images

Images of Biological Molecules

Structures of Proteins

Structures can be visualized through an interactive display by clicking on links that lead to the Protein Data Bank (PDB).

Enzymes

Carbonic anhydrase
one of the fastest enzymes with more than 25,000 reactions / second (1CAH)

carbonic anhydrase

Cellulase; breaks down cellulose, bacterial (1CEC)

HIV Protease; with tripeptide inhibitor (1A30)

Pyruvate Kinase; E.coli (1PKY)

Subtilisin; bacterial serine protease with bound inhibitor eglin (1CSE)

Trypsin; serine protease, digestive tract (1BRB; variant) with bovine pancreatic trypsin inhibitor BPTI (variant)

Amino acyl tRNA-synthetase; in complex with its tRNA (1GTR)

DNA Binding proteins

Nucleosome
histone core particle with bound DNA (1AOI)
1aoi nucleosome

Histone octamer complex without DNA bound (1HIO)

Reverse Transcriptase; from the human immune deficiency virus HIV (1REV)

TATA Box binding Protein; TATA Box Binding Protein with bound DNA (1YTB), and TFIID ( ) the TBP associated factor (1TAF)

Ligand binding proteins, structural proteins

Calmodulin, a calcium binding protein, X-ray at 1.8Å (1CLM)

1clm calmodulin

Brazzein; NMR structure (1BRZ), and an energy minimized structure derived from NMR (2BRZ)

Cytochrome c; from horse heart mitochondria, involved in electron binding using a heme group (1HRC)

Hemoglobin; involved in oxygen binding, deoxy or T-state (1HGA), HbS ( ), sickle cell (1HDS)

N-cadherin; immunoglobulin-like binding domain, end domain involved in dimerization between two cells (1NCH)

Myoglobin, from sperm whale, deoxy , without oxygen (1MBN), oxy, with oxygen (1MBO)

Membrane Proteins

Maltoporin
trimer, specific for oligosaccharides (1MAL)

1mal

Porins are trimeric outer membrane protein transporters with distinct beta-barrel pore structure in each subunit
   a) non-specific trimer (two functional units) OmpF (1OPF)
   b) Osmoporin trimer OmpC (2J1N)
   c) Phosphoporin monomer PhoE, functional unit is a trimer (1PHO);
   d) trimer, specific for oligosaccharides (1MAL) with bound sucrose (1AF6)

Beta-2 Adrenergic Receptor (GPCR) with antibody fragment (24R4); with lysozyme domain (2RH1)

Bacteriorhodopsin, by X-ray diffraction (1AP9) and electron diffraction (1AT9)

Ca-ATPase P-type from muscle sarcoplasmic reticulum membrane (1EUL)

Gap Junction ProteinBeta2 hexamer, connexin 26 hemi-channel or connexon (2ZW)

K-channel Kcsa bacterial potassium selective channel, closed pore, explained K over Na selectivity (1BL8)

Light harvesting complex II surround reaction center feeding photon energy to chlorophyll (1KZU)

Reaction center bacterial photosynthetic reaction center (1PRC)

Rhodopsin, bovine a photosensitive GPCR in the rod cells of the eye at 2.80 Å resolution (1F88)

Channel-forming Peptides
Gramicidin A forms head-to-head beta-helix dimer with single pore (1MAG)
Melittin dimer shown; forms helical multimeric barrel (1MLT);
Molecular dynamics simulation and Channel recording in artificial membrane
(you need QuickTime3 to view movie)

A complete list of known structures of membrane proteins at the Stephen White laboratory at UC Irvine

Structures of Nucleic Acids

DNA oligonucleotide a synthetic oligonucleotide with 11 base pairs (114D)

114d DNA

A-RNA double stranded RNA as found in stem and loop structures of folded RNA enzymes (1SDR)

Transfer RNA yestPhe-tRNA (1TN2) and an anticodon loop ( ) (229D)

Ribosome bacterial ribosome particle, small subunit with bound tRNAs (2WDK)

Polysaccharides, and Lipids
Polysaccharides Hyaluronic acid Disaccharides (KEGG) Polysaccharides (KEGG)	Lipids Plasma Membrane POPC - Palmitoyl-oleoyl-phosphatidyl-choline (view list of phospholipids at KEGG) DHPC - Diheptanoyl-phosphatidyl-choline (detergent cmc 1.4mM; after opening file select 3D rendering) Cholesterol 11-cis-retinal

Links to databases with access to structures of biological molecules

PDB	Protein Data Bank	Tools and resources for studying the structures of biological macromolecules
NCBI	National Center for Biotechnology Information	Resource for molecular biology information, sequences, structures and whole genome maps
KEGG	Kyoto Encyclopedia of Genes and Genomes	Metabolic pathway maps and molecular catalogue
RNA Database	RNA modification database	Post-transcriptionally modified nucleosides from RNA
Gene Cards	Human Gene Compendium	Genes associated with diseases

Please send any questions or comments regarding this class to Lukas Buehler