About PIN db

The Proteins Interacting in the Nucleus database (PIN db) is a relational database containing the compositions of multi-protein complexes in the nucleus of human cells.

Phase I: Proteomic Catalog of the Human Transcriptional Machinery (HTM)

The current version of PIN is limited to information curated from the proteomics literature and primarily comprises of components of the general transcription machinery.

What you will find

Currently, PIN contains 124 general HTM and 30 'other' human protein complexes in the nucleus, totaling 573 proteins. Each complex has a unique composition, though some are partially overlapping.

With the exception of TFIID, the compositional information has all been taken from reports in peer-reviewed literature that describes biochemical-proteomic analyses; ie. protein complex isolation by column chromatography, immuno-affinity methods, or use of epitope tags (eg. FLAG, TAP, GST,...), and identification by mass spectrometry and/or western blotting. The curated experimental data were not derived in a systematic, high-throughput fashion. Rather, they have been generated by different labs, using different types of cells, isolation techniques and read-outs by different mass spectrometrists using various analytical approaches.

Each complex and protein in PIN is linked to a reference that first described the complex biochemically and/or the presence of the protein in a particular complex. Purification or capturing methods are given. Currently, only 462 proteins have links to sequence record(s) in GenBank . The majority of the remaining entries in PIN has been annotated in the original reports as components of a certain complex (usually in the form of bands on a gel) but these proteins have either not been identified or their identities have not been released.

For comparative purposes, 68 nuclear complexes from yeast have also been curated from the published literature, and 122 were imported from MIPS . In yeast, the majority of compositional data has been obtained through experimental means other than proteomic analyses.

PIN DB
STATISTICS PIN MIPS

Human All Yeast

Complex Protein Complex Protein Complex Protein

Nuclear complexes 154 573 222 869 122 578

Transcription complexes 124 493 180 723 0 0

    Chromatin modification 78 320 104 443

    Corepression/Silencing 24 127 26 133

    Elongation 16 48 26 87

    Mediator 11 49 18 84

PIN DB STATISTICS	PIN	MIPS
Human	All	Yeast
Complex	Protein	Complex	Protein	Complex	Protein
Nuclear complexes	154	573	222	869	122	578
Transcription complexes	124	493	180	723	0	0
Chromatin modification	78	320	104	443
Corepression/Silencing	24	127	26	133
Elongation	16	48	26	87
Mediator	11	49	18	84

What you won't find

There is no information on protein-protein interactions derived from yeast two-hybrid (Y2H) analyses. None of the protein complexes were isolated by using specific transcription factors (eg. AP-1, PU.1, .... ) as bait or by assaying for the presence of such specific factors during classical purification. In fact, there are very few specific transcription factors in PIN. There are no protein complexes in PIN from mouse, Drosophila, zebrafish, or any organism other than human and budding yeast.

Browse, Search, Compare Complexes

PIN can be browsed at the complex and/or protein levels (enter from Protein Complexes in the Nucleus ). The first linked page allows viewing of three PIN complex subsets (Human/PIN, Yeast/PIN, and Yeast/MIPS) and viewing of the HTM entries by functional categories, such as chromatin remodeling, mediators, etc.

At PIN Search Page , PIN can be searched by complex name or by subunit proteins (to find any complexes that contain one or more defined proteins).

The Subunit Lineup Tool (PIN Tools Page ) compares HTM complexes with respect to their composition; the result is shown in table format, with links to further information (PIN and/or PubMed and GenBank ). You can enter any two or more (up to all 124 ) complexes in PIN for comparison, or select from a list of HTM complexes (organized by functional sub-categories).

Protein Names and Aliases

The Human Genome Nomenclature Committee (HGNC)-approved names, plus all other common names and aliases, for each set of protein subunits of a complex can be retrieved through the Subunit Alias Finder on PIN Tools Page . Note: The algorithm developed for this tool forms the basis for complex comparison in Subunit Lineup Tool.

For individual proteins, the common and official names can be looked up using the SQL Utilities on PIN Homepage .

Future Additions

New HTM complexes will be curated from the peer-reviewed literature on a continuing basis.
Systematic proteomic interaction profiling of many components of the general HTM is under way at the Protein Center of Memorial Sloan-Kettering, in collaboration with several expert laboratories in the NY / NJ area. Experimental data will be deposited in PIN.
Nuclear protein complexes involved in DNA replication, repair, recombination and telomere function will be added.

Proteomics and Bio-informatics Usage

PINdb is intended for use in 'targeted proteomics' and as a more general resource for modeling of networks. The objective is to archive interactions, modifications and functions in a format allowing easy interactive analysis by query, visualization and modeling, and should lead to an orderly layout of the nuclear protein interaction networks, specifically those involving components of the transcription apparatus.

The comparative tables will initially provide a non-redundant, comprehensive list of HTM components to rationally guide further proteomic profiling efforts. The custom sequence databases can also be used interactively with mass spectrometry-based protein identification applications, ie. by reducing lengthy search result lists, via implementation of web services.

Contact us

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