Stem cell factor

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KIT ligand
Image:PBB Protein KITLG image.jpg
PDB rendering based on 1exz.
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.

Contents

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

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

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

Molecular graphic visualisation tools

Identifiers
Symbol(s) KITLG; SF; DKFZp686F2250; KL-1; Kitl; MGF; SCF
External IDs OMIM: 184745 MGI: 96974 Homologene: 692
RNA expression pattern

Image:PBB GE KITLG 207029 at tn.png

Image:PBB GE KITLG 211124 s at tn.png

More reference expression data

Orthologs
Human Mouse
Entrez 4254 17311
Ensembl ENSG00000049130 ENSMUSG00000019966
Uniprot P21583 Q61854
Refseq NM_000899 (mRNA)
NP_000890 (protein) 		NM_013598 (mRNA)
NP_038626 (protein)
Location Chr 12: 87.41 - 87.5 Mb Chr 10: 99.45 - 99.52 Mb
Pubmed search [9] [10]

Stem cell factor (SCF), otherwise known as KIT ligand or Steel factor[1],is a cytokine which binds CD117 (c-Kit). SCF is also known as "steel factor" or "c-kit ligand". SCF exists in two forms, cell surface bound SCF and soluble (or free) SCF. Soluble SCF is produced by the cleavage of surface bound SCF by metalloproteases.

SCF is a growth factor important for the survival, proliferation, and differentiation of hematopoietic stem cells and other hematopoietic progenitor cells. One of its roles is to change the BFU-E(burst-forming unit-erythroid) cells, which are the earliest erythrocyte precursors in the erythrocytic series, into the CFU-E (colony-forming unit-erythroid)[1]. SCF, along with bFGF (basic fibroblast growth factor) and LIF (lymphocyte inhibitory factor), prevents spontaneous differentiation of primitive embryonic stem cells in cell culture[1].

Ancestim is a recombinant form of SCF.[1]

References


Further reading

  • Broudy VC (1997). "Stem cell factor and hematopoiesis.". Blood 90 (4): 1345-64. PMID 9269751.
  • Andrews RG, Briddell RA, Appelbaum FR, McNiece IK (1999). "Stimulation of hematopoiesis in vivo by stem cell factor.". Curr. Opin. Hematol. 1 (3): 187-96. PMID 9371281.
  • Wehrle-Haller B (2004). "The role of Kit-ligand in melanocyte development and epidermal homeostasis.". Pigment Cell Res. 16 (3): 287-96. PMID 12753403.
  • Rönnstrand L (2004). "Signal transduction via the stem cell factor receptor/c-Kit.". Cell. Mol. Life Sci. 61 (19-20): 2535-48. doi:10.1007/s00018-004-4189-6. PMID 15526160.
  • Mroczko B, Szmitkowski M (2005). "Hematopoietic cytokines as tumor markers.". Clin. Chem. Lab. Med. 42 (12): 1347-54. doi:10.1515/CCLM.2004.253. PMID 15576295.
  • Lev S, Yarden Y, Givol D (1992). "A recombinant ectodomain of the receptor for the stem cell factor (SCF) retains ligand-induced receptor dimerization and antagonizes SCF-stimulated cellular responses.". J. Biol. Chem. 267 (15): 10866-73. PMID 1375232.
  • Huang EJ, Nocka KH, Buck J, Besmer P (1992). "Differential expression and processing of two cell associated forms of the kit-ligand: KL-1 and KL-2.". Mol. Biol. Cell 3 (3): 349-62. PMID 1378327.
  • Toyota M, Hinoda Y, Itoh F, et al. (1992). "Expression of two types of kit ligand mRNAs in human tumor cells.". Int. J. Hematol. 55 (3): 301-4. PMID 1379846.
  • Lu HS, Clogston CL, Wypych J, et al. (1992). "Post-translational processing of membrane-associated recombinant human stem cell factor expressed in Chinese hamster ovary cells.". Arch. Biochem. Biophys. 298 (1): 150-8. PMID 1381905.
  • Sharkey A, Jones DS, Brown KD, Smith SK (1992). "Expression of messenger RNA for kit-ligand in human placenta: localization by in situ hybridization and identification of alternatively spliced variants.". Mol. Endocrinol. 6 (8): 1235-41. PMID 1383693.
  • Mathew S, Murty VV, Hunziker W, Chaganti RS (1992). "Subregional mapping of 13 single-copy genes on the long arm of chromosome 12 by fluorescence in situ hybridization.". Genomics 14 (3): 775-9. PMID 1427906.
  • Geissler EN, Liao M, Brook JD, et al. (1991). "Stem cell factor (SCF), a novel hematopoietic growth factor and ligand for c-kit tyrosine kinase receptor, maps on human chromosome 12 between 12q14.3 and 12qter.". Somat. Cell Mol. Genet. 17 (2): 207-14. PMID 1707188.
  • Anderson DM, Williams DE, Tushinski R, et al. (1992). "Alternate splicing of mRNAs encoding human mast cell growth factor and localization of the gene to chromosome 12q22-q24.". Cell Growth Differ. 2 (8): 373-8. PMID 1724381.
  • Martin FH, Suggs SV, Langley KE, et al. (1990). "Primary structure and functional expression of rat and human stem cell factor DNAs.". Cell 63 (1): 203-11. PMID 2208279.
  • Ramenghi U, Ruggieri L, Dianzani I, et al. (1995). "Human peripheral blood granulocytes and myeloid leukemic cell lines express both transcripts encoding for stem cell factor.". Stem Cells 12 (5): 521-6. PMID 7528592.
  • Saito S, Enomoto M, Sakakura S, et al. (1995). "Localization of stem cell factor (SCF) and c-kit mRNA in human placental tissue and biological effects of SCF on DNA synthesis in primary cultured cytotrophoblasts.". Biochem. Biophys. Res. Commun. 205 (3): 1762-9. doi:10.1006/bbrc.1994.2873. PMID 7529021.
  • Laitinen M, Rutanen EM, Ritvos O (1995). "Expression of c-kit ligand messenger ribonucleic acids in human ovaries and regulation of their steady state levels by gonadotropins in cultured granulosa-luteal cells.". Endocrinology 136 (10): 4407-14. PMID 7545103.
  • Blechman JM, Lev S, Brizzi MF, et al. (1993). "Soluble c-kit proteins and antireceptor monoclonal antibodies confine the binding site of the stem cell factor.". J. Biol. Chem. 268 (6): 4399-406. PMID 7680037.
  • Lu HS, Jones MD, Shieh JH, et al. (1996). "Isolation and characterization of a disulfide-linked human stem cell factor dimer. Biochemical, biophysical, and biological comparison to the noncovalently held dimer.". J. Biol. Chem. 271 (19): 11309-16. PMID 8626683.
  • Vanhaesebroeck B, Welham MJ, Kotani K, et al. (1997). "P110delta, a novel phosphoinositide 3-kinase in leukocytes.". Proc. Natl. Acad. Sci. U.S.A. 94 (9): 4330-5. PMID 9113989.

External links

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Cell signaling: cytokines
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