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(-) Description

Title :  CRYSTAL STRUCTURE OF BONE MORPHOGENETIC PROTEIN-3 (BMP-3)
 
Authors :  G. P. Allendorph
Date :  19 Jun 07  (Deposition) - 23 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.21
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Bmp, Tgf-Beta, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. P. Allendorph, M. J. Isaacs, Y. Kawakami, J. C. Belmonte, S. Choe
Bmp-3 And Bmp-6 Structures Illuminate The Nature Of Binding Specificity With Receptors.
Biochemistry V. 46 12238 2007
PubMed-ID: 17924656  |  Reference-DOI: 10.1021/BI700907K

(-) Compounds

Molecule 1 - BONE MORPHOGENETIC PROTEIN 3
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPET21A
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    GeneBMP3
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymBMP-3, OSTEOGENIN, BMP-3A

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2QCQ)

(-) Sites  (0, 0)

(no "Site" information available for 2QCQ)

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1A:8 -A:75
2A:37 -A:107
3A:41 -A:109
4A:74 -B:74
5B:8 -B:75
6B:37 -B:107
7B:41 -B:109

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ser A:28 -Pro A:29
2Phe A:43 -Pro A:44
3Ser B:28 -Pro B:29
4Phe B:43 -Pro B:44

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QCQ)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TGF_BETA_1PS00250 TGF-beta family signature.BMP3_HUMAN388-403
 
  2A:26-41
B:26-41

(-) Exons   (2, 4)

Asymmetric/Biological Unit (2, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002827011ENSE00001007113chr4:81952119-81952754636BMP3_HUMAN1-1061060--
1.3ENST000002827013ENSE00001007115chr4:81966892-81967802911BMP3_HUMAN106-4093042A:4-47
B:3-47
44
45
1.5bENST000002827015bENSE00001549055chr4:81974499-819786854187BMP3_HUMAN410-472632A:48-110
B:48-110
63
63

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:107
 aligned with BMP3_HUMAN | P12645 from UniProtKB/Swiss-Prot  Length:472

    Alignment length:107
                                   375       385       395       405       415       425       435       445       455       465       
           BMP3_HUMAN   366 EPRNCARRYLKVDFADIGWSEWIISPKSFDAYYCSGACQFPMPKSLKPSNHATIQSIVRAVGVVPGIPEPCCVPEKMSSLSILFFDENKNVVLKVYPNMTVESCACR 472
               SCOP domains d2qcqa_ A: automated matches                                                                                SCOP domains
               CATH domains 2qcqA00 A:4-110 Cystine-knot cytokines                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee..eee.........eee..eee..eee.......hhhhh.hhhhhhhhhhhhh..........eee..eeeeeeeee.....eeeeeeeeeee..eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------TGF_BETA_1      --------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.3  PDB: A:4-47 UniProt: 106-409      Exon 1.5b  PDB: A:48-110 UniProt: 410-472                       Transcript 1
                 2qcq A   4 EPRNCARRYLKVDFADIGWSEWIISPKSFDAYYCSGACQFPMPKSLKPSNHATIQSIVRAVGVVPGIPEPCCVPEKMSSLSILFFDENKNVVLKVYPNMTVESCACR 110
                                    13        23        33        43        53        63        73        83        93       103       

Chain B from PDB  Type:PROTEIN  Length:108
 aligned with BMP3_HUMAN | P12645 from UniProtKB/Swiss-Prot  Length:472

    Alignment length:108
                                   374       384       394       404       414       424       434       444       454       464        
           BMP3_HUMAN   365 IEPRNCARRYLKVDFADIGWSEWIISPKSFDAYYCSGACQFPMPKSLKPSNHATIQSIVRAVGVVPGIPEPCCVPEKMSSLSILFFDENKNVVLKVYPNMTVESCACR 472
               SCOP domains d2qcqb_ B: automated matches                                                                                 SCOP domains
               CATH domains 2qcqB00 B:3-110 Cystine-knot cytokines                                                                       CATH domains
           Pfam domains (1) --TGF_beta-2qcqB01 B:5-110                                                                                   Pfam domains (1)
           Pfam domains (2) --TGF_beta-2qcqB02 B:5-110                                                                                   Pfam domains (2)
         Sec.struct. author ......eee..eee.hhh.....eee..eee..eee.......hhhhh.hhhhhhhhhhhhh..........eee..eeeeeeeee.....eeeeeeeeeee..eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------TGF_BETA_1      --------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.3  PDB: B:3-47 UniProt: 106-409       Exon 1.5b  PDB: B:48-110 UniProt: 410-472                       Transcript 1
                 2qcq B   3 IEPRNCARRYLKVDFADIGWSEWIISPKSFDAYYCSGACQFPMPKSLKPSNHATIQSIVRAVGVVPGIPEPCCVPEKMSSLSILFFDENKNVVLKVYPNMTVESCACR 110
                                    12        22        32        42        52        62        72        82        92       102        

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (BMP3_HUMAN | P12645)
molecular function
    GO:0070700    BMP receptor binding    Interacting selectively and non-covalently with a BMP receptor.
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    GO:0008083    growth factor activity    The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    GO:0005160    transforming growth factor beta receptor binding    Interacting selectively and non-covalently with the transforming growth factor beta receptor.
biological process
    GO:0030509    BMP signaling pathway    A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0060395    SMAD protein signal transduction    The cascade of processes by which a signal interacts with a receptor, causing a change in the activity of a SMAD protein, and ultimately effecting a change in the functioning of the cell.
    GO:0051216    cartilage development    The process whose specific outcome is the progression of a cartilage element over time, from its formation to the mature structure. Cartilage elements are skeletal elements that consist of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.
    GO:0048468    cell development    The process whose specific outcome is the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0007267    cell-cell signaling    Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
    GO:0040007    growth    The increase in size or mass of an entire organism, a part of an organism or a cell.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0001503    ossification    The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance.
    GO:0001649    osteoblast differentiation    The process whereby a relatively unspecialized cell acquires the specialized features of an osteoblast, a mesodermal or neural crest cell that gives rise to bone.
    GO:0010862    positive regulation of pathway-restricted SMAD protein phosphorylation    Any process that increases the rate, frequency or extent of pathway-restricted SMAD protein phosphorylation. Pathway-restricted SMAD proteins and common-partner SMAD proteins are involved in the transforming growth factor beta receptor signaling pathways.
    GO:0043408    regulation of MAPK cascade    Any process that modulates the frequency, rate or extent of signal transduction mediated by the MAP kinase (MAPK) cascade.
    GO:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
    GO:0001501    skeletal system development    The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton).
cellular component
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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