LASP1

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LIM and SH3 protein 1
Image:PBB Protein LASP1 image.jpg
PDB rendering based on 1zfo.
Available structures:
For the file format that describes the 3D structures of molecules found in the Protein Data Bank, see Protein Data Bank (file format).

The Protein Data Bank (PDB) is a repository for 3-D structural data of proteins and nucleic acids. These data, typically obtained by X-ray crystallography or NMR spectroscopy, are submitted by biologists and biochemists from around the world, are released into the public domain, and can be accessed for free.

History

Founded in 1971 by Drs. Edgar Meyer and Walter Hamilton Brookhaven National Laboratory, management of the Protein Data Bank was transferred in 1998 to members of the Research Collaboratory for Structural Bioinformatics (RCSB).

The Worldwide Protein Data Bank (wwPDB) consists of organizations that act as deposition, data processing and distribution centers for PDB data. The founding members are RCSB PDB (USA), MSD-EBI (Europe) and PDBj (Japan). The BMRB (USA) group joined the wwPDB in 2006. The mission of the wwPDB is to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly available to the global community.

The PDB is a key resource in structural biology and is critical to more recent work in structural genomics.

Countless derived databases and projects have been developed to integrate and classify the PDB in terms of protein structure, protein function and protein evolution.

Growth

When the PDB was originally founded it contained just 7 protein structures. Since then it has undergone an approximate exponential growth in the number of structures, which does not show any sign of falling off.

The growth rate of the PDB has been the subject of fairly extensive analysis.

Contents

As of 26 September, 2006, the database contained 39,051 released atomic coordinate entries (or "structures"), 35,767 of that proteins, the rest being nucleic acids, nucleic acid-protein complexes, and a few other molecules. About 5,000 new structures are released each year. Data are stored in the mmCIF format specifically developed for the purpose.

Note that the database stores information about the exact location of all atoms in a large biomolecule (although, usually without the hydrogen atoms, as their positions are more of a statistical estimate); if one is only interested in sequence data, i.e. the list of amino acids making up a particular protein or the list of nucleotides making up a particular nucleic acid, the much larger databases from Swiss-Prot and the International Nucleotide Sequence Database Collaboration should be used.

Statistics

As of 11 September, 2007, the "PDB Holdings List" at RCSB reported the following statistics:

Proteins Nucleic Acids Protein/NA complexes Other Total
X-ray diffraction 36223 983 1684 24 38914
NMR 5665 781 134 7 6587
Electron microscopy 105 10 38 0 153
Other 80 4 4 2 90
Total 42073 1778 1860 33 45744

Note that theoretical models are no longer accepted in the PDB.

22461 structures in the PDB have a structure factor file. 3138 structures in the PDB have an NMR restraint file.

The current breakdown of holdings is updated weekly.

File format

Through the years the PDB file format has undergone many, many changes and revisions. Its original format was dictated by the width of computer punch cards.

This legacy format has caused many problems with the format, and consequently there are 'clean-up' projects;

The MMDB uses ASN.1 (and an XML conversion of this format). The wwPDB members RCSB PDB, MSD-EBI, and PDBj are working together to make the data uniform across the archive. Some believe this to be desirable; others argue that, without a universal repository of information (i.e., a common dictionary), it is not possible to draw comparisons.

Each structure published in PDB receives a four-character alphanumeric identifier, its PDB ID. This should not be used as an identifier for biomolecules, since often several structures for the same molecule (in different environments or conformations) are contained in PDB with different PDB IDs.

If a biologist submits structure data for a protein or nucleic acid, wwPDB staff reviews and annotates the entry. The data are then automatically checked for plausibility. The source code for this validation software has been released for free. The main data base accepts only experimentally derived structures, and not theoretically predicted ones (see protein structure prediction).

Various funding agencies and scientific journals now require scientists to submit their structure data to PDB.

Viewing the data

The structural data can be used to visualize the biomolecules with appropriate software, such as VMD, RasMol, PyMOL, Jmol, MDL Chime, QuteMol, web browser VRML plugin or any web-based software designed to visualize and analyse the protein structures such as STING. A recent desktop software addition is Sirius. The RCSB PDB website also contains resources for education, structural genomics, and related software.

References

Printed

  • H.M. Berman, K. Henrick, H. Nakamura (2003): Announcing the worldwide Protein Data Bank. Nature Structural Biology 10 (12), p. 980 PMID 14634627.
  • H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne: The Protein Data Bank. Nucleic Acids Research, 28 pp. 235-242 (2000). PMID 10592235
  • Bernstein FC, Koetzle TF, Williams GJ, Meyer Jr EF, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol 1977;112:535-542. PMID 875032.
  • E.F. Meyer “The First Years of the Protein Data Bank“, Protein Science 6:1591-1597 (1997)
  • Sussman, JL, Lin, D, Jiang, J, Manning, NO, Prilusky, J, Ritter, O & Abola, EE. Protein data bank (PDB): a database of 3D structural information of biological macromolecules. Acta Cryst 1998; D54:1078-1084. PMID 10089483.

Online

Other external links

Links to enzyme database data

  • [1] The best mapping is provided by Kim Henrick's group at EBI as part of the MSD SIFTS initiative.
  • [2] PDB provide a mapping on their beta site, but it is at the whole PDB level not chain level.
  • [3] Search at BRENDA enzyme database portal.
  • [4] PDBSProtEC:

Molecular graphic visualisation tools

Identifiers
Symbol(s) LASP1; Lasp-1; MLN50
External IDs OMIM: 602920 MGI: 109656 Homologene: 4480
RNA expression pattern

Image:PBB GE LASP1 200618 at tn.png

More reference expression data

Orthologs
Human Mouse
Entrez 3927 16796
Ensembl ENSG00000002834 ENSMUSG00000038366
Uniprot Q14847 Q543N3
Refseq NM_006148 (mRNA)
NP_006139 (protein) 		NM_010688 (mRNA)
NP_034818 (protein)
Location Chr 17: 34.28 - 34.33 Mb Chr 11: 97.62 - 97.65 Mb
Pubmed search [5] [6]

LIM and SH3 protein 1, also known as LASP1, is a human gene.[1]


This gene encodes a member of a LIM protein subfamily which is characterized by a LIM motif and a domain of Src homology region 3. This protein functions as an actin-binding protein and possibly in cytoskeletal organization.[1]


References

Further reading

  • Tomasetto C, Régnier C, Moog-Lutz C, et al. (1996). "Identification of four novel human genes amplified and overexpressed in breast carcinoma and localized to the q11-q21.3 region of chromosome 17.". Genomics 28 (3): 367-76. doi:10.1006/geno.1995.1163. PMID 7490069.
  • Tomasetto C, Moog-Lutz C, Régnier CH, et al. (1995). "Lasp-1 (MLN 50) defines a new LIM protein subfamily characterized by the association of LIM and SH3 domains.". FEBS Lett. 373 (3): 245-9. PMID 7589475.
  • Chew CS, Parente JA, Zhou C, et al. (1998). "Lasp-1 is a regulated phosphoprotein within the cAMP signaling pathway in the gastric parietal cell.". Am. J. Physiol. 275 (1 Pt 1): C56-67. PMID 9688835.
  • Schreiber V, Moog-Lutz C, Régnier CH, et al. (1999). "Lasp-1, a novel type of actin-binding protein accumulating in cell membrane extensions.". Mol. Med. 4 (10): 675-87. PMID 9848085.
  • Chew CS, Chen X, Parente JA, et al. (2003). "Lasp-1 binds to non-muscle F-actin in vitro and is localized within multiple sites of dynamic actin assembly in vivo.". J. Cell. Sci. 115 (Pt 24): 4787-99. PMID 12432067.
  • Strausberg RL, Feingold EA, Grouse LH, et al. (2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.". Proc. Natl. Acad. Sci. U.S.A. 99 (26): 16899-903. doi:10.1073/pnas.242603899. PMID 12477932.
  • Butt E, Gambaryan S, Göttfert N, et al. (2003). "Actin binding of human LIM and SH3 protein is regulated by cGMP- and cAMP-dependent protein kinase phosphorylation on serine 146.". J. Biol. Chem. 278 (18): 15601-7. doi:10.1074/jbc.M209009200. PMID 12571245.
  • Gevaert K, Goethals M, Martens L, et al. (2004). "Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides.". Nat. Biotechnol. 21 (5): 566-9. doi:10.1038/nbt810. PMID 12665801.
  • Ota T, Suzuki Y, Nishikawa T, et al. (2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs.". Nat. Genet. 36 (1): 40-5. doi:10.1038/ng1285. PMID 14702039.
  • Li B, Zhuang L, Trueb B (2004). "Zyxin interacts with the SH3 domains of the cytoskeletal proteins LIM-nebulette and Lasp-1.". J. Biol. Chem. 279 (19): 20401-10. doi:10.1074/jbc.M310304200. PMID 15004028.
  • Keicher C, Gambaryan S, Schulze E, et al. (2004). "Phosphorylation of mouse LASP-1 on threonine 156 by cAMP- and cGMP-dependent protein kinase.". Biochem. Biophys. Res. Commun. 324 (1): 308-16. doi:10.1016/j.bbrc.2004.08.235. PMID 15465019.
  • Gerhard DS, Wagner L, Feingold EA, et al. (2004). "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).". Genome Res. 14 (10B): 2121-7. doi:10.1101/gr.2596504. PMID 15489334.
  • Tao WA, Wollscheid B, O'Brien R, et al. (2005). "Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry.". Nat. Methods 2 (8): 591-8. doi:10.1038/nmeth776. PMID 16094384.
  • Rual JF, Venkatesan K, Hao T, et al. (2005). "Towards a proteome-scale map of the human protein-protein interaction network.". Nature 437 (7062): 1173-8. doi:10.1038/nature04209. PMID 16189514.
  • Grunewald TG, Kammerer U, Schulze E, et al. (2006). "Silencing of LASP-1 influences zyxin localization, inhibits proliferation and reduces migration in breast cancer cells.". Exp. Cell Res. 312 (7): 974-82. doi:10.1016/j.yexcr.2005.12.016. PMID 16430883.
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