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(-) Description

Title :  1.5A CRYSTAL STRUCTURE OF THE NOGO RECEPTOR LIGAND BINDING DOMAIN REVEALS A CONVERGENT RECOGNITION SCAFFOLD MEDIATING INHIBITION OF MYELINATION
 
Authors :  X. He, J. F. Bazan, J. B. Park, G. Mcdermott, Z. He, K. C. Garcia
Date :  09 Apr 03  (Deposition) - 20 May 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.52
Chains :  Asym./Biol. Unit :  A
Keywords :  Nogo Receptor, Mad, Myelination Inhibition, Omgp, Mag, Nogo-66, P75, Signal Transduction, Neuronal Regeneration, Ligand Binding, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. L. He, J. F. Bazan, G. Mcdermott, J. B. Park, K. Wang, M. Tessier-Lavigne, Z. He, K. C. Garcia
Structure Of The Nogo Receptor Ectodomain. A Recognition Module Implicated In Myelin Inhibition.
Neuron V. 38 177 2003
PubMed-ID: 12718853  |  Reference-DOI: 10.1016/S0896-6273(03)00232-0

(-) Compounds

Molecule 1 - RETICULON 4 RECEPTOR
    ChainsA
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System CommonCABBAGE LOOPER
    Expression System PlasmidPACGP67A
    Expression System StrainHI5
    Expression System Taxid7111
    Expression System Vector TypeBACULOVIRUS
    FragmentLIGAND BINDING DOMAIN
    GeneRTN4R OR NOGOR
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNOGO RECEPTOR, NGR, NOGO-66 RECEPTOR

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 10)

Asymmetric/Biological Unit (5, 10)
No.NameCountTypeFull Name
1ACY3Ligand/IonACETIC ACID
2BMA1Ligand/IonBETA-D-MANNOSE
3MAN2Ligand/IonALPHA-D-MANNOSE
4NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
5NDG3Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:45 , ALA A:58 , ARG A:81 , ASN A:82 , ASN A:304 , NDG A:402 , HOH A:675 , HOH A:702 , HOH A:719BINDING SITE FOR RESIDUE NDG A 401
02AC2SOFTWAREGLN A:45 , GLN A:46 , NDG A:401 , MAN A:403 , MAN A:404 , HOH A:505BINDING SITE FOR RESIDUE NDG A 402
03AC3SOFTWAREVAL A:32 , LEU A:289 , NDG A:402 , MAN A:404 , HOH A:573 , HOH A:720BINDING SITE FOR RESIDUE MAN A 403
04AC4SOFTWAREVAL A:263 , ASP A:265 , LEU A:289 , PRO A:290 , GLN A:307 , NDG A:402 , MAN A:403BINDING SITE FOR RESIDUE MAN A 404
05AC5SOFTWAREASP A:122 , ALA A:154 , ALA A:155 , ASN A:179 , NDG A:406 , HOH A:628 , HOH A:689 , HOH A:691 , HOH A:695BINDING SITE FOR RESIDUE NAG A 405
06AC6SOFTWAREALA A:98 , ASP A:122 , NAG A:405 , BMA A:407BINDING SITE FOR RESIDUE NDG A 406
07AC7SOFTWAREALA A:99 , NDG A:406 , HOH A:651BINDING SITE FOR RESIDUE BMA A 407
08AC8SOFTWAREPRO A:290 , ARG A:292 , GLN A:307 , HOH A:466BINDING SITE FOR RESIDUE ACY A 1
09AC9SOFTWAREGLN A:49 , ALA A:50 , ARG A:269 , HOH A:581BINDING SITE FOR RESIDUE ACY A 2
10BC1SOFTWAREGLN A:49 , ARG A:68 , GLY A:308 , HOH A:572 , HOH A:701BINDING SITE FOR RESIDUE ACY A 3

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:27 -A:33
2A:31 -A:43
3A:264 -A:287
4A:266 -A:309

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:36 -Pro A:37
2Leu A:289 -Pro A:290

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1OZN)

(-) PROSITE Motifs  (1, 6)

Asymmetric/Biological Unit (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LRRPS51450 Leucine-rich repeat profile.RTN4R_HUMAN82-103
106-128
155-176
179-200
203-224
227-248
  6A:82-103
A:106-128
A:155-176
A:179-200
A:203-224
A:227-248

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.5aENST000000434025aENSE00001358408chr22:20256054-20255594461RTN4R_HUMAN1-880--
1.8eENST000000434028eENSE00001557601chr22:20230633-202289381696RTN4R_HUMAN8-4734661A:26-309284

(-) 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:284
 aligned with RTN4R_HUMAN | Q9BZR6 from UniProtKB/Swiss-Prot  Length:473

    Alignment length:284
                                    35        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    
          RTN4R_HUMAN    26 PCPGACVCYNEPKVTTSCPQQGLQAVPVGIPAASQRIFLHGNRISHVPAASFRACRNLTILWLHSNVLARIDAAAFTGLALLEQLDLSDNAQLRSVDPATFHGLGRLHTLHLDRCGLQELGPGLFRGLAALQYLYLQDNALQALPDDTFRDLGNLTHLFLHGNRISSVPERAFRGLHSLDRLLLHQNRVAHVHPHAFRDLGRLMTLYLFANNLSALPTEALAPLRALQYLRLNDNPWVCDCRARPLWAWLQKFRGSSSEVPCSLPQRLAGRDLKRLAANDLQGC 309
               SCOP domains d1ozna_ A: Reticulon 4 receptor (Nogo-66 receptor, Ngr)                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1oznA00 A:26-309 Ribonuclease Inhibitor                                                                                                                                                                                                                                                      CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LRR_8-1oznA01 A:202-261                                     ------------------------------------------------ Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LRR_8-1oznA02 A:202-261                                     ------------------------------------------------ Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LRR_8-1oznA03 A:202-261                                     ------------------------------------------------ Pfam domains (3)
         Sec.struct. author ......eee.....eee..................eee.......ee............eee.......ee............eee......................eee.....................eee.....................eee.......ee............eee.......ee............eee.........hhhhhh......eee.....ee.hhhhhhhhhhhhhh..ee....eeehhhhh..hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------LRR  PDB: A:82-103    --LRR  PDB: A:106-128    --------------------------LRR  PDB: A:155-176   --LRR  PDB: A:179-200   --LRR  PDB: A:203-224   --LRR  PDB: A:227-248   ------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.8e  PDB: A:26-309 UniProt: 8-473 [INCOMPLETE]                                                                                                                                                                                                                                         Transcript 1
                 1ozn A  26 PCPGACVCYNEPKVTTSCPQQGLQAVPVGIPAASQRIFLHGNRISHVPAASFRACRNLTILWLHSNVLARIDAAAFTGLALLEQLDLSDNAQLRSVDPATFHGLGRLHTLHLDRCGLQELGPGLFRGLAALQYLYLQDNALQALPDDTFRDLGNLTHLFLHGNRISSVPERAFRGLHSLDRLLLHQNRVAHVHPHAFRDLGRLMTLYLFANNLSALPTEALAPLRALQYLRLNDNPWVCDCRARPLWAWLQKFRGSSSEVPCSLPQRLAGRDLKRLAANDLQGC 309
                                    35        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    

   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/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: LRR (77)
(-)
Family: LRR_8 (41)
1aLRR_8-1oznA01A:202-261
1bLRR_8-1oznA02A:202-261
1cLRR_8-1oznA03A:202-261

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RTN4R_HUMAN | Q9BZR6)
molecular function
    GO:0038131    neuregulin receptor activity    Combining with a neuregulin, a member of the EGF family of growth factors, and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity.
    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:0004860    protein kinase inhibitor activity    Stops, prevents or reduces the activity of a protein kinase, an enzyme which phosphorylates a protein.
    GO:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
biological process
    GO:0007409    axonogenesis    De novo generation of a long process of a neuron, that carries efferent (outgoing) action potentials from the cell body towards target cells. Refers to the morphogenesis or creation of shape or form of the developing axon.
    GO:0019221    cytokine-mediated signaling pathway    A series of molecular signals initiated by the binding of a cytokine to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0046426    negative regulation of JAK-STAT cascade    Any process that stops, prevents, or reduces the frequency, rate or extent of the JAK-STAT signaling pathway activity.
    GO:0030517    negative regulation of axon extension    Any process that stops, prevents, or reduces the frequency, rate or extent of axon outgrowth.
    GO:0050771    negative regulation of axonogenesis    Any process that stops, prevents, or reduces the frequency, rate or extent of axonogenesis.
    GO:0006469    negative regulation of protein kinase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity.
    GO:0023041    neuronal signal transduction    The process in which an activated neuronal cell receptor conveys information down a signaling pathway, resulting in a change in the function or state of a cell. This process may be intracellular or intercellular.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
cellular component
    GO:0031225    anchored component of membrane    The component of a membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
    GO:0044295    axonal growth cone    The migrating motile tip of a growing nerve cell axon.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    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:0030426    growth cone    The migrating motile tip of a growing nerve cell axon or dendrite.
    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:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    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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 Related Entries

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

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        RTN4R_HUMAN | Q9BZR61p8t

(-) Related Entries Specified in the PDB File

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