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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DYNAMIN 3 GTPASE DOMAIN BOUND WITH GDP
 
Authors :  S. Yang, W. Tempel, Y. Tong, L. Nedyalkova, X. Guan, L. Crombet, C. H. Arr A. M. Edwards, C. Bountra, J. Weigelt, A. Bochkarev, H. Park, Structur Genomics Consortium (Sgc)
Date :  18 Dec 09  (Deposition) - 19 Jan 10  (Release) - 11 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.27
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Structural Genomics Consortium, Sgc, Cytoskeleton, Endocytosis, Gtp- Binding, Hydrolase, Microtubule, Motor Protein, Nucleotide-Binding, Phosphoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Yang, W. Tempel, Y. Tong, L. Nedyalkova, X. Guan, L. Crombet, C. H. Arrowsmith, A. M. Edwards, C. Bountra, J. Weigelt, A. Bochkarev, H. Park
Crystal Structure Of The Dynamin 3 Gtpase Domain Bound With Gdp
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DYNAMIN-3
    ChainsA, B, C, D
    EC Number3.6.5.5
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21-V2R-PRARE2
    Expression System Taxid511693
    GeneDNM3, KIAA0820
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDYNAMIN, T-DYNAMIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A  D
Biological Unit 2 (1x) BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1GDP4Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2UNX6Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2UNX4Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2UNX2Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:41 , ALA A:42 , GLY A:43 , LYS A:44 , SER A:45 , SER A:46 , ARG A:59 , LYS A:206 , ASP A:208 , LEU A:209 , ASN A:236 , ARG A:237 , SER A:238 , GLN A:239 , ILE A:242 , HOH A:1003 , ASP D:211BINDING SITE FOR RESIDUE GDP A 901
2AC2SOFTWARESER B:41 , ALA B:42 , GLY B:43 , LYS B:44 , SER B:45 , SER B:46 , ARG B:59 , LYS B:206 , ASP B:208 , LEU B:209 , VAL B:235 , ASN B:236 , ARG B:237 , SER B:238 , GLN B:239 , ILE B:242 , HOH B:1005 , HOH B:1011 , ASP C:211BINDING SITE FOR RESIDUE GDP B 901
3AC3SOFTWAREASP B:211 , SER C:41 , ALA C:42 , GLY C:43 , LYS C:44 , SER C:45 , SER C:46 , ARG C:59 , LYS C:206 , ASP C:208 , LEU C:209 , ASN C:236 , ARG C:237 , SER C:238 , GLN C:239 , ILE C:242BINDING SITE FOR RESIDUE GDP C 901
4AC4SOFTWAREASP A:211 , SER D:41 , ALA D:42 , GLY D:43 , LYS D:44 , SER D:45 , SER D:46 , ARG D:59 , LYS D:206 , ASP D:208 , LEU D:209 , ASN D:236 , ARG D:237 , SER D:238 , GLN D:239 , ILE D:242BINDING SITE FOR RESIDUE GDP D 901

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3L43)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3L43)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3L43)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_DYNAMIN_1PS00410 Dynamin-type guanine nucleotide-binding (G) domain signature.DYN3_HUMAN57-66
 
 
 
  4A:57-66
B:57-66
C:57-66
D:57-66
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_DYNAMIN_1PS00410 Dynamin-type guanine nucleotide-binding (G) domain signature.DYN3_HUMAN57-66
 
 
 
  2A:57-66
-
-
D:57-66
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_DYNAMIN_1PS00410 Dynamin-type guanine nucleotide-binding (G) domain signature.DYN3_HUMAN57-66
 
 
 
  2-
B:57-66
C:57-66
-

(-) Exons   (0, 0)

(no "Exon" information available for 3L43)

(-) 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:242
 aligned with DYN3_HUMAN | Q9UQ16 from UniProtKB/Swiss-Prot  Length:869

    Alignment length:254
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282    
           DYN3_HUMAN    33 QIAVVGGQSAGKSSVLENFVGRDFLPRGSGIVTRRPLVLQLVTSKAEYAEFLHCKGKKFTDFDEVRLEIEAETDRVTGMNKGISSIPINLRVYSPHVLNLTLIDLPGITKVPVGDQPPDIEYQIREMIMQFITRENCLILAVTPANTDLANSDALKLAKEVDPQGLRTIGVITKLDLMDEGTDARDVLENKLLPLRRGYVGVVNRSQKDIDGKKDIKAAMLAERKFFLSHPAYRHIADRMGTPHLQKVLNQQLT 286
               SCOP domains d3l43a_ A: automated matche    s                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....hhhhhhhhhhh......----.....eeeeeee....eeee.........hhhhhhhhhhhhhh--------.....eeeeeee.....eeeee..............hhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhh.....eeeeeehhhhh.....hhhhhh.........eee....hhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------G_DYNAMIN_---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l43 A  33 QIAVVGGQSAGKSSVLENFVGRDFLPR----VTRRPLVLQLITSKAEYAEFLHCKGKKFTDFDEVRLEIEAETD--------ISSIPINLRVYSPHVLNLTLIDLPGITKVPVGDQPPDIEYQIREMIMQFITRENCLILAVTPANTDLANSDALKLAKEVDPQGLRTIGVITKLDLMDEGTDARDVLENKLLPLRRGYVGVVNRSQKDIDGKKDIKAAMLAERKFFLSHPAYRHIADRMGTPHLQKVLNQQLT 286
                                    42        52      |  - |      72        82        92       102   |     -  |    122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282    
                                                     59   64                                       106      115                                                                                                                                                                           

Chain B from PDB  Type:PROTEIN  Length:246
 aligned with DYN3_HUMAN | Q9UQ16 from UniProtKB/Swiss-Prot  Length:869

    Alignment length:255
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281     
           DYN3_HUMAN    32 PQIAVVGGQSAGKSSVLENFVGRDFLPRGSGIVTRRPLVLQLVTSKAEYAEFLHCKGKKFTDFDEVRLEIEAETDRVTGMNKGISSIPINLRVYSPHVLNLTLIDLPGITKVPVGDQPPDIEYQIREMIMQFITRENCLILAVTPANTDLANSDALKLAKEVDPQGLRTIGVITKLDLMDEGTDARDVLENKLLPLRRGYVGVVNRSQKDIDGKKDIKAAMLAERKFFLSHPAYRHIADRMGTPHLQKVLNQQLT 286
               SCOP domains d3l43b_ B: automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhh......----.....eeeeeee....eeee.........hhhhhhhhhhhhhhhhh-----.....eeeeeee.....eeeee..............hhhhhhhhhhhhhhh...eeeeeeee...hhhhhhhhhhhhhhh.....eeeeeehhhhh.....hhhhhh.........eee....hhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------G_DYNAMIN_---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l43 B  32 PQIAVVGGQSAGKSSVLENFVGRDFLPR----VTRRPLVLQLITSKAEYAEFLHCKGKKFTDFDEVRLEIEAETDRVT-----ISSIPINLRVYSPHVLNLTLIDLPGITKVPVGDQPPDIEYQIREMIMQFITRENCLILAVTPANTDLANSDALKLAKEVDPQGLRTIGVITKLDLMDEGTDARDVLENKLLPLRRGYVGVVNRSQKDIDGKKDIKAAMLAERKFFLSHPAYRHIADRMGTPHLQKVLNQQLT 286
                                    41        51       | -  |     71        81        91       101       | -   |   121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281     
                                                      59   64                                          109   115                                                                                                                                                                           

Chain C from PDB  Type:PROTEIN  Length:238
 aligned with DYN3_HUMAN | Q9UQ16 from UniProtKB/Swiss-Prot  Length:869

    Alignment length:251
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282 
           DYN3_HUMAN    33 QIAVVGGQSAGKSSVLENFVGRDFLPRGSGIVTRRPLVLQLVTSKAEYAEFLHCKGKKFTDFDEVRLEIEAETDRVTGMNKGISSIPINLRVYSPHVLNLTLIDLPGITKVPVGDQPPDIEYQIREMIMQFITRENCLILAVTPANTDLANSDALKLAKEVDPQGLRTIGVITKLDLMDEGTDARDVLENKLLPLRRGYVGVVNRSQKDIDGKKDIKAAMLAERKFFLSHPAYRHIADRMGTPHLQKVLNQ 283
               SCOP domains d3l43c_ C: automated matche     s                                                                                                                                                                                                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....hhhhhhhhhhh......-----....eeeeeee....eeee.........hhhhhhhhhhhhh.--------.....eeeeeee.....eeeee..............hhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhh.....eeeeeehhhhh.....hhhhhh.........eee....hhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------G_DYNAMIN_------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l43 C  33 QIAVVGGQSAGKSSVLENFVGRDFLPR-----TRRPLVLQLITSKAEYAEFLHCKGKKFTDFDEVRLEIEAETD--------ISSIPINLRVYSPHVLNLTLIDLPGITKVPVGDQPPDIEYQIREMIMQFITRENCLILAVTPANTDLANSDALKLAKEVDPQGLRTIGVITKLDLMDEGTDARDVLENKLLPLRRGYVGVVNRSQKDIDGKKDIKAAMLAERKFFLSHPAYRHIADRMGTPHLQKVLNQ 283
                                    42        52      |  -  |     72        82        92       102   |     -  |    122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282 
                                                     59    65                                      106      115                                                                                                                                                                        

Chain D from PDB  Type:PROTEIN  Length:239
 aligned with DYN3_HUMAN | Q9UQ16 from UniProtKB/Swiss-Prot  Length:869

    Alignment length:252
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282  
           DYN3_HUMAN    33 QIAVVGGQSAGKSSVLENFVGRDFLPRGSGIVTRRPLVLQLVTSKAEYAEFLHCKGKKFTDFDEVRLEIEAETDRVTGMNKGISSIPINLRVYSPHVLNLTLIDLPGITKVPVGDQPPDIEYQIREMIMQFITRENCLILAVTPANTDLANSDALKLAKEVDPQGLRTIGVITKLDLMDEGTDARDVLENKLLPLRRGYVGVVNRSQKDIDGKKDIKAAMLAERKFFLSHPAYRHIADRMGTPHLQKVLNQQ 284
               SCOP domains d3l43d_ D: automated matche     s                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -Dynamin_N-3l43D01 D:34-207                                                                                                                                                    --------Dynamin_M-3l43D05 D:216-284                                           Pfam domains (1)
           Pfam domains (2) -Dynamin_N-3l43D02 D:34-207                                                                                                                                                    --------Dynamin_M-3l43D06 D:216-284                                           Pfam domains (2)
           Pfam domains (3) -Dynamin_N-3l43D03 D:34-207                                                                                                                                                    --------Dynamin_M-3l43D07 D:216-284                                           Pfam domains (3)
           Pfam domains (4) -Dynamin_N-3l43D04 D:34-207                                                                                                                                                    --------Dynamin_M-3l43D08 D:216-284                                           Pfam domains (4)
         Sec.struct. author .eeee.....hhhhhhhhhhh......-----....eeeeeee....eeee......ee.hhhhhhhhhhhhhh--------.....eeeeeee.....eeeee..............hhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhh.....eeeeeehhhhh.....hhhhhh.........eee....hhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------G_DYNAMIN_-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3l43 D  33 QIAVVGGQSAGKSSVLENFVGRDFLPR-----TRRPLVLQLITSKAEYAEFLHCKGKKFTDFDEVRLEIEAETD--------ISSIPINLRVYSPHVLNLTLIDLPGITKVPVGDQPPDIEYQIREMIMQFITRENCLILAVTPANTDLANSDALKLAKEVDPQGLRTIGVITKLDLMDEGTDARDVLENKLLPLRRGYVGVVNRSQKDIDGKKDIKAAMLAERKFFLSHPAYRHIADRMGTPHLQKVLNQQ 284
                                    42        52      |  -  |     72        82        92       102   |     -  |    122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282  
                                                     59    65                                      106      115                                                                                                                                                                         

   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, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3L43)

(-) Pfam Domains  (2, 8)

Asymmetric Unit

(-) Gene Ontology  (28, 28)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (DYN3_HUMAN | Q9UQ16)
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:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0050998    nitric-oxide synthase binding    Interacting selectively and non-covalently with the enzyme nitric-oxide synthase.
    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:0031798    type 1 metabotropic glutamate receptor binding    Interacting selectively and non-covalently with a type 1 metabotropic glutamate receptor.
    GO:0031802    type 5 metabotropic glutamate receptor binding    Interacting selectively and non-covalently with a type 5 metabotropic glutamate receptor.
biological process
    GO:0006897    endocytosis    A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
    GO:0046847    filopodium assembly    The assembly of a filopodium, a thin, stiff protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal growth cone.
    GO:0061002    negative regulation of dendritic spine morphogenesis    Any process that decreases the rate, frequency, or extent of dendritic spine morphogenesis, the process in which the anatomical structures of a dendritic spine are generated and organized. A dendritic spine is a protrusion from a dendrite and a specialized subcellular compartment involved in synaptic transmission.
    GO:0051491    positive regulation of filopodium assembly    Any process that activates or increases the frequency, rate or extent of the assembly of a filopodium, a thin, stiff protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal growth cone.
    GO:0061001    regulation of dendritic spine morphogenesis    Any process that modulates the rate, frequency, or extent of dendritic spine morphogenesis, the process in which the anatomical structures of a dendritic spine are generated and organized. A dendritic spine is a protrusion from a dendrite and a specialized subcellular compartment involved in synaptic transmission.
    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:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    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:0043197    dendritic spine    A small, membranous protrusion from a dendrite that forms a postsynaptic compartment - typically receiving input from a single presynapse. They function as partially isolated biochemical and an electrical compartments. Spine morphology is variable including "thin", "stubby", "mushroom", and "branched", with a continuum of intermediate morphologies. They typically terminate in a bulb shape, linked to the dendritic shaft by a restriction. Spine remodeling is though to be involved in synaptic plasticity.
    GO:0044327    dendritic spine head    Distal part of the dendritic spine, that carries the post-synaptic density.
    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:0005874    microtubule    Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    GO:0001917    photoreceptor inner segment    The inner segment of a vertebrate photoreceptor containing mitochondria, ribosomes and membranes where opsin molecules are assembled and passed to be part of the outer segment discs.
    GO:0014069    postsynaptic density of dendrite    An electron dense network of proteins within and adjacent to the postsynaptic membrane of the dendrite of asymetric synapses. Its major components include neurotransmitter receptors and the proteins that spatially and functionally organize them such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components.
    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:0043083    synaptic cleft    The narrow gap that separates the presynaptic and postsynaptic membranes, into which neurotransmitter is released.

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