What is PDB is all about???
A Resource for Studying Biological MacromoleculesThe PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. These molecules are visualized, downloaded, and analyzed by users who range from students to specialized scientists. |
Examples of structures:
Human telomerase RNA(Htr A)
Telomerase isa unique ribonucleoprotein complex that catalyzes the addition of telomeric DNA repeatsonto the 3' ends of linear chromosomes. All vertebrate telomerase RNAs contain a catalytically essentialcore domain that includes the template and a pseudoknot with extended helical subdomains. Withinthese helical regions is an asymmetric 5-nt internal bulge loop (J2a/b) flanked by helices (P2a and P2b)that is highly conserved in its location but not sequence. NMR structure determination reveals thatJ2a/b forms a defined S-shape and creates an ?90 ° bend with a surprisingly low twist (?10 °) betweenthe flanking helices. A search of RNA structures revealed only one other example of a 5-nt bulge, fromhepatitis C virus internal ribosome entry site, with a different sequence but the same structure. J2a/b is intrinsically flexible but the interhelical motions across the loop are remarkably restricted. Nucleotidesubstitutions in J2a/b that affect the bend angle, direction, and interhelical dynamics are correlated with telomerase activity. Based on the structures of P2ab (J2a/b and flanking helices), the conserved region of the pseudoknot (P2b/P3, previously determined) and the remaining helical segment (P2a.1-J2a.1refined using residual dipolar couplings and the modeling program MC-Sym) we have calculated an NMR-based model of the full-length pseudoknot. The model and dynamics analysis show that J2a/b serves as a dominant structural and dynamical element in defining the overall topology of the core domain, andsuggest that interhelical motions in P2ab facilitate nucleotide addition along the template and templatetranslocation.
Lon protease (Lon A)
Lon is an oligomeric ATP-dependent protease that degrades defective or denatured proteins as well as some folded proteins for the control of cellular protein quality and metabolism. Lon fromThermococcus onnurineus NA1 was purified and crystallized at 295 K. A 2.0 Å resolution data set was collected using synchrotron radiation. The crystals belonged to space group P63, with unit-cell parameters a = 121.45, b = 121.45, c = 195.24 Å. Assuming the presence of two monomers in the asymmetric unit, the solvent content was estimated to be about 60.7%.
Plasmodium vivax geranylgeranylpyrophosphate synthase and IPP bound (CIpP)
Humans and other animals produce IPP and DMAPP via the mevalonic acid (MVA) pathway, which are used to make longer-chained pyrophosphates by enzymes such as farnesyl pyrophosphate synthase (FPPS) and geranylgeranylpyrophosphate synthase. Both of these human enzymes have been characterized and found to profuce strictly one product - respectively FPP and GGPP. The proteins encoded by the gene PF11_0295 and Pv092040 respectively in the Plasmodium falciparum and Plasmodium vivax genomes are sequentially homologous to both human FPPS and GGPPS, but slightly closer to FPPS. Our crystallographic structure of Pv092040 also shows a fold that more closely resembles hFPPS. Interestingly, our experiments show that these proteins from malaria parasites produce GGPPS in biochemical assays. Furthermore, this Plasmodium enzyme can be inhibited by nitrogen-containing bisphosphonates at mid-nanomolar concentrations, which is common of FPPS but not GGPPS from other orgnanisms.
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