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(-) Description

Title :  SOLUTION STRUCTURE OF RIM2 ZINC FINGER DOMAIN
 
Authors :  I. Dulubova, X. Lou, J. Lu, I. Huryeva, A. Alam, R. Schneggenburger, T. C. Sudhof, J. Rizo
Date :  21 Jun 05  (Deposition) - 16 Aug 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Zinc-Finger Domain, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  I. Dulubova, X. Lou, J. Lu, I. Huryeva, A. Alam, R. Schneggenburger, T. C. Sudhof, J. Rizo
A Munc13/Rim/Rab3 Tripartite Complex: From Priming To Plasticity?
Embo J. V. 24 2839 2005
PubMed-ID: 16052212  |  Reference-DOI: 10.1038/SJ.EMBOJ.7600753
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - REGULATING SYNAPTIC MEMBRANE EXOCYTOSIS PROTEIN 2
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPGEX-KT
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentZINC-FINGER DOMAIN, FYVE-TYPE, RESIDUES 83-142
    GeneRIMS2, RIM2
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymRAB3-INTERACTING MOLECULE 2, RIM 2

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

NMR Structure (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:92 , ILE A:94 , CYS A:95 , CYS A:116 , CYS A:119BINDING SITE FOR RESIDUE ZN A 292
2AC2SOFTWARECYS A:108 , CYS A:111 , CYS A:134 , CYS A:137BINDING SITE FOR RESIDUE ZN A 308

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2A20)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2A20)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2A20)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_FYVEPS50178 Zinc finger FYVE/FYVE-related type profile.RIMS2_RAT86-142  1A:86-142

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000507531ENSRNOE00000454594chr7:74757003-74757229227RIMS2_RAT1-59590--
1.4ENSRNOT000000507534ENSRNOE00000223871chr7:74862495-74862705211RIMS2_RAT59-129711A:83-12947
1.5ENSRNOT000000507535ENSRNOE00000223852chr7:74922056-74922366311RIMS2_RAT130-2331041A:130-14213
1.7ENSRNOT000000507537ENSRNOE00000245525chr7:75007836-75008761926RIMS2_RAT233-5423100--
1.8ENSRNOT000000507538ENSRNOE00000236412chr7:75022293-7502236068RIMS2_RAT542-564230--
1.10ENSRNOT0000005075310ENSRNOE00000309334chr7:75024249-75024368120RIMS2_RAT565-604400--
1.11ENSRNOT0000005075311ENSRNOE00000313303chr7:75026216-75026315100RIMS2_RAT605-638340--
1.12ENSRNOT0000005075312ENSRNOE00000342737chr7:75027291-75027414124RIMS2_RAT638-679420--
1.13ENSRNOT0000005075313ENSRNOE00000310460chr7:75029686-7502973247RIMS2_RAT679-695170--
1.14ENSRNOT0000005075314ENSRNOE00000300188chr7:75032477-75032589113RIMS2_RAT695-732380--
1.15ENSRNOT0000005075315ENSRNOE00000328054chr7:75038397-7503844448RIMS2_RAT733-748160--
1.16ENSRNOT0000005075316ENSRNOE00000236330chr7:75041602-75041732131RIMS2_RAT749-792440--
1.17ENSRNOT0000005075317ENSRNOE00000236358chr7:75048205-75048376172RIMS2_RAT792-849580--
1.18ENSRNOT0000005075318ENSRNOE00000236351chr7:75050571-75050724154RIMS2_RAT850-901520--
1.19ENSRNOT0000005075319ENSRNOE00000236324chr7:75081091-7508115969RIMS2_RAT901-924240--
1.20ENSRNOT0000005075320ENSRNOE00000236341chr7:75090877-75091033157RIMS2_RAT924-976530--
1.21ENSRNOT0000005075321ENSRNOE00000045881chr7:75092194-75092304111RIMS2_RAT976-1013380--
1.22ENSRNOT0000005075322ENSRNOE00000329316chr7:75098602-7509866766RIMS2_RAT1013-1035230--
1.23ENSRNOT0000005075323ENSRNOE00000046081chr7:75109786-75109965180RIMS2_RAT1035-1095610--
1.24ENSRNOT0000005075324ENSRNOE00000350038chr7:75110820-75110929110RIMS2_RAT1095-1132380--
1.25ENSRNOT0000005075325ENSRNOE00000359488chr7:75130866-7513090742RIMS2_RAT1132-1146150--
1.26ENSRNOT0000005075326ENSRNOE00000223420chr7:75139420-75139520101RIMS2_RAT1146-1179340--
1.28ENSRNOT0000005075328ENSRNOE00000248632chr7:75159578-75159750173RIMS2_RAT1180-1237580--
1.30ENSRNOT0000005075330ENSRNOE00000248608chr7:75196983-75197224242RIMS2_RAT1237-1318820--
1.32aENSRNOT0000005075332aENSRNOE00000248577chr7:75250727-75250868142RIMS2_RAT1318-1365480--
1.33ENSRNOT0000005075333ENSRNOE00000321148chr7:75268338-75268450113RIMS2_RAT1365-1403390--
1.34ENSRNOT0000005075334ENSRNOE00000248520chr7:75268763-75268864102RIMS2_RAT1403-1437350--
1.35ENSRNOT0000005075335ENSRNOE00000248504chr7:75270057-75270196140RIMS2_RAT1437-1483470--
1.36ENSRNOT0000005075336ENSRNOE00000045670chr7:75270633-752717711139RIMS2_RAT1484-1555720--

(-) Sequences/Alignments

NMR Structure
   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:60
 aligned with RIMS2_RAT | Q9JIS1 from UniProtKB/Swiss-Prot  Length:1555

    Alignment length:60
                                    92       102       112       122       132       142
            RIMS2_RAT    83 QEQKGDAPTCGICHKTKFADGCGHNCSYCQTKFCARCGGRVSLRSNKVMWVCNLCRKQQE 142
               SCOP domains ------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author .......................ee......ee....eeeee.....eeeeehhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---ZF_FYVE  PDB: A:86-142 UniProt: 86-142                    PROSITE
               Transcript 1 Exon 1.4  PDB: A:83-129 UniProt: 59-129        Exon 1.5      Transcript 1
                 2a20 A  83 QEQKGDAPTCGICHKTKFADGCGHNCSYCQTKFCARCGGRVSLRSNKVMWVCNLCRKQQE 142
                                    92       102       112       122       132       142

   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 2A20)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2A20)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2A20)

(-) Gene Ontology  (29, 29)

NMR Structure(hide GO term definitions)
Chain A   (RIMS2_RAT | Q9JIS1)
molecular function
    GO:0017137    Rab GTPase binding    Interacting selectively and non-covalently with Rab protein, any member of the Rab subfamily of the Ras superfamily of monomeric GTPases.
    GO:0044325    ion channel binding    Interacting selectively and non-covalently with one or more specific sites on an ion channel, a protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
    GO:0019933    cAMP-mediated signaling    Any intracellular signal transduction in which the signal is passed on within the cell via cyclic AMP (cAMP). Includes production of cAMP, and downstream effectors that further transmit the signal within the cell.
    GO:0017156    calcium ion regulated exocytosis    The release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle by fusion of the vesicle with the plasma membrane of a cell, induced by a rise in cytosolic calcium-ion levels.
    GO:0048791    calcium ion-regulated exocytosis of neurotransmitter    The release of a neurotransmitter into the synaptic cleft by exocytosis of synaptic vesicles, where the release step is dependent on a rise in cytosolic calcium ion levels.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0006887    exocytosis    A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell.
    GO:0030073    insulin secretion    The regulated release of proinsulin from secretory granules (B granules) in the B cells of the pancreas; accompanied by cleavage of proinsulin to form mature insulin.
    GO:0006886    intracellular protein transport    The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.
    GO:0006836    neurotransmitter transport    The directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Neurotransmitters are any chemical substance that is capable of transmitting (or inhibiting the transmission of) a nerve impulse from a neuron to another cell.
    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:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0097151    positive regulation of inhibitory postsynaptic potential    Any process that activates or increases the frequency, rate or extent of inhibitory postsynaptic potential (IPSP). IPSP is a temporary decrease in postsynaptic membrane potential due to the flow of negatively charged ions into the postsynaptic cell. The flow of ions that causes an IPSP is an inhibitory postsynaptic current (IPSC) and makes it more difficult for the neuron to fire an action potential.
    GO:0017157    regulation of exocytosis    Any process that modulates the frequency, rate or extent of exocytosis.
    GO:0042391    regulation of membrane potential    Any process that modulates the establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane.
    GO:0061669    spontaneous neurotransmitter secretion    Neurotransmitter secretion that occurs in the absence of the action of a secretagogue or a presynaptic action potential.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
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:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    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:0048786    presynaptic active zone    A specialized region of the plasma membrane and cell cortex of a presynaptic neuron; encompasses a region of the plasma membrane where synaptic vesicles dock and fuse, and a specialized cortical cytoskeletal matrix.
    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.

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 Related Entries

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

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        RIMS2_RAT | Q9JIS12bwq 2cjs

(-) Related Entries Specified in the PDB File

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