Wikipedia:WikiProject Molecular and Cellular Biology/protbox usage

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This guide explains how to build a protbox, a table setting the properties of proteins using Template:protbox.


Contents

[edit] Quick start and examples

[edit] Enzyme

2-oxoglutarate dehydrogenase E1 component (α-Ketoglutarate dehydrogenase)
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

Insulin crystals
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

Ternary Complex Of Bmp-2 Bound To Bmpr-Ia-Ecd And Actrii-Ecd
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) Mendelian Inheritance in Man (OMIM) 174900; Cowden disease (CD) Mendelian Inheritance in Man (OMIM) 158350; Hereditary mixed polyposis syndrome 2 (HMPS2) 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

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=
}}
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