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(-) Description

Title :  CRYSTAL STRUCTURE OF PLEXIN A2 RBD IN COMPLEX WITH RND1
 
Authors :  H. Wang, W. Tempel, Y. Tong, X. Guan, L. Shen, L. Buren, N. Zhang, A. K. Wer L. Crombet, C. H. Arrowsmith, A. M. Edwards, C. Bountra, J. Weigelt, H. Structural Genomics Consortium (Sgc)
Date :  21 Dec 10  (Deposition) - 12 Jan 11  (Release) - 12 Jan 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.97
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (4x)
Keywords :  Ras-Binding Domain, Plexin, Small Gtpase, Structural Genomics Consortium, Sgc, Membrane Protein-Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Wang, W. Tempel, Y. Tong, X. Guan, L. Shen, L. Buren, N. Zhang, A. K. Wernimont, L. Crombet, C. H. Arrowsmith, A. M. Edwards, C. Bountra, J. Weigelt, H. Park
Crystal Structure Of Plexin A2 Rbd In Complex With Rnd1
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PLEXIN-A2
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21-V2R-PRARE2
    Expression System Taxid511693
    FragmentUNP RESIDUES 1490-1600
    GenePLXNA2, KIAA0463, OCT, PLXN2, UNQ209/PRO235
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSEMAPHORIN RECEPTOR OCT
 
Molecule 2 - RHO-RELATED GTP-BINDING PROTEIN RHO6
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21-V2R-PRARE2
    Expression System Taxid511693
    FragmentUNP RESIDUES 5-200
    GeneRND1, RHO6
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRHO FAMILY GTPASE 1, RND1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (4x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
1GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG1Ligand/IonMAGNESIUM ION
3UNX9Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 1 (2, 40)
No.NameCountTypeFull Name
1GNP4Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
3UNX36Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL B:22 , GLN B:23 , CYS B:24 , GLY B:25 , LYS B:26 , THR B:27 , ALA B:28 , TYR B:38 , PRO B:39 , GLU B:40 , THR B:41 , TYR B:42 , THR B:45 , GLY B:70 , LYS B:126 , ASP B:128 , LEU B:129 , SER B:168 , ALA B:169 , PHE B:170 , MG B:201 , HOH B:218 , HOH B:224 , HOH B:225 , HOH B:228 , HOH B:232BINDING SITE FOR RESIDUE GNP B 500
2AC2SOFTWARETHR B:27 , THR B:45 , HOH B:224 , HOH B:225 , GNP B:500BINDING SITE FOR RESIDUE MG B 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3Q3J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3Q3J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_020188P44RRND1_HUMANPolymorphism2270577BP44R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_020188P44RRND1_HUMANPolymorphism2270577BP44R

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3Q3J)

(-) Exons   (5, 5)

Asymmetric Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003097391ENSE00001187861chr12:49259681-49259431251RND1_HUMAN1-40401B:13-4028
1.2ENST000003097392ENSE00001273828chr12:49258653-4925856688RND1_HUMAN41-70301B:41-70 (gaps)30
1.3ENST000003097393ENSE00001273819chr12:49255901-49255792110RND1_HUMAN70-106371B:70-10637
1.4ENST000003097394ENSE00001293879chr12:49254914-49254780135RND1_HUMAN107-151451B:107-15145
1.5ENST000003097395ENSE00001313310chr12:49252024-492509311094RND1_HUMAN152-232811B:152-18938

(-) 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:102
 aligned with PLXA2_HUMAN | O75051 from UniProtKB/Swiss-Prot  Length:1894

    Alignment length:111
                                  1499      1509      1519      1529      1539      1549      1559      1569      1579      1589      1599 
         PLXA2_HUMAN   1490 LIRQQIEYKTLILNCVNPDNENSPEIPVKVLNCDTITQVKEKILDAVYKNVPYSQRPRAVDMDLEWRQGRIARVVLQDEDITTKIEGDWKRLNTLMHYQVSDRSVVALVPK 1600
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Plexin_cytopl-3q3jA01 A:1490-1600                                                                               Pfam domains
         Sec.struct. author .........eeeeee..........eeeeee...hhhhhhhhhhhhhh.-----...hhh.eeeeeee...eeeee.........----....hhhhhh.....eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                3q3j A 1490 LIRQQIEYKTLILNCVNPDNENSPEIPVKVLNCDTITQVKEKILDAVYK-----QRPRAVDMDLEWRQGRIARVVLQDEDITTKI----KRLNTLMHYQVSDRSVVALVPK 1600
                                  1499      1509      1519      1529        |-    | 1549      1559      1569    | 1579      1589      1599 
                                                                         1538  1544                          1574 1579                     

Chain B from PDB  Type:PROTEIN  Length:175
 aligned with RND1_HUMAN | Q92730 from UniProtKB/Swiss-Prot  Length:232

    Alignment length:177
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       
          RND1_HUMAN     13 RCKLVLVGDVQCGKTAMLQVLAKDCYPETYVPTVFENYTACLETEEQRVELSLWDTSGSPYYDNVRPLCYSDSDAVLLCFDISRPETVDSALKKWRTEILDYCPSTRVLLIGCKTDLRTDLSTLMELSHQKQAPISYEQGCAIAKQLGAEIYLEGSAFTSEKSIHSIFRTASMLCLN  189
               SCOP domains d3q3jb_ B: automated matches                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --Ras-3q3jB01 B:15-189                                                                                                                                                            Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhh..........eeeeeeee..--..eeeeeeee..hhhhh.hhhhhh....eeeeeee...hhhhhhhhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------R------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: B:13-40      Exon 1.2  PDB: B:41-70 (gaps) ------------------------------------Exon 1.4  PDB: B:107-151 UniProt: 107-151    Exon 1.5  PDB: B:152-189 [INCOMPLETE]  Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------Exon 1.3  PDB: B:70-106              ----------------------------------------------------------------------------------- Transcript 1 (2)
                3q3j B   13 RCKLVLVGDVQCGKTAMLQVLAKDCYPETYVPTVFENYTACLET--QRVELSLWDTSGSPYYDNVRPLCYSDSDAVLLCFDISRPETVDSALKKWRTEILDYCPSTRVLLIGCKTDLRTDLSTLMELSHQKQAPISYEQGCAIAKQLGAEIYLEGSAFTSEKSIHSIFRTASMLCLN  189
                                    22        32        42        52   |  | 62        72        82        92       102       112       122       132       142       152       162       172       182       
                                                                      56 59                                                                                                                                  

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (1, 1)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3Q3J)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Family: Ras (176)

(-) Gene Ontology  (32, 35)

Asymmetric Unit(hide GO term definitions)
Chain A   (PLXA2_HUMAN | O75051)
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: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.

Chain B   (RND1_HUMAN | Q92730)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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: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.
biological process
    GO:0007015    actin filament organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments. Includes processes that control the spatial distribution of actin filaments, such as organizing filaments into meshworks, bundles, or other structures, as by cross-linking.
    GO:0007162    negative regulation of cell adhesion    Any process that stops, prevents, or reduces the frequency, rate or extent of cell adhesion.
    GO:0016322    neuron remodeling    The developmentally regulated remodeling of neuronal projections such as pruning to eliminate the extra dendrites and axons projections set up in early stages of nervous system development.
    GO:0007264    small GTPase mediated signal transduction    Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
cellular component
    GO:0005912    adherens junction    A cell junction at which anchoring proteins (cadherins or integrins) extend through the plasma membrane and are attached to actin filaments.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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.

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        RND1_HUMAN | Q927302cls 2rex

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