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(-) Description

Title :  CRYSTAL STRUCTURE OF BETA-NEUREXIN 1 WITH THE SPLICE INSERT 4
 
Authors :  X. Jin, L. Shapiro
Date :  05 May 10  (Deposition) - 28 Jul 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.69
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Neurexin, Lns Domain, Calcium-Binding, Cell Adhesion, Glycoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Koehnke, P. S. Katsamba, G. Ahlsen, F. Bahna, J. Vendome, B. Honig, L. Shapiro, X. Jin
Splice Form Dependence Of Beta-Neurexin/Neuroligin Binding Interactions.
Neuron V. 67 61 2010
PubMed-ID: 20624592  |  Reference-DOI: 10.1016/J.NEURON.2010.06.001

(-) Compounds

Molecule 1 - NEUREXIN-1-ALPHA
    ChainsA, B
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHEK293
    Expression System CommonHUMAN
    Expression System Taxid9606
    FragmentUNP RESIDUES 1132 TO 1334
    GeneNRXN1, KIAA0578
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymNEUREXIN I-ALPHA

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
3PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
3PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
3PO4-1Ligand/IonPHOSPHATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:181 , ASN A:184 , TRP A:226 , LEU A:228 , NAG A:292 , BMA A:293 , HOH A:319BINDING SITE FOR RESIDUE NAG A 291
2AC2SOFTWAREHOH A:35 , NAG A:291 , HOH A:319BINDING SITE FOR RESIDUE NAG A 292
3AC3SOFTWARETRP A:226 , NAG A:291BINDING SITE FOR RESIDUE BMA A 293
4AC4SOFTWARELYS A:91 , ARG A:105 , SER A:132 , SER A:133BINDING SITE FOR RESIDUE PO4 A 1
5AC5SOFTWAREASN B:103 , SER B:181 , GLY B:182 , ASN B:184 , TRP B:226 , NAG B:292 , BMA B:293BINDING SITE FOR RESIDUE NAG B 291
6AC6SOFTWAREHOH B:13 , ASN B:103 , NAG B:291BINDING SITE FOR RESIDUE NAG B 292
7AC7SOFTWAREVAL A:222 , TRP B:226 , NAG B:291BINDING SITE FOR RESIDUE BMA B 293

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3MW2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3MW2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3MW2)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LAM_G_DOMAINPS50025 Laminin G domain profile.NRX1A_MOUSE30-217
283-480
487-679
725-898
912-1087
1133-1331
 
  2-
-
-
-
-
A:87-285
B:87-285
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LAM_G_DOMAINPS50025 Laminin G domain profile.NRX1A_MOUSE30-217
283-480
487-679
725-898
912-1087
1133-1331
 
  1-
-
-
-
-
A:87-285
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LAM_G_DOMAINPS50025 Laminin G domain profile.NRX1A_MOUSE30-217
283-480
487-679
725-898
912-1087
1133-1331
 
  1-
-
-
-
-
-
B:87-285

(-) Exons   (0, 0)

(no "Exon" information available for 3MW2)

(-) 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:195
 aligned with NRX1A_MOUSE | Q9CS84 from UniProtKB/Swiss-Prot  Length:1514

    Alignment length:205
                                  1139      1149      1159      1169      1179      1189      1199      1209      1219      1229      1239      1249      1259      1269      1279      1289      1299      1309      1319      1329     
         NRX1A_MOUSE   1130 GTTYIFSKGGGQITYKWPPNDRPSTRADRLAIGFSTVQKEAVLVRVDSSSGLGDYLELHIHQGKIGVKFNVGTDDIAIEESNAIINDGKYHVVRFTRSGGNATLQVDSWPVIERYPAGNNDNERLAIARQRIPYRLGRVVDEWLLDKGRQLTIFNSQATIIIGGKEQGQPFQGQLSGLYYNGLKVLNMAAENDANIAIVGNVRLV 1334
               SCOP domains d3mw2a_ A: automated matches                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................................................................................................................----------.......................................hhhhh...............hhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---LAM_G_DOMAIN  PDB: A:87-285 UniProt: 1133-1331                                                                                                                                                         --- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3mw2 A   84 GSTYIFSKGGGQITYKWPPNDRPSTRADRLAIGFSTVQKEAVLVRVDSSSGLGDYLELHIHQGKIGVKFNVGTDDIAIEESNAIINDGKYHVVRFTRSGGNATLQVDSWPVIER----------LAIARQRIPYRLGRVVDEWLLDKGRQLTIFNSQATIIIGGKEQGQPFQGQLSGLYYNGLKVLNMAAENDANIAIVGNVRLV  288
                                    93       103       113       123       133       143       153       163       173       183       193   |     -    |  213       223       233       243       253       263       273       283     
                                                                                                                                           197        208                                                                                

Chain B from PDB  Type:PROTEIN  Length:198
 aligned with NRX1A_MOUSE | Q9CS84 from UniProtKB/Swiss-Prot  Length:1514

    Alignment length:205
                                  1139      1149      1159      1169      1179      1189      1199      1209      1219      1229      1239      1249      1259      1269      1279      1289      1299      1309      1319      1329     
         NRX1A_MOUSE   1130 GTTYIFSKGGGQITYKWPPNDRPSTRADRLAIGFSTVQKEAVLVRVDSSSGLGDYLELHIHQGKIGVKFNVGTDDIAIEESNAIINDGKYHVVRFTRSGGNATLQVDSWPVIERYPAGNNDNERLAIARQRIPYRLGRVVDEWLLDKGRQLTIFNSQATIIIGGKEQGQPFQGQLSGLYYNGLKVLNMAAENDANIAIVGNVRLV 1334
               SCOP domains d3mw2b_ B: automated matches                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------Laminin_G_2-3mw2B01 B:117-266                                                                                                                         ---------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------Laminin_G_2-3mw2B02 B:117-266                                                                                                                         ---------------------- Pfam domains (2)
         Sec.struct. author .................hhhhh.............................................................................................-------.........................................hhhhh................hhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---LAM_G_DOMAIN  PDB: B:87-285 UniProt: 1133-1331                                                                                                                                                         --- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3mw2 B   84 GSTYIFSKGGGQITYKWPPNDRPSTRADRLAIGFSTVQKEAVLVRVDSSSGLGDYLELHIHQGKIGVKFNVGTDDIAIEESNAIINDGKYHVVRFTRSGGNATLQVDSWPVIERY-------ERLAIARQRIPYRLGRVVDEWLLDKGRQLTIFNSQATIIIGGKEQGQPFQGQLSGLYYNGLKVLNMAAENDANIAIVGNVRLV  288
                                    93       103       113       123       133       143       153       163       173       183       193    |    -  |    213       223       233       243       253       263       273       283     
                                                                                                                                            198     206                                                                                  

   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, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MW2)

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (41, 41)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NRX1A_MOUSE | Q9CS84)
molecular function
    GO:0033130    acetylcholine receptor binding    Interacting selectively and non-covalently with an acetylcholine receptor.
    GO:0005246    calcium channel regulator activity    Modulates the activity of a calcium channel.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0050839    cell adhesion molecule binding    Interacting selectively and non-covalently with a cell adhesion molecule.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0097109    neuroligin family protein binding    Interacting selectively and non-covalently with a member of the neuroligin protein family, neuronal cell surface proteins that mediate synapse formation.
    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).
biological process
    GO:0030534    adult behavior    Behavior in a fully developed and mature organism.
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0007268    chemical synaptic transmission    The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.
    GO:0097116    gephyrin clustering involved in postsynaptic density assembly    The clustering process in which gephyrin molecules are localized to distinct domains in the postsynaptic density as part of postsynaptic density assembly. Gephyrin is a component of the postsynaptic protein network of inhibitory synapses.
    GO:0007612    learning    Any process in an organism in which a relatively long-lasting adaptive behavioral change occurs as the result of experience.
    GO:0097118    neuroligin clustering involved in postsynaptic membrane assembly    The receptor clustering process involved in assembly of the postsynaptic membrane in which neuroligins are localized to distinct domains in the cell membrane. Neuroligins are neuronal cell surface proteins on the postsynaptic membrane that mediate synapse formation between neurons.
    GO:0050885    neuromuscular process controlling balance    Any process that an organism uses to control its balance, the orientation of the organism (or the head of the organism) in relation to the source of gravity. In humans and animals, balance is perceived through visual cues, the labyrinth system of the inner ears and information from skin pressure receptors and muscle and joint receptors.
    GO:0007269    neurotransmitter secretion    The regulated release of neurotransmitter from the presynapse into the synaptic cleft via calcium regualated exocytosis during synaptic transmission.
    GO:2000463    positive regulation of excitatory postsynaptic potential    Any process that enhances the establishment or increases the extent of the excitatory postsynaptic potential (EPSP) which is a temporary increase in postsynaptic potential due to the flow of positively charged ions into the postsynaptic cell. The flow of ions that causes an EPSP is an excitatory postsynaptic current (EPSC) and makes it easier for the neuron to fire an action potential.
    GO:0051965    positive regulation of synapse assembly    Any process that activates, maintains or increases the frequency, rate or extent of synapse assembly, the aggregation, arrangement and bonding together of a set of components to form a synapse.
    GO:0090129    positive regulation of synapse maturation    Any process that increases the extent of synapse maturation, the process that organizes a synapse so that it attains its fully functional state.
    GO:0051968    positive regulation of synaptic transmission, glutamatergic    Any process that activates, maintains or increases the frequency, rate or extent of glutamatergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter glutamate.
    GO:0097119    postsynaptic density protein 95 clustering    The clustering process in which postsynaptic density protein 95 (PSD-95) molecules are localized to distinct domains in the cell membrane. PSD-95 is mostly located in the post synaptic density of neurons, and is involved in anchoring synaptic proteins.
    GO:0097104    postsynaptic membrane assembly    The aggregation, arrangement and bonding together of a set of components to form a postsynaptic membrane, a specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft).
    GO:0060134    prepulse inhibition    The process in which a startle magnitude is reduced when the startling stimulus is preceded by a low-intensity prepulse.
    GO:2000821    regulation of grooming behavior    Any process that modulates the frequency, rate or extent of grooming behavior.
    GO:0061178    regulation of insulin secretion involved in cellular response to glucose stimulus    Any process that modulates the frequency, rate or extent of the regulated release of insulin that contributes to the response of a cell to glucose.
    GO:0035176    social behavior    Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group.
    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).
    GO:0006904    vesicle docking involved in exocytosis    The initial attachment of a vesicle membrane to a target membrane, mediated by proteins protruding from the membrane of the vesicle and the target membrane, that contributes to exocytosis.
    GO:0042297    vocal learning    A behavioral process whose outcome is a relatively long-lasting behavioral change whereby an organism modifies innate vocalizations to imitate sounds produced by others.
    GO:0071625    vocalization behavior    The behavior in which an organism produces sounds by a mechanism involving its respiratory system.
cellular component
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    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: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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    GO:0031965    nuclear membrane    Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
    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:0042734    presynaptic membrane    A specialized area of membrane of the axon terminal that faces the plasma membrane of the neuron or muscle fiber with which the axon terminal establishes a synaptic junction; many synaptic junctions exhibit structural presynaptic characteristics, such as conical, electron-dense internal protrusions, that distinguish it from the remainder of the axon plasma membrane.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
    GO:0045202    synapse    The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.
    GO:0031982    vesicle    Any small, fluid-filled, spherical organelle enclosed by membrane.

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        NRX1A_MOUSE | Q9CS843bod

(-) Related Entries Specified in the PDB File

3mw3 3mw4