Download An Introduction to Protein Structure Databases

An Introduction to Protein
Structure Databases
Michael Tress
CNIO
The Protein Data Bank
Small targets
To the
PDB …
The Protein Data Bank
The PDB is the only repository for proteins and related biological macromolecules.
It provides links to a variety of tools and resources for studying the structures and their
relationship to sequence, function, and disease.
The RSCB Protein Data Bank
The RSCB Protein Data Bank
The RSCB Protein Data Bank
The RSCB Protein Data Bank
The RSCB Protein Data Bank
The RSCB Protein Data Bank
The RSCB Protein Data Bank
The RSCB Protein Data Bank
Sequence Tab
Uniprot Sequence
Cross-reference
Missing (disordered)
residues
Secondary
structure
The RSCB Protein Data Bank
Other Tabs …
Statistical scores
showing deviations
Structural features
Mean deviation
from norm
The RSCB Protein Data Bank
The RSCB Protein Data Bank
The RSCB Protein Data Bank
Header …
Chain ID
Journal
The RSCB Protein Data Bank
Atom
Residue
Co-ordinates
Chain ID
Flexibility
The RSCB Protein Data Bank
SCOP (Structural Classification of Proteins)‫‏‬
A detailed description of structural relationships between proteins, classified
mostly by eye.
FAMILY: Clear evolutionary relationship.
Proteins in families are clearly
evolutionarily related. Generally the
pairwise residue identities are greater than
30%.
SUPERFAMILY: Probable common
evolutionary origin. Proteins often have
low sequences identities, but structural
and functional features suggest a common
evolutionary origin.
FOLD: Major structural similarity. Proteins
are defined as having a common fold if
they have the same secondary structures
arrangement and the same topological
connections.
The CATH Database
The same idea as SCOP, another classification of proteins, except there are 4
levels. The CATH classification system is semi-automatic.
Class: Secondary structure and packing
Architecture: overall shape, domain structure
and orientation (no connectivities between the
secondary structures)‫‏‬
Topology (FOLD family): overall shape and
connectivities.
Homologous superfamily: proteins are thought to
share common ancestor. Similarities by sequence
alignment and then by structure comparison
using the SSAP structural alignment program.
Structural Classification by 3D Alignments
The superposition of 2 (or more) 3D structures,
so that as many atoms as possible match.
Alignment usually only by c-alpha atoms.
3D alignments are not sequence alignments, but
they can converted into sequence alignments.
Structural alignment also important for evolutionary
comparisons and functional studies.
There are many different methods, all of
which have different principles.
For example, DALI (contact maps),
Mammoth (secondary structure),
SSAP (dynamic programming), LGA
(longest segment).
Measurements of Structural Similarity
The two structures being compared can be experimental
structures or predicted models.
RMSD: Root Mean Squared Deviation
is the total distance between all the
equivalent atoms in two structures. It
is measured in Angstroms.