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Biomolecular Structural Biology

methods for determining atomic structures

Scientists use a variety of experimental methods to discover the inner workings of biological molecules. These include X-ray crystallography, NMR spectroscopy, and electron microscopy. Each method has specific advantages for the exploration of biological molecules.

Molecule of the Month Articles (12)

Adenine Riboswitch in Action

Fifty Years of Open Access to PDB Structures

Lysozyme

Myoglobin

	Adenine Riboswitch in Action XFEL serial crystallography reveals what happens when adenine binds to a riboswitch
	Fifty Years of Open Access to PDB Structures The Protein Data Bank is celebrating its golden anniversary!
	Lysozyme Lysozyme attacks the cell walls of bacteria
	Myoglobin Myoglobin was the first protein to have its atomic structure determined, revealing how it stores oxygen in muscle cells.
	Nanodiscs and HDL Nanodiscs conveniently package a small piece of membrane for experimental studies.
	PDB Pioneers A dozen historic structures set the foundation for the PDB archive
	Pepsin Pepsin digests proteins in strong stomach acid
	Photoactive Yellow Protein Researchers use synchrotrons and X-ray lasers to reveal the rapid processes of light sensing.
	Ribonuclease A Ribonuclease cuts and controls RNA
	Selenocysteine Synthase Selenium is used in place of sulfur to build proteins for special tasks
	Trypsin An activated serine amino acid in trypsin cleaves protein chains
	Twenty Years of Molecules Celebrating the structural biology revolution

Learning Resources (14)

Quasisymmetry in Icosahedral Viruses

(Activity Page)

Expanding Boundaries of Complexity with 3DEM

(Flyer)

200 Icosahedral Viruses

(Poster)

Photoactive Yellow Protein and XFEL/SFX

(GIF)

	Quasisymmetry in Icosahedral Viruses Activity Page Build 3D paper models of several viruses to explore how quasisymmetry builds capsids with different sizes.
	Expanding Boundaries of Complexity with 3DEM Flyer 3D electron microscopy (3DEM) is revolutionizing the field of structural biology.
	200 Icosahedral Viruses Poster
	Photoactive Yellow Protein and XFEL/SFX GIF Structures of photoactive yellow protein were determined by serial femtosecond crystallography after illumination, capturing the isomerization of the chromophore after it absorbs light. Structures included in this movie include: 5hd3 (ground state), 5hdc (100-400 femtoseconds after illumination), 5hdd (800-1200 femtoseconds), 5hds (3 picoseconds), 4b9o (100 picoseconds), 5hd5 (200 nanoseconds) and 1ts0 (1 millisecond). For more, see the Molecule of the Month on Photoactive Yellow Protein and Guide to Understanding PDB Data: Methods for Determining Atomic Structures
	Celebrating 50 Years of the Protein Data Bank Archive Video In 1971, the structural biology community established the single worldwide archive for macromolecular structure data–the Protein Data Bank (PDB). From its inception, the PDB has embraced a culture of open access, leading to its widespread use by the research community. PDB data are used by hundreds of data resources and millions of users exploring fundamental biology, energy, and biomedicine. This video looks at the history and the milestones that shaped the PDB into the leading resource for research and education it is today.
	Discovering Biology Through Crystallography Coloring Book Color the diverse 3D shapes studied by crystallographers. Created with support from the ACA. Available as a PDF and individual images.
	Biological Assemblies Guide
	Methods for Determining Structure Guide
	Computed Structure Models Guide New machine-learning methods for predicting protein structures build on and complement the PDB archive of experimentally-determined structures.
	Resolution Guide
	R-value and R-free Guide
	Structure Factors and Electron Density Guide
	Molecular Backgrounds For Virtual Meetings Other Resources Download images created by David Goodsell to add a molecular backdrop to your next virtual meeting. Click on the image to expand.
	PDB50 the Game Other Resource A PDB “worker placement” board game that explores the process of structure discovery

Curriculum Resources (11)

Exploring a Protein Structure in the RCSB PDB: Antibodies Advanced

Exploring a Protein Structure in the RSCB PDB: Insulin Introductory

Exploring a Protein Structure in the RCSB PDB: T-Cell Receptor Introductory

Exploring a Protein Structure in the RSCB PDB: Insulin Advanced

Community-Nominated Targets

Deciphering Microbial DUFs

Discovering Deaminases

Disordered Proteins

	Myoglobin Geis highlights the hundreds of chemical bonds in the lattice of myoglobin.
	Myoglobin Fold Geis illustrated the structure of myoglobin, focusing on the folding pattern of the secondary structure of the protein. Unlike previous myoglobin Illustrations, this painting focuses on the tertiary structure of the molecule rather than the sequence or surface.
	Ribonuclease S Geis illustrates the structure of the ribonuclease S that highlights the dinucleotide RNA substrate in red and the four disulfide bonds in yellow.
	Trypsin Geis illustrates the structure of bovine trypsin, an enzyme that breaks down proteins, which was first revealed by X-ray crystallography in 1971 and further explored in 1974 (Krieger et al., 1974). This illustration was originally published in Scientific American (Stroud, 1984). Trypsin is a protease, an enzyme that catalyzes cleavage of polypeptide chains (Stroud, 1984). Geis' sketch depicts the structure with a ball-and-stick model and displays the sidechains of aspartic acid (Asp102), histidine (His57), and serine (Ser195), known as the catalytic triad.
	Crambin In Hendrickson and Teeter's molecular study in 1981, the crystal structure of crambin, a small seed storage protein, was determined based on the location of sulfur atoms in the protein. Using an artistic approach, Geis utilizes bright yellow shading and orange coloring to highlight the importance of these 6 sulfur atoms in this ball-and-stick representation. The backbone of the protein is depicted in blue.
	Myohemerythrin The colored print depicts the structure of myohemerythrin, which was first revealed by X-ray crystallography in 1975 (Hendrickson et al., 1975) and further refined in 1987 (Sheriff et al., 1987). Geis's illustration depicts the tertiary structure of the protein, highlighting the four anti-parallel alpha-helices and the presence of mu-oxo-diiron (iron atoms in red and oxygen atom in pink) located within the core of the macromolecule (Myohemerythrin).

	Exploring a Protein Structure in the RCSB PDB: Antibodies Advanced
	Exploring a Protein Structure in the RSCB PDB: Insulin Introductory
	Exploring a Protein Structure in the RCSB PDB: T-Cell Receptor Introductory
	Exploring a Protein Structure in the RSCB PDB: Insulin Advanced
	Bioinformatics of Green Fluorescent Protein
	Exploring a Protein Structure in the RCSB PDB: Green Fluorescent Protein Introductory
	Exploring a Protein Structure in the RCSB PDB: Major Histocompatibility Complex Introductory
	Exploring a Protein Structure in the RCSB PDB: Fluorescent Proteins Advanced
	Visual Comprehension: Humoral and Cell Mediated Adaptvie Immune Response
	Exploring a Protein Structure in the RCSB PDB: Antibodies Introductory
	Exploring a Protein Structure in the RCSB PDB: Major Histocompatibility Complex Advanced

Biomolecular Structural Biology

Molecule of the Month Articles (12)

Learning Resources (14)

Curriculum Resources (11)

Structural Biology Highlights (6)

Geis Digital Archive (6)