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(-) Description

Title :  MOUSE PLEXIN A2, EXTRACELLULAR DOMAINS 1-4
 
Authors :  B. J. C. Janssen, R. A. Robinson, C. H. Bell, C. Siebold, E. Y. Jones
Date :  25 Aug 10  (Deposition) - 13 Oct 10  (Release) - 02 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Transmembrane, Receptor, Sema-Domain, Cell-Cell Signalling, Semaphorin-6A, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. J. Janssen, R. A. Robinson, F. Perez-Branguli, C. H. Bell, K. J. Mitchell, C. Siebold, E. Y. Jones
Structural Basis Of Semaphorin-Plexin Signalling.
Nature V. 467 1118 2010
PubMed-ID: 20877282  |  Reference-DOI: 10.1038/NATURE09468

(-) Compounds

Molecule 1 - PLEXIN-A2
    ChainsA
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHEK293
    Expression System CommonHUMAN
    Expression System PlasmidPHLSEC
    Expression System Taxid9606
    FragmentRESIDUES 33-703, EXTRACELLULAR DOMAINS 1-4
    GenePLXNA2, KIAA0463
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymPLEXIN-2, PLEX 2

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric Unit (4, 12)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2GOL4Ligand/IonGLYCEROL
3NA1Ligand/IonSODIUM ION
4NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (2, 9)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL4Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION
4NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (2, 18)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL8Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION
4NAG10Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:74 , GLY A:75 , ASN A:76 , THR A:78BINDING SITE FOR RESIDUE NAG A 1076
02AC2SOFTWARELYS A:92 , ASN A:163BINDING SITE FOR RESIDUE NAG A 1163
03AC3SOFTWAREASN A:327BINDING SITE FOR RESIDUE NAG A 1327
04AC4SOFTWAREASN A:598BINDING SITE FOR RESIDUE NAG A 1598
05AC5SOFTWAREILE A:624 , ASN A:655 , SER A:657 , ALA A:658 , GLN A:660BINDING SITE FOR RESIDUE NAG A 1655
06AC6SOFTWAREGLN A:345 , TYR A:346 , HIS A:347 , ALA A:549 , HOH A:2151BINDING SITE FOR RESIDUE CL A 2001
07AC7SOFTWAREARG A:459BINDING SITE FOR RESIDUE CL A 2002
08AC8SOFTWAREASP A:273 , ASN A:550BINDING SITE FOR RESIDUE NA A 2003
09AC9SOFTWAREILE A:118 , ILE A:119 , GLY A:170 , VAL A:171 , ILE A:172 , GOL A:2005 , HOH A:2186BINDING SITE FOR RESIDUE GOL A 2004
10BC1SOFTWARETHR A:54 , LEU A:117 , ILE A:118 , ILE A:119 , GOL A:2004BINDING SITE FOR RESIDUE GOL A 2005
11BC2SOFTWAREHIS A:348 , PRO A:349 , ASP A:351 , ASN A:587 , HOH A:2148BINDING SITE FOR RESIDUE GOL A 2006
12BC3SOFTWAREARG A:459 , GLY A:524BINDING SITE FOR RESIDUE GOL A 2007

(-) SS Bonds  (14, 14)

Asymmetric Unit
No.Residues
1A:94 -A:103
2A:129 -A:137
3A:284 -A:405
4A:300 -A:356
5A:374 -A:393
6A:511 -A:528
7A:517 -A:559
8A:520 -A:537
9A:531 -A:543
10A:594 -A:613
11A:656 -A:672
12A:662 -A:701
13A:665 -A:681
14A:675 -A:688

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Gly A:86 -Pro A:87
2Tyr A:95 -Pro A:96
3Ser A:237 -His A:238
4Gln A:411 -Pro A:412
5Pro A:463 -Pro A:464
6His A:565 -Pro A:566

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3OKT)

(-) 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:656
 aligned with PLXA2_MOUSE | P70207 from UniProtKB/Swiss-Prot  Length:1894

    Alignment length:667
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       
          PLXA2_MOUSE    36 PQYSTFHSENRDWTFNHLTVHRRTGAVYVGAINRVYKLTGNLTIQVAHKTGPEEDNKACYPPLIVQPCSEVLTLTNNVNKLLIIDYSENRLLACGSLYQGVCKLLRLDDLFILVEPSHKKEHYLSSVNKTGTMYGVIVRSEGEDGKLFIGTAVDGKQDYFPTLSSRKLPRDPESSAMLDYELHSDFVSSLIKIPSDTLALVSHFDIFYIYGFASGGFVYFLTVQPETPDGMAINSAGDLFYTSRIVRLCKDDPKFHSYVSLPFGCTRAGVEYRLLQAAYLAKPGEALAQAFNISSDEDVLFAIFSKGQKQYHHPPDDSALCAFPIRAINLQIKERLQSCYHGEGNLELNWLLGKDVQCTKAPVPIDDNFCGLDINQPLGGSTPVEGLTLYTTSRDRLTSVASYVYNGYSVVFVGTKSGKLKKIRADGPPHGGVQYEMVSVFKDGSPILRDMAFSINQLYLYVMSERQVTRVPVESCEQYTTCGECLSSGDPHCGWCALHNMCSRRDKCQRAWEANRFAASISQCMSLEVHPNSISVSDHSRLLSLVVNDAPNLSEGIACAFGNLTEVEGQVSGSQVICISPGPKDVPVIPLDQDWFGLELQLRSKETGKIFVSTEFKFYNCSAHQLCLSCVNSAFRCHWCKYRNLCTHDPTTCSFQEGRINVSEDCP 702
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------Sema-3oktA03 A:50-491                                                                                                                                                                                                                                                                                                                                                                                                                                     ---------------------------------------------------------------------------------------------------------------------------------------  --------------------------PSI-3oktA01 A:655-702                            Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PSI-3oktA02 A:655-702                            Pfam domains (2)
         Sec.struct. author ...eeee.......eeeeee......eeeee..eeeee.....eeeeee...eee.................eee...eeeeeeehhh.eeeeee.hhhh.eeeee.....eee....hhhhh.........eeeeee.......eeeeee...........eeeee......................ee..hhhhhhhh.....eeeeeeee..eeeeeeeee...---------...eeeeeeeee.........eeeeeeeee..eeeeeeeeeeee..hhhhhhhhh......eeeeeeee...........eeeeeeehhhhhhhhhhhhhhhh.......hhhhhh..............................ee.eeeeee....eeeeeeeee..eeeeeeee...eeeeeee......eeeeeeee............ee.....eeeee...eeeeee..hhhhh.hhhhhh.......eee....eeehhhhh........ee.hhhhh.eeeee..eee......eeeeeee........eeeee...eeee.eee..eeeee............--.eeeeeeeeee.....eeeeeeeeee.hhhh.hhhhhhh.....eee....eee.hhhhh.hhh.ee.hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3okt A  36 PQYSTFHSENRDWTFNHLTVHRRTGAVYVGAINRVYKLTGNLTIQVAHKTGPEEDNKACYPPLIVQPCSEVLTLTNNVNKLLIIDYSENRLLACGSLYQGVCKLLRLDDLFILVEPSHKKEHYLSSVNKTGTMYGVIVRSEGEDGKLFIGTAVDGKQDYFPTLSSRKLPRDPESSAMLDYELHSDFVSSLIKIPSDTLALVSHFDIFYIYGFASGGFVYFLTVQPETP---------DLFYTSRIVRLCKDDPKFHSYVSLPFGCTRAGVEYRLLQAAYLAKPGEALAQAFNISSDEDVLFAIFSKGQKQYHHPPDDSALCAFPIRAINLQIKERLQSCYHGEGNLELNWLLGKDVQCTKAPVPIDDNFCGLDINQPLGGSTPVEGLTLYTTSRDRLTSVASYVYNGYSVVFVGTKSGKLKKIRADGPPHGGVQYEMVSVFKDGSPILRDMAFSINQLYLYVMSERQVTRVPVESCEQYTTCGECLSSGDPHCGWCALHNMCSRRDKCQRAWEANRFAASISQCMSLEVHPNSISVSDHSRLLSLVVNDAPNLSEGIACAFGNLTEVEGQVSGSQVICISPGPKDVPVIPL--DWFGLELQLRSKETGKIFVSTEFKFYNCSAHQLCLSCVNSAFRCHWCKYRNLCTHDPTTCSFQEGRINVSEDCP 702
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       | -       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625|  |   635       645       655       665       675       685       695       
                                                                                                                                                                                                                                                             263       273                                                                                                                                                                                                                                                                                                                                                              626  |                                                                         
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           629                                                                         

   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 3)

Asymmetric Unit
(-)
Family: PSI (9)
1aPSI-3oktA01A:655-702
1bPSI-3oktA02A:655-702

(-) Gene Ontology  (19, 19)

Asymmetric Unit(hide GO term definitions)
Chain A   (PLXA2_MOUSE | P70207)
molecular function
    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: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:0007166    cell surface receptor signaling pathway    A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0051642    centrosome localization    Any process in which a centrosome is transported to, and/or maintained in, a specific location within the cell.
    GO:0021935    cerebellar granule cell precursor tangential migration    The early migration of granule cell precursors in which cells move orthogonal to the direction of radial migration and ultimately cover the superficial zone of the cerebellar primordium.
    GO:0060174    limb bud formation    The process pertaining to the initial formation of a limb bud from unspecified parts. This process begins with the formation of a local condensation of mesenchyme cells within the prospective limb field, and ends when a limb bud is recognizable.
    GO:0021915    neural tube development    The process whose specific outcome is the progression of the neural tube over time, from its formation to the mature structure. The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium.
    GO:0060037    pharyngeal system development    The process whose specific outcome is the progression of the pharyngeal system over time, from its formation to the mature structure. The pharyngeal system is a transient embryonic complex that is specific to vertebrates. It comprises the pharyngeal arches, bulges of tissues of mesoderm and neural crest derivation through which pass nerves and pharyngeal arch arteries. The arches are separated internally by pharyngeal pouches, evaginations of foregut endoderm, and externally by pharyngeal clefts, invaginations of surface ectoderm. The development of the system ends when the stucture it contributes to are forming: the thymus, thyroid, parathyroids, maxilla, mandible, aortic arch, cardiac outflow tract, external and middle ear.
    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:0001756    somitogenesis    The formation of mesodermal clusters that are arranged segmentally along the anterior posterior axis of an embryo.
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: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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 Related Entries

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

UniProtKB/Swiss-Prot
        PLXA2_MOUSE | P702073al8 3al9 3oky 4gza 5l5g 5l74

(-) Related Entries Specified in the PDB File

3okw 3oky