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(-) Description

Title :  CRYSTAL STRUCTURE OF THE UBIQUITIN-LIKE DOMAIN OF PLEXIN D1
 
Authors :  Y. Tong, L. Nedyalkova, W. Tempel, F. Mackenzie, C. H. Arrowsmith, A. M. Edwards, C. Bountra, J. Weigelt, A. Bochkarev, M. Buck, H. Park, Structural Genomics Consortium (Sgc)
Date :  23 Apr 09  (Deposition) - 19 May 09  (Release) - 19 May 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Structural Genomics Consortium, Sgc, Membrane, Transmembrane, Receptor, Alternative Splicing, Cell Membrane, Glycoprotein, Polymorphism, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Tong, L. Nedyalkova, W. Tempel, F. Mackenzie, C. H. Arrowsmith, A. M. Edwards, C. Bountra, J. Weigelt, A. Bochkarev, M. Buck, H. Park
Crystal Structure Of The Ubiquitin-Like Domain Of Plexin D1
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PLEXIN-D1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28-MHL
    Expression System StrainBL21(DE3)-V2R-PRARE2
    Expression System Taxid562
    FragmentUBIQUITIN-LIKE DOMAIN (UNP RESIDUES 1553-1678)
    GenePLXND1, KIAA0620
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1ARS2Ligand/IonARSENIC
2MSE3Mod. Amino AcidSELENOMETHIONINE
3UNX1Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1ARS4Ligand/IonARSENIC
2MSE6Mod. Amino AcidSELENOMETHIONINE
3UNX2Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:1592BINDING SITE FOR RESIDUE ARS A 1
2AC2SOFTWARECYS A:1565BINDING SITE FOR RESIDUE ARS A 2

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3H6N)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3H6N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3H6N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3H6N)

(-) Exons   (0, 0)

(no "Exon" information available for 3H6N)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:104
 aligned with PLXD1_HUMAN | Q9Y4D7 from UniProtKB/Swiss-Prot  Length:1925

    Alignment length:104
                                  1562      1572      1582      1592      1602      1612      1622      1632      1642      1652    
         PLXD1_HUMAN   1553 AKPRNLNVSFQGCGMDSLSVRAMDTDTLTQVKEKILEAFCKNVPYSQWPRAEDVDLEWFASSTQSYILRDLDDTSVVEDGRKKLNTLAHYKIPEGASLAMSLID 1656
               SCOP domains -------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee......eeeeee...hhhhhhhhhhhhhh...hhhhh.hhh.eeeeee.....eee.........ee..ee..............eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                3h6n A 1553 AKPRNLNVSFQGCGmDSLSVRAmDTDTLTQVKEKILEAFCKNVPYSQWPRAEDVDLEWFASSTQSYILRDLDDTSVVEDGRKKLNTLAHYKIPEGASLAmSLID 1656
                                  1562    | 1572  |   1582      1592      1602      1612      1622      1632      1642      1652    
                                       1567-MSE   |                                                                         1652-MSE
                                               1575-MSE                                                                             

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  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  (0, 0)

(no "SCOP Domain" information available for 3H6N)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3H6N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3H6N)

(-) Gene Ontology  (27, 27)

Asymmetric Unit(hide GO term definitions)
Chain A   (PLXD1_HUMAN | Q9Y4D7)
molecular function
    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:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
    GO:0017154    semaphorin receptor activity    Combining with a semaphorin, and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity.
biological process
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0035904    aorta development    The progression of the aorta over time, from its initial formation to the mature structure. An aorta is an artery that carries blood from the heart to other parts of the body.
    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:0021785    branchiomotor neuron axon guidance    The process in which a branchiomotor neuron growth cone is directed to a specific target site. Branchiomotor neurons are located in the hindbrain and innervate branchial arch-derived muscles that control jaw movements, facial expression, the larynx, and the pharynx.
    GO:0003279    cardiac septum development    The progression of a cardiac septum over time, from its initial formation to the mature structure.
    GO:0060976    coronary vasculature development    The process whose specific outcome is the progression of the blood vessels of the heart over time, from its formation to the mature structure.
    GO:0060666    dichotomous subdivision of terminal units involved in salivary gland branching    The process in which a salivary epithelial cord bifurcates at its end.
    GO:0043542    endothelial cell migration    The orderly movement of an endothelial cell into the extracellular matrix to form an endothelium.
    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:0003151    outflow tract morphogenesis    The process in which the anatomical structures of the outflow tract are generated and organized. The outflow tract is the portion of the heart through which blood flows into the arteries.
    GO:0032092    positive regulation of protein binding    Any process that activates or increases the frequency, rate or extent of protein binding.
    GO:0045765    regulation of angiogenesis    Any process that modulates the frequency, rate or extent of angiogenesis.
    GO:0048841    regulation of axon extension involved in axon guidance    Any process that modulates the frequency, rate or extent of axon extension involved in axon guidance.
    GO:0030334    regulation of cell migration    Any process that modulates the frequency, rate or extent of cell migration.
    GO:0071526    semaphorin-plexin signaling pathway    A series of molecular signals generated as a consequence of a semaphorin receptor (composed of a plexin and a neurophilin) binding to a semaphorin ligand.
    GO:1902287    semaphorin-plexin signaling pathway involved in axon guidance    Any semaphorin-plexin signaling pathway that is involved in axon guidance.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0007416    synapse assembly    The aggregation, arrangement and bonding together of a set of components to form a synapse. This process ends when the synapse is mature (functional).
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0030027    lamellipodium    A thin sheetlike process extended by the leading edge of a migrating cell or extending cell process; contains a dense meshwork of actin filaments.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0002116    semaphorin receptor complex    A stable binary complex of a neurophilin and a plexin, together forming a functional semaphorin receptor.

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