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(-) Description

Title :  CRYSTAL STRUCTURE OF BMP9
 
Authors :  M. A. Brown, Q. Zhao, K. A. Baker, C. Naik, C. Chen, L. Pukac, M. Singh, T. T Y. Parice, A. Mahoney, V. Roschke, I. Sanyal, S. Choe
Date :  04 May 05  (Deposition) - 24 May 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.33
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Glycoprotein, Growth Factor, Cytokine, Hormone-Growth Factor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. A. Brown, Q. Zhao, K. A. Baker, C. Naik, C. Chen, L. Pukac, M. Singh, T. Tsareva, Y. Parice, A. Mahoney, V. Roschke, I. Sanyal, S. Choe
Crystal Structure Of Bmp-9 And Functional Interactions With Pro-Region And Receptors
J. Biol. Chem. V. 280 25111 2005
PubMed-ID: 15851468  |  Reference-DOI: 10.1074/JBC.M503328200

(-) Compounds

Molecule 1 - GROWTH/DIFFERENTIATION FACTOR 2
    ChainsA
    EngineeredYES
    Expression SystemCRICETULUS GRISEUS
    Expression System CommonCHINESE HAMSTER
    Expression System PlasmidPC4
    Expression System StrainCHO-DG44
    Expression System Taxid10029
    Expression System TissueOVARY CELLS
    Expression System Vector TypePLASMID
    FragmentGROWTH/DIFFERENTIATION FACTOR 2, RESIDUES 320-429
    GeneGDF2, BMP9
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymGDF-2, BONE MORPHOGENETIC PROTEIN 9, BMP-9

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1ZKZ)

(-) Sites  (0, 0)

(no "Site" information available for 1ZKZ)

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:8 -A:74
2A:37 -A:107
3A:41 -A:109

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:28 -Pro A:29
2Phe A:43 -Pro A:44

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_070691R333WGDF2_HUMANDisease (HHT5)35129734AR14W

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_070691R333WGDF2_HUMANDisease (HHT5)35129734AR14W

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TGF_BETA_1PS00250 TGF-beta family signature.GDF2_HUMAN345-360  1A:26-41
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TGF_BETA_1PS00250 TGF-beta family signature.GDF2_HUMAN345-360  2A:26-41

(-) Exons   (0, 0)

(no "Exon" information available for 1ZKZ)

(-) Sequences/Alignments

Asymmetric 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 GDF2_HUMAN | Q9UK05 from UniProtKB/Swiss-Prot  Length:429

    Alignment length:107
                                   332       342       352       362       372       382       392       402       412       422       
           GDF2_HUMAN   323 AGSHCQKTSLRVNFEDIGWDSWIIAPKEYEAYECKGGCFFPLADDVTPTKHAIVQTLVHLKFPTKVGKACCVPTKLSPISVLYKDDMGVPTLKYHYEGMSVAECGCR 429
               SCOP domains d1zkza_ A: automated matches                                                                                SCOP domains
               CATH domains 1zkzA00 A:4-110 Cystine-knot cytokines                                                                      CATH domains
               Pfam domains -TGF_beta-1zkzA01 A:5-110                                                                                   Pfam domains
         Sec.struct. author .....eeeeeeee.........eee..eeeeeeee.............hhhhhhhhhhhhhh........eeeeeeeeeeeeee.....eeeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------W------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------TGF_BETA_1      --------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 1zkz A   4 AGSHCQKTSLRVNFEDIGWDSWIIAPKEYEAYECKGGCFFPLADDVTPTKHAIVQTLVHLKFPTKVGKACCVPTKLSPISVLYKDDMGVPTLKYHYEGMSVAECGCR 110
                                    13        23        33        43        53        63        73        83        93       103       

   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, 1)

Asymmetric Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (43, 43)

Asymmetric Unit(hide GO term definitions)
Chain A   (GDF2_HUMAN | Q9UK05)
molecular function
    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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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:0032924    activin receptor signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to an activin receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0048514    blood vessel morphogenesis    The process in which the anatomical structures of blood vessels are generated and organized. The blood vessel is the vasculature carrying blood.
    GO:0001569    branching involved in blood vessel morphogenesis    The process of coordinated growth and sprouting of blood vessels giving rise to the organized vascular system.
    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:0006879    cellular iron ion homeostasis    Any process involved in the maintenance of an internal steady state of iron ions at the level of a cell.
    GO:0071773    cellular response to BMP stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a bone morphogenetic protein (BMP) stimulus.
    GO:0040007    growth    The increase in size or mass of an entire organism, a part of an organism or a cell.
    GO:2000279    negative regulation of DNA biosynthetic process    Any process that stops, prevents or reduces the frequency, rate or extent of DNA biosynthetic process.
    GO:0008156    negative regulation of DNA replication    Any process that stops, prevents, or reduces the frequency, rate or extent of DNA replication.
    GO:0016525    negative regulation of angiogenesis    Any process that stops, prevents, or reduces the frequency, rate or extent of angiogenesis.
    GO:0043537    negative regulation of blood vessel endothelial cell migration    Any process that stops, prevents, or reduces the frequency, rate or extent of the migration of the endothelial cells of blood vessels.
    GO:0030308    negative regulation of cell growth    Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth.
    GO:0010596    negative regulation of endothelial cell migration    Any process that decreases the rate, frequency, or extent of the orderly movement of an endothelial cell into the extracellular matrix to form an endothelium.
    GO:0001937    negative regulation of endothelial cell proliferation    Any process that stops, prevents, or reduces the rate or extent of endothelial cell proliferation.
    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:0060389    pathway-restricted SMAD protein phosphorylation    The process of introducing a phosphate group on to a pathway restricted SMAD protein. A pathway restricted SMAD protein is an effector protein that acts directly downstream of the transforming growth factor family receptor.
    GO:0030513    positive regulation of BMP signaling pathway    Any process that activates or increases the frequency, rate or extent of BMP signaling pathway activity.
    GO:0045766    positive regulation of angiogenesis    Any process that activates or increases angiogenesis.
    GO:0061036    positive regulation of cartilage development    Any process that increases the rate, frequency, or extent of cartilage development, the process whose specific outcome is the progression of the cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.
    GO:0045603    positive regulation of endothelial cell differentiation    Any process that activates or increases the frequency, rate or extent of endothelial cell differentiation.
    GO:0001938    positive regulation of endothelial cell proliferation    Any process that activates or increases the rate or extent of endothelial cell proliferation.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0032757    positive regulation of interleukin-8 production    Any process that activates or increases the frequency, rate, or extent of interleukin-8 production.
    GO:0045669    positive regulation of osteoblast differentiation    Any process that activates or increases the frequency, rate or extent of osteoblast differentiation.
    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:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    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:0001570    vasculogenesis    The differentiation of endothelial cells from progenitor cells during blood vessel development, and the de novo formation of blood vessels and tubes.
cellular component
    GO:0005623    cell    The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
    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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        GDF2_HUMAN | Q9UK054fao 4mpl 4ycg 4yci 5hzw 5i05

(-) Related Entries Specified in the PDB File

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