | Authors: | Liberman, J.A, Jenkins, J.L, Krucinska, J, Wedekind, J.E. | | Deposit date: | 2012-07-19 | | Release date: | 2012-08-08 | | Last modified: | 2024-02-28 | | Method: | X-RAY DIFFRACTION (2.84 Å) | | Cite: | A Transition-State Interaction Shifts Nucleobase Ionization toward Neutrality To Facilitate Small Ribozyme Catalysis.
J.Am.Chem.Soc., 134, 2012
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4FXW
 | | Structure of phosphorylated SF1 complex with U2AF65-UHM domain | | Descriptor: | SULFATE ION, Splicing factor 1, Splicing factor U2AF 65 kDa subunit | | Authors: | Wang, W, Bauer, W.J, Wedekind, J.E, Kielkopf, C.L. | | Deposit date: | 2012-07-03 | | Release date: | 2013-01-16 | | Last modified: | 2017-11-15 | | Method: | X-RAY DIFFRACTION (2.29 Å) | | Cite: | Structure of Phosphorylated SF1 Bound to U2AF(65) in an Essential Splicing Factor Complex.
Structure, 21, 2013
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4G6R
 | | Minimal Hairpin Ribozyme in the Transition State with G8I Variation | | Descriptor: | Loop A Ribozyme strand, Loop A Substrate strand, Loop B Ribozyme Strand, ... | | Authors: | Liberman, J.A, Jenkins, J.L, Krucinska, J, Wedekind, J.E. | | Deposit date: | 2012-07-19 | | Release date: | 2012-08-15 | | Last modified: | 2024-02-28 | | Method: | X-RAY DIFFRACTION (2.832 Å) | | Cite: | A Transition-State Interaction Shifts Nucleobase Ionization toward Neutrality To Facilitate Small Ribozyme Catalysis.
J.Am.Chem.Soc., 134, 2012
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4JF2
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3Q50
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1R5T
 | | The Crystal Structure of Cytidine Deaminase CDD1, an Orphan C to U editase from Yeast | | Descriptor: | Cytidine deaminase, ZINC ION | | Authors: | Xie, K, Sowden, M.P, Dance, G.S.C, Torelli, A.T, Smith, H.C, Wedekind, J.E. | | Deposit date: | 2003-10-13 | | Release date: | 2004-05-25 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | The structure of a yeast RNA-editing deaminase provides insight into the fold and function of activation-induced deaminase and APOBEC-1.
Proc.Natl.Acad.Sci.Usa, 101, 2004
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2P7F
 | | The Novel Use of a 2',5'-Phosphodiester Linkage as a Reaction Intermediate at the Active Site of a Small Ribozyme | | Descriptor: | COBALT HEXAMMINE(III), Loop A ribozyme strand, Loop B S-turn strand, ... | | Authors: | Torelli, A.T, Krucinska, J, Wedekind, J.E. | | Deposit date: | 2007-03-20 | | Release date: | 2007-05-22 | | Last modified: | 2023-08-30 | | Method: | X-RAY DIFFRACTION (2.35 Å) | | Cite: | A comparison of vanadate to a 2'-5' linkage at the active site of a small ribozyme suggests a role for water in transition-state stabilization
Rna, 13, 2007
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2P7E
 | | Vanadate at the Active Site of a Small Ribozyme Suggests a Role for Water in Transition-State Stabilization | | Descriptor: | 3' substrate strand, octameric fragment, 5' substrate strand, ... | | Authors: | Torelli, A.T, Krucinska, J, Wedekind, J.E. | | Deposit date: | 2007-03-20 | | Release date: | 2007-05-22 | | Last modified: | 2023-08-30 | | Method: | X-RAY DIFFRACTION (2.05 Å) | | Cite: | A comparison of vanadate to a 2'-5' linkage at the active site of a small ribozyme suggests a role for water in transition-state stabilization
Rna, 13, 2007
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2P7D
 | | A Minimal, 'Hinged' Hairpin Ribozyme Construct Solved with Mimics of the Product Strands at 2.25 Angstroms Resolution | | Descriptor: | 3' substrate strand, octameric fragment, 5' substrate strand, ... | | Authors: | Torelli, A.T, Krucinska, J, Wedekind, J.E. | | Deposit date: | 2007-03-20 | | Release date: | 2007-05-22 | | Last modified: | 2023-08-30 | | Method: | X-RAY DIFFRACTION (2.25 Å) | | Cite: | A comparison of vanadate to a 2'-5' linkage at the active site of a small ribozyme suggests a role for water in transition-state stabilization
Rna, 13, 2007
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6CMN
 | | Co-Crystal Structure of HIV-1 TAR Bound to Lab-Evolved RRM TBP6.7 | | Descriptor: | TAR-Binding Protein 6.7, Trans-Activation Response RNA Element | | Authors: | Belashov, I.A, Wedekind, J.E. | | Deposit date: | 2018-03-05 | | Release date: | 2018-06-06 | | Last modified: | 2023-10-04 | | Method: | X-RAY DIFFRACTION (1.796 Å) | | Cite: | Structure of HIV TAR in complex with a Lab-Evolved RRM provides insight into duplex RNA recognition and synthesis of a constrained peptide that impairs transcription.
Nucleic Acids Res., 46, 2018
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7REX
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1U7H
 | | Structure and a Proposed Mechanism for Ornithine Cyclodeaminase from Pseudomonas putida | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, SODIUM ION, ... | | Authors: | Alam, S, Goodman, J.L, Wang, S, Ruzicka, F.J, Frey, P.A, Wedekind, J.E. | | Deposit date: | 2004-08-03 | | Release date: | 2004-11-09 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Ornithine Cyclodeaminase: Structure, Mechanism of Action, and Implications for
the u-Crystallin Family;
Biochemistry, 43, 2004
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1T2Q
 | | The Crystal Structure of an NNA7 Fab that recognizes an N-type blood group antigen | | Descriptor: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, Fab NNA7 Heavy Chain, Fab NNA7 Light Chain, ... | | Authors: | Xie, K, Song, S.C, Spitalnik, S.L, Wedekind, J.E. | | Deposit date: | 2004-04-22 | | Release date: | 2005-06-07 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (1.83 Å) | | Cite: | Crystal Structure and Mutational Analysis of an Antibody that Recognizes an N-type Blood Group Antigen
To be Published
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2D03
 | | Crystal structure of the G91S mutant of the NNA7 Fab | | Descriptor: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, DI(HYDROXYETHYL)ETHER, GLYCEROL, ... | | Authors: | Xie, K, Song, S.C, Spitalnik, S.L, Wedekind, J.E. | | Deposit date: | 2005-07-23 | | Release date: | 2006-01-24 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.97 Å) | | Cite: | Crystallographic analysis of the NNA7 Fab and proposal for the mode of human blood-group recognition.
Acta Crystallogr.,Sect.D, 61, 2005
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2D2L
 | | Crystal Structure of a minimal, all-RNA hairpin ribozyme with a propyl linker (C3) at position U39 | | Descriptor: | 5'-R(*CP*GP*GP*UP*GP*AP*GP*AP*AP*GP*GP*G)-3', 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3', 5'-R(*UP*CP*CP*CP*(A2M)P*GP*UP*CP*CP*AP*CP*CP*G)-3', ... | | Authors: | Alam, S, Grum-Tokars, V, Krucinska, J, Kundracik, M.L, Wedekind, J.E. | | Deposit date: | 2005-09-11 | | Release date: | 2005-11-01 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Conformational heterogeneity at position U37 of an all-RNA hairpin ribozyme with implications for metal binding and the catalytic structure of the S-turn
Biochemistry, 44, 2005
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2BCY
 | | Crystal Structure of a minimal, mutant all-RNA hairpin ribozyme (U39C, G8MTU) | | Descriptor: | 5'-R(*CP*GP*GP*UP*GP*AP*(MTU)P*AP*AP*GP*GP*G)-3', 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3', 5'-R(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*G)-3', ... | | Authors: | Salter, J.D, Wedekind, J.E. | | Deposit date: | 2005-10-19 | | Release date: | 2006-02-14 | | Last modified: | 2023-08-23 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Water in the Active Site of an All-RNA Hairpin Ribozyme and Effects of Gua8 Base Variants on the Geometry of Phosphoryl Transfer.
Biochemistry, 45, 2006
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2BCZ
 | | Crystal Structure of a minimal, mutant all-RNA hairpin ribozyme (U39C, G8I, 2'deoxy A-1) | | Descriptor: | 5'-R(*CP*GP*GP*UP*GP*AP*IP*AP*AP*GP*GP*G)-3', 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3', 5'-R(*UP*CP*CP*CP*(DA)P*GP*UP*CP*CP*AP*CP*CP*G)-3'), ... | | Authors: | Salter, J.D, Wedekind, J.E. | | Deposit date: | 2005-10-19 | | Release date: | 2006-02-14 | | Last modified: | 2023-08-23 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Water in the Active Site of an All-RNA Hairpin Ribozyme and Effects of Gua8 Base Variants on the Geometry of Phosphoryl Transfer.
Biochemistry, 45, 2006
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2D2K
 | | Crystal Structure of a minimal, native (U39) all-RNA hairpin ribozyme | | Descriptor: | 5'-R(*CP*GP*GP*UP*GP*AP*GP*AP*AP*GP*GP*G)-3', 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3', 5'-R(*UP*CP*CP*CP*(A2M)P*GP*UP*CP*CP*AP*CP*CP*G)-3', ... | | Authors: | Alam, S, Grum-Tokars, V, Krucinska, J, Kundracik, M.L, Wedekind, J.E. | | Deposit date: | 2005-09-11 | | Release date: | 2005-11-01 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.65 Å) | | Cite: | Conformational heterogeneity at position U37 of an all-RNA hairpin ribozyme with implications for metal binding and the catalytic structure of the S-turn
Biochemistry, 44, 2005
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1ONE
 | | YEAST ENOLASE COMPLEXED WITH AN EQUILIBRIUM MIXTURE OF 2'-PHOSPHOGLYCEATE AND PHOSPHOENOLPYRUVATE | | Descriptor: | 2-PHOSPHOGLYCERIC ACID, ENOLASE, MAGNESIUM ION, ... | | Authors: | Larsen, T.M, Wedekind, J.E, Rayment, I, Reed, G.H. | | Deposit date: | 1995-12-05 | | Release date: | 1997-01-11 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | A carboxylate oxygen of the substrate bridges the magnesium ions at the active site of enolase: structure of the yeast enzyme complexed with the equilibrium mixture of 2-phosphoglycerate and phosphoenolpyruvate at 1.8 A resolution.
Biochemistry, 35, 1996
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1X9C
 | | An all-RNA Hairpin Ribozyme with mutation U39C | | Descriptor: | 5'-R(*CP*GP*GP*UP*GP*AP*GP*AP*AP*GP*GP*G)-3', 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3', 5'-R(*UP*CP*CP*CP*(A2M)P*GP*UP*CP*CP*AP*CP*CP*G)-3', ... | | Authors: | Alam, S, Grum-Tokars, V, Krucinska, J, Kundracik, M.L, Wedekind, J.E. | | Deposit date: | 2004-08-20 | | Release date: | 2005-11-22 | | Last modified: | 2023-08-23 | | Method: | X-RAY DIFFRACTION (2.19 Å) | | Cite: | Conformational Heterogeneity at Position U37 of an All-RNA Hairpin Ribozyme with Implications for Metal Binding and the Catalytic Structure of the S-Turn.
Biochemistry, 44, 2005
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1X9K
 | | An all-RNA Hairpin Ribozyme with mutation U39C | | Descriptor: | 5'-R(*AP*AP*UP*AP*GP*AP*GP*AP*AP*GP*CP*GP*A)-3', 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3', 5'-R(*UP*CP*GP*CP*AP*GP*UP*CP*CP*UP*AP*UP*U)-3', ... | | Authors: | Alam, S, Grum-Tokars, V, Krucinska, J, Kundracik, M.L, Wedekind, J.E. | | Deposit date: | 2004-08-21 | | Release date: | 2005-11-22 | | Last modified: | 2023-08-23 | | Method: | X-RAY DIFFRACTION (3.17 Å) | | Cite: | Conformational Heterogeneity at Position U37 of an All-RNA Hairpin Ribozyme with Implications for Metal Binding and the Catalytic Structure of the S-Turn.
Biochemistry, 44, 2005
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