Some definitions

• Class: α, β, α/β, α+β

• Topology: spatial properties preserved under
deformation (qualitative spatial properties).

2D and 1D schematic
representation of the topology
of a protein structure
• Architecture: structure disregarding topology
• Fold: type of domain structure (2D + topology)
• Family: group of obvious homologs (>30% IDE)
• Homologs: proteins derived from common ancestor
• Domain: basic unit of protein architecture
 Structural domains

• Fundamental units of protein architecture

• ~90% of proteins in eukaryotes are multidomain
• Challenge of domain identification
• Even bigger challange of domain prediction
• Domains can be continuous or discontinuous
• Resistent to mild proteolysis (solvent accessibility, flexibility)
• Independent folding: stay folded after cut, fold in isolation
(often even if discontinuous, i.e. more than one fragment)
• Independent evolutionary units
(Orengo and Thornton 2005 Ann. Rev. Biochem. 74, 867-900)
The Swissprot sequence database

Rich annotation (biological function)

Bibliography
Sequence
Secondary structure
Active site
Links to other databases
 The pfam database
http://pfam.sanger.ac.uk/

(Bateman et al. 2004 NAR 32, D138-D141; 2002 NAR 30, 276-280; 2000 NAR 28, 263-266)
• High-quality Pfam-A families are represented by large, single-colour boxes .
Mouseover to see domain descriptions; click on box to enter family page.

Examples:

• Pfam-B families (represented by small three-colour boxes ) are made

automatically from Prodom, and are of much lower quality (less reliable
alignments) with no annotation.

Example:

Click on domain box:

3D if available
N of chains
Clan (superfamily)
Interactions (crystallography)
Alignments
Residue conservation
Species tree
Links to other databases
National Center for Biotechnology Information
 The diagram shows the Entrez databases and the connections between
them. Each database is represented by a colored circle, where the color
indicates the approximate number of records in the database. Mouse over
a circle to see which databases are linked to the one selected, and how
many links exist between those databases.
 The hexameric DNA
arginine repressor L-Arg
(argr_ecoli)

1F9N

156 residues
Hexamer 108 kDa
wHTH
Arg X Allosteric repressor
Recombination factor
promoter/operator Hydrophobic interface
Search „3D domains“ for „arginine repressor“
Cn3D view 1F9N
try all...

try all...
Map sequence
regions onto
structure
The PDB structure database
PDB entries
ArgR still image from PDB
(1F9N)
Select chain, sequence stretch => map onto structure
Cursor on structure => residue identity
Then double click on rashelp.exe to extract RASMOL.HLP and RASWIN.HLP
Mouse L rotate
Mouse R translate
Shift + mouse L zoom
Strg + mouse L slab
Try
all...
 Try
all...

CPK by atom type

Shapely by amino-acid properties
Group N-term red, C-term blue
Chain by protein molecule
Temperature by B-value (mobility) from blue to red
Structure by secondary structure
User colour scheme stored in the PDB file
Command Reference
Using rasmol commands
RasMol allows the execution of interactive commands typed at the "RasMol>"
prompt in the terminal window. Each command must be given on a separate
line. Keywords are case insensitive and may be entered in either upper or lower
case letters. All whitespace characters are ignored except to separate keywords
and their arguments.

The commands/keywords currently recognised by RasMol are given below.

backbone background centre clipboard

colour connect cpk dots
define echo exit hbonds
help label load print
quit renumber reset restrict
ribbon rotate save script
select set show slab
source spacefill ssbonds strands
structure trace translate wireframe
write zap zoom
Select
Select atom sets
Syntax: select {<expression>}

Define the currently selected region of the molecule. All subsequent RasMol
commands that manipulate a molecule or modify its colour or representation, only
effects the currently selected region. The parameter of a select command is a
RasMol expression that is evaluated for every atom of the current molecule. The
currently selected (active) region of the molecule are those atoms that cause the
expression to evaluate true. To select the whole molecule use the RasMol
command select all. The behaviour of the select command without any parameters
is determined by the RasMol hetero and hydrogen parameters.

Type "help expression" for more information on RasMol atom expressions.

Select complementaries categories

Syntax: select not {<expression>}

... Display Ribbons
Predefined Sets

RasMol atom expressions may contain predefined sets. These sets are single
keywords that represent portions of a molecule of interest. Predefined sets are
often abbreviations primitive atom expressions, and in some cases of selecting
areas of a molecule that could not otherwise be distinguished. A list of the
currently predefined sets is given below. In addition to the sets listed here, RasMol
also treats element names (and their plurals) as predefined sets containing all
atoms of that element type, i.e. the command select oxygen is equivalent to the
command select elemno=8.

at acidic acyclic aliphatic

alpha amino aromatic backbone
basic bonded buried cg
charged cyclic cystine helix
hetero hydrogen hydrophobic ions
large ligand medium neutral
Nucleic polar protein purine
pyrimidine selected sheet sidechain
small solvent surface turn
water
... Display Spacefill
For fragment 1-10 of chain a:
>restrict 1-10a
Click on atom to get info
 To save...

Export picture

Write script

> write script filename

> script filename
 Animated images
(http://www.dkfz.de/spec/pdb2mgif/)