Wikipedia:WikiProject Molecular and Cellular Biology/protbox usage
From Wikipedia, the free encyclopedia
This guide explains how to build a protbox, a table setting the properties of proteins using Template:protbox.
Contents[hide]
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[edit] Quick start and examples
[edit] Enzyme
2-oxoglutarate dehydrogenase E1 component (α-Ketoglutarate dehydrogenase) | |
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Other names: | Alpha-ketoglutarate dehydrogenase |
Genetic data | |
Gene type: | protein coding |
Protein Structure/Function | |
Molecular Weight: | 115942 (Da) |
Protein type: | Enzyme: Dehydrogenase |
Functions: | converts Alpha ketoglutarate to succinyl CoA |
Domains: | Transketolase central region, Dehydrogenase E1 component |
Other | |
Taxa expressing: | Homo sapiens; homologs: ubiquitous among oxidatively respiring organisms |
Cell types: | ubiquitous among aerobic cells |
Subcellular localization: | mitochondrion, mitochondrial matrix |
Pathway(s): | Citric acid cycle, Lysine degradation, Tryptophan metabolism |
Enzymatic Data | |
Catalytic activity: | 2-oxoglutarate + [dihydrolipoyllysine-residue succinyltransferase] lipoyllysine = [dihydrolipoyllysine-residue succinyltransferase] S-succinyldihydrolipoyllysine + CO(2) |
Cofactor(s): | Thiamine pyrophosphate |
Enzyme Regulation: | Catabolite repressed |
Medical/Biotechnological data | |
Diseases: | Alpha-Ketoglutarate Dehydrogenase Deficiency |
{{Protbox |Name= |Photo= |Caption= |Gene_type= |Molecular_weight= |Structure= |Type= |Functions= |Domains= |Motifs= |Alternative_products= |Catalytic_activity= |Cofactors= |Enzyme_regulation= |Diseases= |Pharmaceuticals= |Taxa= |Cells= |Location= |Names= |Pathways= |Interactions= |Pages= |Review= }}
[edit] Hormone/Cytokine
Insulin | |
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Insulin crystals |
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Other names: | proinsulin |
Genetic data | |
Gene code: | HUGO code:INS |
Gene type: | Protein coding |
Protein Structure/Function | |
Molecular Weight: | 11982 (Da) |
Structure: | Solution Structure of Human pro-Insulin Polypeptide |
Protein type: | insulin family |
Functions: | glucose regulation |
Domains: | INS domain |
Motifs: | SP motif |
Other | |
Taxa expressing: | Homo sapiens; homologs: many metazoan taxa |
Cell types: | pancreas |
Subcellular localization: | extracellular |
Covalent modifications: | glycation, proteolytic cleavage |
Pathway(s): | Insulin signaling pathway (KEGG); Type II diabetes mellitus (KEGG); Type I diabetes mellitus (KEGG); Maturity onset diabetes of the young(KEGG); Regulation of actin cytoskeleton (KEGG) |
Medical/Biotechnological data | |
Diseases: | familial hyperproinsulinemia, Diabetes |
Pharmaceuticals: | Humulin, Humalog (Eli Lilly) and Novolin(Novo Nordisk) |
[edit] Receptor
Bone morphogenetic protein receptor, type IA | |
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Ternary Complex Of Bmp-2 Bound To Bmpr-Ia-Ecd And Actrii-Ecd |
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Other names: | Serine/threonine-protein kinase receptor R5, SKR5, Activin receptor-like kinase 3, ALK-3, CD292 antigen |
Genetic data | |
Gene code: | HUGO code:BMPR1A |
Protein Structure/Function | |
Protein type: | Receptor serine/threonine kinase |
Domains: | TM domain S/T domain, GS domain |
Other | |
Taxa expressing: | Homo sapiens: homologs: many metazoan phyla |
Cell types: | many; prostate. cornea, brain |
Subcellular localization: | Plasma membrane |
Enzymatic Data | |
Catalytic activity: | ATP + (receptor-protein) = ADP + receptor-protein phosphate |
Cofactor(s): | Magnesium or manganese |
Receptor/Ligand data | |
Actions: | Involved in TGF beta superfamily ligand signaling |
Agonists: | BMP2, BMP6, BMP7, GDF6 |
Antagonists: | Noggin |
Medical/Biotechnological data | |
Diseases: | Juvenile polyposis syndrome (JPS) Online 'Mendelian Inheritance in Man' (OMIM) 174900; Cowden disease (CD) Online 'Mendelian Inheritance in Man' (OMIM) 158350; Hereditary mixed polyposis syndrome 2 (HMPS2) Online 'Mendelian Inheritance in Man' (OMIM) 610069 |
{{Protbox |Name= |Photo= |Caption= |Gene = |Structure = |Review = |Type= |Functions= |Domains= |Diseases= |Taxa = | Cells = | Location = |Catalytic_activity= |Cofactors= |Enzyme_regulation= |Actions= |Agonists= |Antagonists= |Mods= |Names= |Interactions= |Pages= }}
[edit] Field Descriptions
[edit] Nomenclature/Symbols/Images
[edit] Name
The official name of the protein is preferable in this field. The most common name may be placed in brackets. Many proteins have several names, however the official name is preferable in this field. Sources of the name of proteins include uniprot and HGNC. Alternate names may go in the alternate name field.
| Name =
[edit] Photo
A photo of the molecular structure may go in this field or an appropriate related photo. Sources of molecular structure include PDB. When entering the image name just write the name of the image do not precede with Image: .
|Photo=
[edit] Caption
If a photo is include make sure to include a caption to describe the picture.
|Caption=
[edit] Names
List the alternate names that protein has.
[edit] Symbol(s)
The official HGNC symbol is placed here(Human proteins). In order for the symbol to link to the HGNC site, you will need to fill two fields. The HGNCid is official HGNC identification number for that protein/gene. The symbol field and the HGNCid field. Alternate symbols may also be listed here using the AltSymbols field.
|HGNCid = |Symbol = |AltSymbols =
[edit] Gene Information
[edit] Gene
The "Gene" field represents the official gene code. For human proteins this can be retrieved from the HGNC.
- |Gene =
[edit] Gene type
The "Gene type" field referes to the type of gene ie what is its role or what it codes for. The gene type may be:
- Protein coding
- Pseudogenes
- RNA genes
- Genetic loci
- Gene clusters
- Unclasified or Unknown or Other
- |Gene_type=
[edit] Structural/functional information
[edit] Protein length
In this field enter the length of the protein - the amount of amino acids in the protein.
|Protein_length=
[edit] Molecular_weight
The Molecular weight of the protein given in Daltons.
[edit] Structure
In this field links to the molecular structure is given.
[edit] Type
This field describes the type of protein
[edit] Functions
The major funtion of the protein is described here.
[edit] Domains
The major protein domains. eg. MH1 domain, MH2 domain
[edit] Motifs
List the major motifs that are present in the protein.
[edit] Alternative_products
If the protein has other isoforms list them here.
[edit] Other information
[edit] Taxa
List species, genus or phyla that express the protein. If a
[edit] Cells
List the cell types that express the protein.
[edit] Location
List the location in the cell that the mature protein is expressed in. There may be several places. May be listed as: Primary Region A, Region B. Seconday: Region C, Region D. The regions of protein expression include: Extracellular, Membrane protein, Cytoplasm, mitochondria, chloroplast, nucleus.
[edit] Mods
Describe what types of Post translational modifications that the protein undergoes. This may be: Phosphorylation , Sumoylation, Ubiquitination. See PTM for a list of Post translational modifications that a protein may undergo. Sources of PTM information include Uniprot and Human protein reference database.
[edit] Pathways
List any cellular pathways that the protein is involved in. It is useful to include a link to the Kyoto encyclopedia of genes and genomes pathway in parenthesis following the name of the pathway. eg. Hedgehog signaling pathway (KEGG).
- |Pathway=
[edit] Interactions
List any major protein interactions.
[edit] Enzymes
Enzymes have special properties that are unique to them these fields may be used to describe them.
[edit] Catalytic_activity
This field describes what reaction is catalyzed by the enzyme.
[edit] Cofactors
If the enzyme requires cofactors list them here
[edit] Enzyme_regulation
Describe how the enzyme is regulated here.
[edit] Medical/Biotechnological uses
If the protein has any medically related information this can be listed here.
[edit] Diseases
List any diseases that are related to the protein. It is also useful to list with the disease the related OMIM article using
{{OMIM | #OMIM_reference number}}
[edit] Pharmaceuticals
List any pharmaceutical uses of the protein or related medications.
[edit] Biotechnology
List any biotechnology uses of the protein.
[edit] Receptor related information
[edit] Actions
Describe the general actions of the receptor.
[edit] Agonists
List the receptor agonists
[edit] Antagonists
List the receptor antagonists
[edit] Database links
[edit] Identifiers
There are many databases online that catalog proteins and the genes that produce them. The identifier fields may be used to describe them:
|Symbol = |AltSymbols = |EntrezGene = |OMIM = |RefSeq= |UniProt= |PDB = |ECnumber= |Chromosome= |Arm = |Band = |LocusSupplementaryData=
[edit] Codes
The code section is an alternative to the individual gene identifier codes. In this field you can include the various identifiers using the templates that link to the websites that describe the protein/gene.
|codes =
[edit] Aditional information
This section lists sources
[edit] Pages
Here you can list pages that are related to the protein on wikipedia
[edit] Review
List here any recent scholarly papers that talk about the protein.
[edit] All Parameters
This lists all the parameters in a protbox in the order that they appear.
Name | |
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Caption |
|
Symbol(s): | Symbol AltSymbols |
Other names: | Names |
Genetic data | |
Locus: | Chr. Chromosome ArmBandqtr13-54 |
Gene code: | Gene |
Gene type: | Gene_type |
Protein Structure/Function | |
Protein length: | Protein_length (Amino Acids) |
Molecular Weight: | Molecular_weight (Da) |
Structure: | Structure |
Protein type: | Type |
Functions: | Functions |
Domains: | Domains |
Motifs: | Motifs |
Alternative Products: | Alternative_products |
Other | |
Taxa expressing: | Taxa |
Cell types: | Cells |
Subcellular localization: | Location |
Covalent modifications: | Mods |
Pathway(s): | Pathways |
Molecular interactions: | Interactions |
Biophysicochemical properties: | Biophysicochemical_properties |
Enzymatic Data | |
Catalytic activity: | Catalytic_activity |
Cofactor(s): | Cofactors |
Enzyme Regulation: | Enzyme_regulation |
KM: | Km |
VMax: | Vmax |
Receptor/Ligand data | |
Actions: | Actions |
Agonists: | Agonists |
Antagonists: | Antagonists |
Medical/Biotechnological data | |
Diseases: | Diseases |
Pharmaceuticals: | Pharmaceuticals |
Biotechnological uses: | Biotechnology |
Database Links | |
Accession Numbers: | Accession_numbers |
EC number: | ECnumber |
Entrez: | EntrezGene |
OMIM: | OMIM |
PDB: | PDB |
RefSeq: | RefSeq |
UniProt: | UniProt |
Codes: | Codes |
Related information | |
Related articles: | Pages |
Recent publications: | Review |
{{Protbox |Name= |Photo= |Caption= |HGNCid = |Symbol = |AltSymbols = |Chromosome = |Arm = |Band = |LocusSupplementaryData = |Gene= |Gene_type= |Protein_length= |Molecular_weight= |Structure= |Type= |Functions= |Domains= |Motifs= |Alternative_products= |Catalytic_activity= |Cofactors= |Enzyme_regulation= |Km= |Vmax= |Biophysicochemical_properties= |Diseases= |Pharmaceuticals= |Biotechnology= |Taxa= |Cells= |Location= |Mods= |Names= |Pathways= |Interactions= |Actions= |Agonists= |Antagonists= |Accession_numbers= |EntrezGene = |OMIM = |RefSeq = |UniProt = |PDB = |ECnumber = |Codes= |Review= |Pages= }}