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(-) Description

Title :  CRYSTAL STRUCTURE OF THE NEURONAL T-SNARE SYNTAXIN-1A
 
Authors :  J. C. Lerman, J. Robblee, R. Fairman, F. M. Hughson
Date :  09 May 00  (Deposition) - 07 Jun 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Three Helix Bundle, Endocytosis/Exocytosis Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. C. Lerman, J. Robblee, R. Fairman, F. M. Hughson
Structural Analysis Of The Neuronal Snare Protein Syntaxin-1A.
Biochemistry V. 39 8470 2000
PubMed-ID: 10913252  |  Reference-DOI: 10.1021/BI0003994
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SYNTAXIN-1A
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PLM1 T7 PROMOTER PLASMID
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DOMAIN
    Organ: BRAIN
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: SYNAPTOTAGMIN ASSOCIATED 35 KDA PROTEIN, P35A, NEURON-SPECIFIC ANTIGEN HPC-1

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1EZ3)

(-) Sites  (0, 0)

(no "Site" information available for 1EZ3)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1EZ3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1EZ3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1EZ3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1EZ3)

(-) Exons   (5, 15)

Asymmetric Unit (5, 15)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000496011ENSRNOE00000287178chr12:22765064-2276500461STX1A_RAT1-10100--
1.2ENSRNOT000000496012ENSRNOE00000361256chr12:22752097-2275202078STX1A_RAT11-36263A:26-36
B:27-36
C:26-36		11
10
11
1.3ENSRNOT000000496013ENSRNOE00000279130chr12:22751752-22751653100STX1A_RAT37-70343A:37-70
B:37-70
C:37-70		34
34
34
1.4ENSRNOT000000496014ENSRNOE00000343385chr12:22748087-2274801375STX1A_RAT70-95263A:70-95
B:70-95
C:70-95		26
26
26
1.5ENSRNOT000000496015ENSRNOE00000295520chr12:22747334-2274726174STX1A_RAT95-119253A:95-119
B:95-119
C:95-119		25
25
25
1.6ENSRNOT000000496016ENSRNOE00000302188chr12:22747159-22747051109STX1A_RAT120-156373A:120-149
B:120-150
C:120-149		30
31
30
1.7ENSRNOT000000496017ENSRNOE00000358330chr12:22746606-2274653374STX1A_RAT156-180250--
1.8ENSRNOT000000496018ENSRNOE00000316992chr12:22743199-22743062138STX1A_RAT181-226460--
1.9ENSRNOT000000496019ENSRNOE00000335636chr12:22739362-22739252111STX1A_RAT227-263370--
1.10ENSRNOT0000004960110ENSRNOE00000345574chr12:22738422-227371121311STX1A_RAT264-288250--

(-) 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:124
 aligned with STX1A_RAT | P32851 from UniProtKB/Swiss-Prot  Length:288

    Alignment length:124
                                    35        45        55        65        75        85        95       105       115       125       135       145    
            STX1A_RAT    26 RDRFMDEFFEQVEEIRGFIDKIAENVEEVKRKHSAILASPNPDEKTKEELEELMSDIKKTANKVRSKLKSIEQSIEQEEGLNRSSADLRIRKTQHSTLSRKFVEVMSEYNATQSDYRERCKGRI 149
               SCOP domains d1ez3a_ A: Syntaxin 1A N-terminal domain                                                                                     SCOP domains
               CATH domains 1ez3A00 A:26-149  [code=1.20.58.70, no name defined]                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2   Exon 1.3  PDB: A:37-70            ------------------------Exon 1.5  PDB: A:95-119  Exon 1.6  PDB: A:120-149       Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------Exon 1.4  PDB: A:70-95    ------------------------------------------------------ Transcript 1 (2)
                 1ez3 A  26 RDRFMDEFFEQVEEIRGFIDKIAENVEEVKRKHSAILASPNPDEKTKEELEELMSDIKKTANKVRSKLKSIEQSIEQEEGLNRSSADLRIRKTQHSTLSRKFVEVMSEYNATQSDYRERCKGRI 149
                                    35        45        55        65        75        85        95       105       115       125       135       145    


Chain B from PDB  Type:PROTEIN  Length:124
 aligned with STX1A_RAT | P32851 from UniProtKB/Swiss-Prot  Length:288

    Alignment length:124
                                    36        46        56        66        76        86        96       106       116       126       136       146    
            STX1A_RAT    27 DRFMDEFFEQVEEIRGFIDKIAENVEEVKRKHSAILASPNPDEKTKEELEELMSDIKKTANKVRSKLKSIEQSIEQEEGLNRSSADLRIRKTQHSTLSRKFVEVMSEYNATQSDYRERCKGRIQ 150
               SCOP domains d1ez3b_ B: Syntaxin 1A N-terminal domain                                                                                     SCOP domains
               CATH domains 1ez3B00 B:27-150  [code=1.20.58.70, no name defined]                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  Exon 1.3  PDB: B:37-70            ------------------------Exon 1.5  PDB: B:95-119  Exon 1.6  PDB: B:120-150        Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.4  PDB: B:70-95    ------------------------------------------------------- Transcript 1 (2)
                 1ez3 B  27 DRFMDEFFEQVEEIRGFIDKIAENVEEVKRKHSAILASPNPDEKTKEELEELMSDIKKTANKVRSKLKSIEQSIEQEEGLNRSSADLRIRKTQHSTLSRKFVEVMSEYNATQSDYRERCKGRIQ 150
                                    36        46        56        66        76        86        96       106       116       126       136       146    


Chain C from PDB  Type:PROTEIN  Length:124
 aligned with STX1A_RAT | P32851 from UniProtKB/Swiss-Prot  Length:288

    Alignment length:124
                                    35        45        55        65        75        85        95       105       115       125       135       145    
            STX1A_RAT    26 RDRFMDEFFEQVEEIRGFIDKIAENVEEVKRKHSAILASPNPDEKTKEELEELMSDIKKTANKVRSKLKSIEQSIEQEEGLNRSSADLRIRKTQHSTLSRKFVEVMSEYNATQSDYRERCKGRI 149
               SCOP domains d1ez3c_ C: Syntaxin 1A N-terminal domain                                                                                     SCOP domains
               CATH domains 1ez3C00 C:26-149  [code=1.20.58.70, no name defined]                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2   Exon 1.3  PDB: C:37-70            ------------------------Exon 1.5  PDB: C:95-119  Exon 1.6  PDB: C:120-149       Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------Exon 1.4  PDB: C:70-95    ------------------------------------------------------ Transcript 1 (2)
                 1ez3 C  26 RDRFMDEFFEQVEEIRGFIDKIAENVEEVKRKHSAILASPNPDEKTKEELEELMSDIKKTANKVRSKLKSIEQSIEQEEGLNRSSADLRIRKTQHSTLSRKFVEVMSEYNATQSDYRERCKGRI 149
                                    35        45        55        65        75        85        95       105       115       125       135       145
   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, 3)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 3)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1EZ3)

(-) Gene Ontology  (51, 51)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (STX1A_RAT | P32851)
molecular function
    GO:0043008    ATP-dependent 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) using energy from the hydrolysis of ATP.
    GO:0005484    SNAP receptor activity    Acting as a marker to identify a membrane and interacting selectively with one or more SNAREs on another membrane to mediate membrane fusion.
    GO:0000149    SNARE binding    Interacting selectively and non-covalently with a SNARE (soluble N-ethylmaleimide-sensitive factor attached protein receptor) protein.
    GO:0019855    calcium channel inhibitor activity    Stops, prevents, or reduces the activity of a calcium channel.
    GO:0048306    calcium-dependent 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), in the presence of calcium.
    GO:0019869    chloride channel inhibitor activity    Stops, prevents, or reduces the activity of a chloride channel.
    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:0019900    kinase binding    Interacting selectively and non-covalently with a kinase, any enzyme that catalyzes the transfer of a phosphate group.
    GO:0017022    myosin binding    Interacting selectively and non-covalently with any part of a myosin complex; myosins are any of a superfamily of molecular motor proteins that bind to actin and use the energy of ATP hydrolysis to generate force and movement along actin filaments.
    GO:0032028    myosin head/neck binding    Interacting selectively and non-covalently with the head/neck region of a myosin heavy chain.
    GO:0047485    protein N-terminus binding    Interacting selectively and non-covalently with a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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:0030674    protein binding, bridging    The binding activity of a molecule that brings together two or more protein molecules, or a protein and another macromolecule or complex, through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.
    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: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: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: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:0045956    positive regulation of calcium ion-dependent exocytosis    Any process that activates or increases the frequency, rate or extent of calcium ion-dependent exocytosis.
    GO:0033605    positive regulation of catecholamine secretion    Any process that activates or increases the frequency, rate or extent of the regulated release of a catecholamine.
    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:0045921    positive regulation of exocytosis    Any process that activates or increases the frequency, rate or extent of exocytosis.
    GO:0001956    positive regulation of neurotransmitter secretion    Any process that activates or increases the frequency, rate or extent of the regulated release of a neurotransmitter.
    GO:0010701    positive regulation of norepinephrine secretion    Any process that increases the frequency, rate or extent of the regulated release of norepinephrine.
    GO:0017157    regulation of exocytosis    Any process that modulates the frequency, rate or extent of exocytosis.
    GO:0010807    regulation of synaptic vesicle priming    Any process that modulates the frequency, rate or extent of synaptic vesicle priming. Synaptic vesicle priming is the formation of SNARE-containing complexes, bringing synaptic vesicle membrane and plasma membranes into close proximity and thereby facilitating membrane fusion.
    GO:0009629    response to gravity    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a gravitational stimulus.
    GO:0032940    secretion by cell    The controlled release of a substance by a cell.
    GO:0016081    synaptic vesicle docking    The initial (indirect) attachment of a synaptic vesicle membrane to the presynaptic active zone membrane, mediated by proteins protruding from the membrane and proteins of the presynaptic active zone cytoplasmic component. Synaptic vesicle tethering is the first step in this process.
    GO:0031629    synaptic vesicle fusion to presynaptic active zone membrane    Fusion of the membrane of a synaptic vesicle with the presynaptic active zone membrane, thereby releasing its cargo neurotransmitters into the synaptic cleft.
    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.
    GO:0016192    vesicle-mediated transport    A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
cellular component
    GO:0031201    SNARE complex    A protein complex involved in membrane fusion; a stable ternary complex consisting of a four-helix bundle, usually formed from one R-SNARE and three Q-SNAREs with an ionic layer sandwiched between hydrophobic layers. One well-characterized example is the neuronal SNARE complex formed of synaptobrevin 2, syntaxin 1a, and SNAP-25.
    GO:0042641    actomyosin    Any complex of actin, myosin, and accessory proteins.
    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:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    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:0043229    intracellular organelle    Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma 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: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: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:0030141    secretory granule    A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules.
    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:0008021    synaptic vesicle    A secretory organelle, typically 50 nm in diameter, of presynaptic nerve terminals; accumulates in high concentrations of neurotransmitters and secretes these into the synaptic cleft by fusion with the 'active zone' of the presynaptic plasma membrane.
    GO:0030672    synaptic vesicle membrane    The lipid bilayer surrounding a synaptic vesicle.
    GO:0070044    synaptobrevin 2-SNAP-25-syntaxin-1a complex    A SNARE complex that contains synaptobrevin 2 (VAMP2), SNAP-25, and syntaxin 1a (or orthologs thereof).
    GO:0070032    synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex    A SNARE complex that contains synaptobrevin 2 (VAMP2), SNAP-25, syntaxin 1a, and complexin I (or orthologs thereof).
    GO:0070033    synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex    A SNARE complex that contains synaptobrevin 2 (VAMP2), SNAP-25, syntaxin 1a, and complexin II (or orthologs thereof).
    GO:0008076    voltage-gated potassium channel complex    A protein complex that forms a transmembrane channel through which potassium ions may cross a cell membrane in response to changes in membrane potential.

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  STX1A_RAT | P32851
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 Related Entries

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

UniProtKB/Swiss-Prot
        STX1A_RAT | P32851: 1br0 1hvv 1jth 1kil 1n7s 1sfc 1urq 2bu0 2m8r 2n1t 3c98 3hd7 3ipd 3j96 3j97 3j98 3j99 3rk2 3rk3 3rl0 4jeh 4jeu 5ccg 5cch 5cci 5kj7 5kj8

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1EZ3)