PDB: 5653 resultsInfo pagesStatus searchChemie searchBIRD

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6UU4	E. coli sigma-S transcription initiation complex with a 3-nt RNA ("old" crystal soaked with GTP and dinucleotide GpA for 30 minutes) Descriptor: DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase subunit beta', ... Authors: Zuo, Y, De, S, Steitz, T.A. Deposit date: 2019-10-30 Release date: 2020-08-26 Last modified: 2023-10-11 Method: X-RAY DIFFRACTION (4.305 Å) Cite: Structural Insights into Transcription Initiation from De Novo RNA Synthesis to Transitioning into Elongation. Iscience, 23, 2020
6UU7	E. coli sigma-S transcription initiation complex with a 6-nt RNA and an NTP ("Old" crystal soaked with UTP, CTP, ddGTP, and dinucleotide ApG for 30 minutes) Descriptor: 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE, DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, ... Authors: Zuo, Y, De, S, Steitz, T.A. Deposit date: 2019-10-30 Release date: 2020-08-26 Last modified: 2023-10-11 Method: X-RAY DIFFRACTION (4.4 Å) Cite: Structural Insights into Transcription Initiation from De Novo RNA Synthesis to Transitioning into Elongation. Iscience, 23, 2020
6UUC	E. coli sigma-S transcription initiation complex with a 3-nt RNA and a mismatching ATP ("Fresh" crystal soaked with ATP for 2 hours) Descriptor: ADENOSINE-5'-TRIPHOSPHATE, DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, ... Authors: Zuo, Y, De, S, Steitz, T.A. Deposit date: 2019-10-30 Release date: 2020-08-26 Last modified: 2023-10-11 Method: X-RAY DIFFRACTION (4.096 Å) Cite: Structural Insights into Transcription Initiation from De Novo RNA Synthesis to Transitioning into Elongation. Iscience, 23, 2020
6UU5	E. coli sigma-S transcription initiation complex with a 6-nt RNA ("Old" crystal soaked with GTP, UTP, CTP, and dinucleotide GpA for 30 minutes) Descriptor: DIPHOSPHATE, DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, ... Authors: Zuo, Y, De, S, Steitz, T.A. Deposit date: 2019-10-30 Release date: 2020-08-26 Last modified: 2023-10-11 Method: X-RAY DIFFRACTION (5.403 Å) Cite: Structural Insights into Transcription Initiation from De Novo RNA Synthesis to Transitioning into Elongation. Iscience, 23, 2020
8AP1	Cryo-EM structure of yeast mitochondrial RNA polymerase transcription initiation complex with two GTP molecules poised for de novo initiation (IC2) Descriptor: DNA-directed RNA polymerase, mitochondrial, GUANOSINE-5'-TRIPHOSPHATE, ... Authors: Goovaerts, Q, Shen, J, Patel, S.S, Das, K. Deposit date: 2022-08-09 Release date: 2023-08-23 Last modified: 2023-11-01 Method: ELECTRON MICROSCOPY (3.47 Å) Cite: Structures illustrate step-by-step mitochondrial transcription initiation. Nature, 622, 2023
6KOS	Crystal structure of SUWA (Super WA20), a hyper-stable de novo protein with a dimeric bisecting topology Descriptor: SUWA (Super WA20) Authors: Kimura, N, Arai, R. Deposit date: 2019-08-13 Release date: 2020-01-29 Last modified: 2023-11-22 Method: X-RAY DIFFRACTION (2 Å) Cite: HyperstableDe NovoProtein with a Dimeric Bisecting Topology. Acs Synth Biol, 9, 2020
6EGM	Crystal Structure of a de novo Three-stranded Coiled Coil Peptide Containing D-Leu in a d-site Position of a Tris-thiolate Binding Site Descriptor: Apo-(GRAND CoilSerL16CL19(DLE))3, ZINC ION Authors: Ruckthong, L, Stuckey, J.A, Pecoraro, V.L. Deposit date: 2018-08-20 Release date: 2019-04-03 Last modified: 2019-12-18 Method: X-RAY DIFFRACTION (1.84 Å) Cite: How Outer Coordination Sphere Modifications Can Impact Metal Structures in Proteins: A Crystallographic Evaluation. Chemistry, 25, 2019
7N1J	Crystal structure of FGFR4 domain 3 in complex with a de novo-designed mini-binder Descriptor: Binder, Fibroblast growth factor receptor 4 Authors: Park, J.S, Lee, S. Deposit date: 2021-05-27 Release date: 2022-04-06 Last modified: 2023-10-18 Method: X-RAY DIFFRACTION (2.99 Å) Cite: Design of protein-binding proteins from the target structure alone. Nature, 605, 2022
6GFW	Cryo-EM structure of bacterial RNA polymerase-sigma54 holoenzyme initial transcribing complex Descriptor: DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase subunit beta', ... Authors: Glyde, R, Ye, F.Z, Zhang, X.D. Deposit date: 2018-05-02 Release date: 2018-07-04 Last modified: 2024-05-15 Method: ELECTRON MICROSCOPY (3.7 Å) Cite: Structures of Bacterial RNA Polymerase Complexes Reveal the Mechanism of DNA Loading and Transcription Initiation. Mol. Cell, 70, 2018
1HQJ	CRYSTAL STRUCTURE OF A DE NOVO DESIGNED TRIMERIC COILED-COIL PEPTIDE Descriptor: LEAD (II) ION, SULFATE ION, ZJU-GLU-LEU-GLU-ALA-ARG-ILE-ARG-GLU-LEU-GLU-ALA-ARG-ILE-LYS-NH2 Authors: Burkhard, P, Meier, M, Lustig, A. Deposit date: 2000-12-18 Release date: 2001-03-14 Last modified: 2024-04-24 Method: X-RAY DIFFRACTION (1.2 Å) Cite: Design of a minimal protein oligomerization domain by a structural approach. Protein Sci., 9, 2000
6TMS	Crystal structure of a de novo designed hexameric helical-bundle protein Descriptor: SULFATE ION, a novel designed pore protein, affinity purification tag Authors: Xu, C, Pei, X.Y, Luisi, B.F, Baker, D. Deposit date: 2019-12-05 Release date: 2020-04-29 Last modified: 2024-05-01 Method: X-RAY DIFFRACTION (2.7 Å) Cite: Computational design of transmembrane pores. Nature, 585, 2020
4GVW	Three-dimensional structure of the de novo designed serine hydrolase 2bfq_3, Northeast Structural Genomics Consortium (NESG) Target OR248 Descriptor: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, ACETIC ACID, De novo designed serine hydrolase, ... Authors: Kuzin, A, Lew, S, Seetharaman, J, Rajagopalan, S, Everett, J.K, Acton, T.B, Montelione, G.T, Tong, L, Hunt, J.F, Northeast Structural Genomics Consortium (NESG) Deposit date: 2012-08-31 Release date: 2012-09-12 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (2.113 Å) Cite: Northeast Structural Genomics Consortium Target OR248 To be Published
8QNJ	Folded alpha helical de novo proteins from Apilactobacillus kunkeei Descriptor: Lenovo Protein Authors: Celestine, C. Deposit date: 2023-09-26 Release date: 2024-02-21 Last modified: 2024-05-08 Method: SOLUTION NMR Cite: Folded Alpha Helical Putative New Proteins from Apilactobacillus kunkeei. J.Mol.Biol., 436, 2024
4QBQ	Crystal structure of DNMT3a ADD domain bound to H3 peptide Descriptor: DNA (cytosine-5)-methyltransferase 3A, Histone H3, ZINC ION Authors: Li, H, Patel, D.J. Deposit date: 2014-05-08 Release date: 2015-05-13 Method: X-RAY DIFFRACTION (2.406 Å) Cite: Engineering of a histone-recognition domain in a de novo DNA methyltransferase alters the epigenetic landscape of ESCs To be Published
4QBS	Crystal structure of DNMT3a ADD domain E545R mutant bound to H3T3ph peptide Descriptor: DNA (cytosine-5)-methyltransferase 3A, Histone H3, SULFATE ION, ... Authors: Wang, H, Li, H. Deposit date: 2014-05-08 Release date: 2015-05-13 Method: X-RAY DIFFRACTION (1.8 Å) Cite: Engineering of a histone-recognition domain in a de novo DNA methyltransferase alters the epigenetic landscape of ESCs To be Published
4QBR	Crystal structure of DNMT3a ADD domain G550D mutant bound to H3 peptide Descriptor: DNA (cytosine-5)-methyltransferase 3A, Histone H3, ZINC ION Authors: Wang, H, Li, H. Deposit date: 2014-05-08 Release date: 2015-05-13 Last modified: 2024-03-20 Method: X-RAY DIFFRACTION (1.902 Å) Cite: Engineering of a histone-recognition domain in a de novo DNA methyltransferase alters the epigenetic landscape of ESCs To be Published
7BG1	Structure of anti-FLAG M2 Fab domain remodeled based on proteomic sequencing Descriptor: CHLORIDE ION, SULFATE ION, anti-FLAG M2 heavy chain, ... Authors: Pronker, M.F, Snijder, J. Deposit date: 2021-01-05 Release date: 2021-07-21 Last modified: 2024-01-31 Method: X-RAY DIFFRACTION (1.86 Å) Cite: Mass Spectrometry-Based De Novo Sequencing of Monoclonal Antibodies Using Multiple Proteases and a Dual Fragmentation Scheme. J.Proteome Res., 20, 2021
3Q7W	Crystal structure of Symfoil-4P/PV1: de novo designed beta-trefoil architecture with symmetric primary structure, primitive version 1 Descriptor: SULFATE ION, de novo designed beta-trefoil architecture with symmetric primary structure Authors: Blaber, M, Lee, J. Deposit date: 2011-01-05 Release date: 2012-01-11 Last modified: 2024-02-21 Method: X-RAY DIFFRACTION (1.5 Å) Cite: Simplified protein design biased for prebiotic amino acids yields a foldable, halophilic protein. Proc.Natl.Acad.Sci.USA, 110, 2013
3O4C	Crystal structure of Symfoil-4V: de novo designed beta-trefoil architecture with symmetric primary structure Descriptor: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, CHLORIDE ION, SULFATE ION, ... Authors: Lee, J, Blaber, M. Deposit date: 2010-07-26 Release date: 2010-12-22 Last modified: 2024-02-21 Method: X-RAY DIFFRACTION (1.75 Å) Cite: Experimental support for the evolution of symmetric protein architecture from a simple peptide motif. Proc.Natl.Acad.Sci.USA, 108, 2011
3O4B	Crystal structure of Symfoil-4T: de novo designed beta-trefoil architecture with symmetric primary structure Descriptor: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, CHLORIDE ION, SULFATE ION, ... Authors: Lee, J, Blaber, M. Deposit date: 2010-07-26 Release date: 2010-12-22 Last modified: 2024-02-21 Method: X-RAY DIFFRACTION (1.8 Å) Cite: Experimental support for the evolution of symmetric protein architecture from a simple peptide motif. Proc.Natl.Acad.Sci.USA, 108, 2011
3O4A	Crystal structure of Symfoil-2: de novo designed beta-trefoil architecture with symmetric primary structure Descriptor: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, SULFATE ION, de novo designed beta-trefoil architecture with symmetric primary structure Authors: Lee, J, Blaber, M. Deposit date: 2010-07-26 Release date: 2010-12-22 Last modified: 2024-02-21 Method: X-RAY DIFFRACTION (1.45 Å) Cite: Experimental support for the evolution of symmetric protein architecture from a simple peptide motif. Proc.Natl.Acad.Sci.USA, 108, 2011
3O49	Crystal structure of Symfoil-1: de novo designed beta-trefoil architecture with symmetric primary structure Descriptor: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, SULFATE ION, de novo designed beta-trefoil architecture with symmetric primary structure Authors: Lee, J, Blaber, M. Deposit date: 2010-07-26 Release date: 2010-12-22 Last modified: 2024-02-21 Method: X-RAY DIFFRACTION (1.45 Å) Cite: Experimental support for the evolution of symmetric protein architecture from a simple peptide motif. Proc.Natl.Acad.Sci.USA, 108, 2011
3OL0	Crystal structure of Monofoil-4P homo-trimer: de novo designed monomer trefoil-fold sub-domain which forms homo-trimer assembly Descriptor: SULFATE ION, de novo designed monomer trefoil-fold sub-domain which forms homo-trimer assembly Authors: Lee, J, Blaber, M. Deposit date: 2010-08-25 Release date: 2010-12-22 Last modified: 2024-02-21 Method: X-RAY DIFFRACTION (1.483 Å) Cite: Experimental support for the evolution of symmetric protein architecture from a simple peptide motif. Proc.Natl.Acad.Sci.USA, 108, 2011
3OGF	Crystal structure of Difoil-4P homo-trimer: de novo designed dimeric trefoil-fold sub-domain which forms homo-trimer assembly Descriptor: SULFATE ION, de novo designed dimeric trefoil-fold sub-domain which forms homo-trimer assembly Authors: Lee, J, Blaber, M. Deposit date: 2010-08-16 Release date: 2010-12-22 Last modified: 2024-02-21 Method: X-RAY DIFFRACTION (2.864 Å) Cite: Experimental support for the evolution of symmetric protein architecture from a simple peptide motif. Proc.Natl.Acad.Sci.USA, 108, 2011
3O4D	Crystal structure of Symfoil-4P: de novo designed beta-trefoil architecture with symmetric primary structure Descriptor: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, CHLORIDE ION, SULFATE ION, ... Authors: Lee, J, Blaber, M. Deposit date: 2010-07-26 Release date: 2010-12-22 Last modified: 2024-02-21 Method: X-RAY DIFFRACTION (1.65 Å) Cite: Experimental support for the evolution of symmetric protein architecture from a simple peptide motif. Proc.Natl.Acad.Sci.USA, 108, 2011

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