1. The Complex Portal Birgit Meldal
IntAct & Complex Portal Database Curator

2. A couple of definitions…
Protein-protein interactions (PPIs): physical and selective contacts that happen between pairs of proteins, in certain molecular regions and in a defined biological context.
Protein A
Protein B
binds

3. A couple of definitions…
Protein-protein interactions (PPIs): physical and selective contacts that happen between pairs of proteins, in certain molecular regions and in a defined biological context.
Protein-protein interaction network (PPIN): Graphical representation of a group of PPIs in which proteins are represented as nodes and interactions as edges. A B

4. From Networks to Complexes
PPI Networks can provide evidence for large structures that cannot be isolated in its entirety, e.g. Human proteasome
Hook, B. and Schagat, T. [Internet] 2011.
Available from:

5. A complex entry has many source databases

6. A complex entry has many source databases

7. Common Curation pipeline & QC
Sanity Checks (nightly)
Release (monthly)
reject
Public web site
FTP site
accept
annotate p1 p2 I
exp
Publication(s)
(full text) .
Web Service
(complexes)
CVs
Curation manual
check
curator
Super curator
Other DBs
report

8. Mission statement
To provide freely accessible, high quality, manually curated annotations of macromolecular complexes.

9. Definition of a complex
A stable set of (2 or more) interacting protein molecules which
can be co-purified and
have been shown to exist as a functional unit in vivo.
Non-protein molecules (e.g. small molecules, nucleic acids) may also be present in the complex if they are an integral part of the complex.

10. What is not a stable complex?
Enzyme/substrate, receptor/ligand or similar transient interactions,
Unless:
one element is a complex in its own right, and/or
it is an obligate complex that requires substrate/ligand binding,
maltose transporter requires maltose binding for holo-enzyme formation (EBI , EBI )

11. Maltose transport complex
Core subunit, no maltose binding protein (MBP) or maltose
Holo-enzyme with MBP and maltose (and ATP)
EBI , 3fh6
EBI , 3puy

12. What is not a stable complex?
Enzyme/substrate, receptor/ligand or similar transient interactions,
Unless:
one element is a complex in its own right, and/or
it is an obligate complex that requires substrate/ligand binding,
maltose transporter requires maltose binding for holo-enzyme formation (EBI , EBI )
PDGF receptors: ligands are obligate dimer and receptors require ligand binding for dimerisation forming an obligate tetramer

13. PDGF receptor complex
PMID: : Fig. 2: Structure of the PDGF-B:PDGFRβ complex. (A) Side view of the ribbon model of the complex, with the PDGF-B protomers in green and blue, and the PDGFRβ protomers in pink and orange. The N-linked glycans attached to PDGFRβ are depicted as sticks. (B) Top view of the PDGF-B:PDGFRβ complex in surface representation.

14. What is not a stable complex?
Enzyme/substrate, receptor/ligand or similar transient interactions,
Unless:
one element is a complex in its own right, and/or
it is an obligate complex that requires substrate/ligand binding,
maltose transporter requires maltose binding for holo-enzyme formation (EBI , EBI )
PDGF receptors: ligands are obligate dimer and receptors require ligand binding for dimerisation forming an obligate tetramer
Two proteins associated in a pulldown / coimmunoprecipitation with no functional link

15. Evidence Code Ontology

16. Evidence Code Ontology

17. Species coverage
Arabidopsis thaliana
Danio rerio

18. Complex search

19. Complex search http://www.ebi.ac.uk/complexportal Search examples
Identifiers, names and synonyms of molecules (protein, gene, small molecule)
Identifiers, names and synonyms of complexes
Cross-references of complexes
Species
Gene Ontology terms

20. Complex search for all complexes (“*”)
Filters:
Species
Biological role
Molecule type

21. Demo: Overview of an entry
Hemoglobin HbA EBI
Integrin alphaIIb-beta3 complex EBI
Shelterin EBI
Telomerase EBI
GO: , EBI
PCNA EBI

22. Downloads via ftp From http://www.ebi.ac.uk/complexportal/download
ftp://ftp.ebi.ac.uk/pub/databases/intact/complex/current/
Folder per species
In PSI-XML 2.5 & 3.0  please use XML 3.0!
ComplexTab – tab-del format

23. Web service REST-API http://www.ebi.ac.uk/intact/complex-ws/
3 methods:
~/search/
~/display/
~/export/
Returns a JSON object
Complex Viewer queries the WS for the JSON object

24. Curation Requests and Contact
Found a bug? Report it!
(GitHub)
What to get updates? Sign up to our Newsletter or follow us on Twitter
We tweet about releases, Complex of the Month (#CotM), usage tips and other curiosities
Can’t find a complex? Request it!
(generates to helpdesk, will become a tracker)

25. A Service brought to you by EMBL-EBI in collaboration with…
@ UCL
Sandra Orchard
Henning Hermjakob
PDBe
Max
Koch
past members…
Noemi del Toro Ayllon
Birgit Meldal

26. Thank you! ?