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(-) Description

Title :  CRYSTAL STRUCTURE OF RAT SYNAPSIN I C DOMAIN COMPLEXED TO CA.ATP (FORM 1)
 
Authors :  C. A. Brautigam, Y. Chelliah, J. Deisenhofer
Date :  02 Jul 03  (Deposition) - 23 Mar 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.23
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Atp Binding, Atp Grasp, Calcium (Ii) Ion, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. A. Brautigam, Y. Chelliah, J. Deisenhofer
Tetramerization And Atp Binding By A Protein Comprising The A, B, And C Domains Of Rat Synapsin I.
J. Biol. Chem. V. 279 11948 2004
PubMed-ID: 14688264  |  Reference-DOI: 10.1074/JBC.M312015200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SYNAPSIN I
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPSYNABC
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPGEX
    Expression System Vector TypePLASMID
    FragmentA, B, & C DOMAINS
    GeneSYN1
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2CA2Ligand/IonCALCIUM ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1ATP4Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2CA-1Ligand/IonCALCIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:373 , GLU A:386 , ATP A:800BINDING SITE FOR RESIDUE CA A 817
2AC2SOFTWAREGLU B:373 , GLU B:386 , ATP B:800 , HOH B:883BINDING SITE FOR RESIDUE CA B 817
3AC3SOFTWARELYS A:225 , LYS A:269 , HIS A:274 , SER A:275 , GLY A:276 , LYS A:279 , GLU A:305 , PRO A:306 , PHE A:307 , ILE A:308 , LYS A:336 , LEU A:375 , GLU A:386 , CA A:817 , HOH A:832 , HOH A:905BINDING SITE FOR RESIDUE ATP A 800
4AC4SOFTWARELYS B:225 , ILE B:247 , VAL B:267 , LYS B:269 , ALA B:273 , HIS B:274 , SER B:275 , GLY B:276 , LYS B:279 , GLU B:305 , PRO B:306 , PHE B:307 , ILE B:308 , TRP B:335 , THR B:337 , GLU B:373 , LEU B:375 , ILE B:385 , GLU B:386 , CA B:817 , HOH B:857 , HOH B:863 , HOH B:883 , HOH B:916BINDING SITE FOR RESIDUE ATP B 800

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1PX2)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Val A:213 -Asn A:214
2Tyr A:264 -Pro A:265
3Val B:213 -Asn B:214
4Tyr B:264 -Pro B:265

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PX2)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SYNAPSIN_2PS00416 Synapsins signature 2.SYN1_RAT271-281
 
  2A:271-281
B:271-281
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SYNAPSIN_2PS00416 Synapsins signature 2.SYN1_RAT271-281
 
  4A:271-281
B:271-281

(-) Exons   (8, 16)

Asymmetric Unit (8, 16)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000142501ENSRNOE00000447489X:12512210-125122178SYN1_RAT1-330--
1.2ENSRNOT000000142502ENSRNOE00000097479X:12512244-1251230158SYN1_RAT3-22200--
1.3ENSRNOT000000142503ENSRNOE00000097614X:12512392-1251248392SYN1_RAT23-53310--
1.4ENSRNOT000000142504ENSRNOE00000097742X:12513717-12513873157SYN1_RAT53-105530--
1.5ENSRNOT000000142505ENSRNOE00000097879X:12515168-1251525790SYN1_RAT106-135302A:112-135
B:113-135
24
23
1.6ENSRNOT000000142506ENSRNOE00000098024X:12551213-1255127563SYN1_RAT136-156212A:136-156
B:136-156
21
21
1.7ENSRNOT000000142507ENSRNOE00000098221X:12552134-12552276143SYN1_RAT157-204482A:157-204
B:157-204
48
48
1.8ENSRNOT000000142508ENSRNOE00000098378X:12552359-1255243375SYN1_RAT204-229262A:204-229
B:204-229
26
26
1.9ENSRNOT000000142509ENSRNOE00000098563X:12552528-12552630103SYN1_RAT229-263352A:229-263
B:229-263
35
35
1.10ENSRNOT0000001425010ENSRNOE00000098754X:12553682-12553822141SYN1_RAT264-310472A:264-310
B:264-310
47
47
1.11ENSRNOT0000001425011ENSRNOE00000099054X:12554138-1255422588SYN1_RAT311-340302A:311-336 (gaps)
B:311-337 (gaps)
26
27
1.12bENSRNOT0000001425012bENSRNOE00000289921X:12554323-12554914592SYN1_RAT340-5371982A:344-417
B:344-417
74
74
1.13ENSRNOT0000001425013ENSRNOE00000209968X:12555820-12556160341SYN1_RAT537-581450--

(-) 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:294
 aligned with SYN1_RAT | P09951 from UniProtKB/Swiss-Prot  Length:704

    Alignment length:306
                                   121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411      
             SYN1_RAT   112 AARVLLVIDEPHTDWAKYFKGKKIHGEIDIKVEQAEFSDLNLVAHANGGFSVDMEVLRNGVKVVRSLKPDFVLIRQHAFSMARNGDYRSLVIGLQYAGIPSVNSLHSVYNFCDKPWVFAQMVRLHKKLGTEEFPLIDQTFYPNHKEMLSSTTYPVVVKMGHAHSGMGKVKVDNQHDFQDIASVVALTKTYATAEPFIDAKYDVRVQKIGQNYKAYMRTSVSGNWKTNTGSAMLEQIAMSDRYKLWVDTCSEIFGGLDICAVEALHGKDGRDHIIEVVGSSMPLIGDHQDEDKQLIVELVVNKMTQA 417
               SCOP domains d1px2a1 A:112-213 Synapsin I                                                                          d1px2a2 A:214-417 Synapsin                                                                                                                                                                                   SCOP domains
               CATH domains 1px2A02 A:112-214,A:394-406  [code=3.40.50.20, no name defined]                                        1px2A03 A:215-247,A:308-393      1px2A01 A:248-307 ATP-grasp fold, A domain                  1px2A03 A:215-247,A:30     8-       393 ATP-grasp fold, B domain                      1px2A02      ----------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhh..eehhheeeeeeeehhh.eeeeee....eeeeeeeee..eeeeeee...eeee............hhhhhhhhhhh...ee.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.....eee.hhhhh.......eeeee........eeee.hhhhhhhhhhhhhhhh..eeeee...eeeeeeeeee..eeeeeee.-----..-------.eee..hhhhhhhhhhhhhhhhh..eeeeeeeee....eeeeeee......hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------SYNAPSIN_2 ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5  PDB: A:112-135Exon 1.6             Exon 1.7  PDB: A:157-204 UniProt: 157-204       ------------------------Exon 1.9  PDB: A:229-263           Exon 1.10  PDB: A:264-310 UniProt: 264-310     Exon 1.11 UniProt: 311-340    ----------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------Exon 1.8  PDB: A:204-229  --------------------------------------------------------------------------------------------------------------Exon 1.12b  PDB: A:344-417 UniProt: 340-537 [INCOMPLETE]                       Transcript 1 (2)
                 1px2 A 112 AARVLLVIDEPHTDWAKYFKGKKIHGEIDIKVEQAEFSDLNLVAHANGGFSVDMEVLRNGVKVVRSLKPDFVLIRQHAFSMARNGDYRSLVIGLQYAGIPSVNSLHSVYNFCDKPWVFAQMVRLHKKLGTEEFPLIDQTFYPNHKEMLSSTTYPVVVKMGHAHSGMGKVKVDNQHDFQDIASVVALTKTYATAEPFIDAKYDVRVQKIGQNYKAYMRT-----WK-------LEQIAMSDRYKLWVDTCSEIFGGLDICAVEALHGKDGRDHIIEVVGSSMPLIGDHQDEDKQLIVELVVNKMTQA 417
                                   121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       | -   ||    -  |    351       361       371       381       391       401       411      
                                                                                                                                                                                                                                                   329   335|     344                                                                         
                                                                                                                                                                                                                                                          336                                                                                 

Chain B from PDB  Type:PROTEIN  Length:294
 aligned with SYN1_RAT | P09951 from UniProtKB/Swiss-Prot  Length:704

    Alignment length:305
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412     
             SYN1_RAT   113 ARVLLVIDEPHTDWAKYFKGKKIHGEIDIKVEQAEFSDLNLVAHANGGFSVDMEVLRNGVKVVRSLKPDFVLIRQHAFSMARNGDYRSLVIGLQYAGIPSVNSLHSVYNFCDKPWVFAQMVRLHKKLGTEEFPLIDQTFYPNHKEMLSSTTYPVVVKMGHAHSGMGKVKVDNQHDFQDIASVVALTKTYATAEPFIDAKYDVRVQKIGQNYKAYMRTSVSGNWKTNTGSAMLEQIAMSDRYKLWVDTCSEIFGGLDICAVEALHGKDGRDHIIEVVGSSMPLIGDHQDEDKQLIVELVVNKMTQA 417
               SCOP domains d1px2b1 B:113-213 Synapsin I                                                                         d1px2b2 B:214-417 Synapsin                                                                                                                                                                                   SCOP domains
               CATH domains 1px2B02 B:113-214,B:394-406  [code=3.40.50.20, no name defined]                                       1px2B03 B:215-247,B:308-393      1px2B01 B:248-307 ATP-grasp fold, A domain                  1px2B03 B:215-247,B:30     8-3      93 ATP-grasp fold, B domain                       1px2B02      ----------- CATH domains
           Pfam domains (1) Synapsin-1px2B03 B:113-212                                                                          -Synapsin_C-1px2B01 B:214-416                                                                                                                                                                               - Pfam domains (1)
           Pfam domains (2) Synapsin-1px2B04 B:113-212                                                                          -Synapsin_C-1px2B02 B:214-416                                                                                                                                                                               - Pfam domains (2)
         Sec.struct. author .eeeeee.....hhhhhhh..eehhheeeeeeeehhh.eeeeee....eeeeeeeee..eeeeeee...eeee............hhhhhhhhhhh...ee.hhhhhhhh.hhhhhhhhhhhhhhhhh.........eee.hhhhh.......eeeee........eeee.hhhhhhhhhhhhhhhh..eeeee...eeeeeeeeee..eeeeeee.-----...------.eee..hhhhhhhhhhhhhhhhh..eeeeeeeee....eeeeeee......hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------SYNAPSIN_2 ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5  PDB: B:113-13Exon 1.6             Exon 1.7  PDB: B:157-204 UniProt: 157-204       ------------------------Exon 1.9  PDB: B:229-263           Exon 1.10  PDB: B:264-310 UniProt: 264-310     Exon 1.11 UniProt: 311-340    ----------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------Exon 1.8  PDB: B:204-229  --------------------------------------------------------------------------------------------------------------Exon 1.12b  PDB: B:344-417 UniProt: 340-537 [INCOMPLETE]                       Transcript 1 (2)
                 1px2 B 113 ARVLLVIDEPHTDWAKYFKGKKIHGEIDIKVEQAEFSDLNLVAHANGGFSVDMEVLRNGVKVVRSLKPDFVLIRQHAFSMARNGDYRSLVIGLQYAGIPSVNSLHSVYNFCDKPWVFAQMVRLHKKLGTEEFPLIDQTFYPNHKEMLSSTTYPVVVKMGHAHSGMGKVKVDNQHDFQDIASVVALTKTYATAEPFIDAKYDVRVQKIGQNYKAYMRT-----WKT------LEQIAMSDRYKLWVDTCSEIFGGLDICAVEALHGKDGRDHIIEVVGSSMPLIGDHQDEDKQLIVELVVNKMTQA 417
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322      |  -  | |    - |     352       362       372       382       392       402       412     
                                                                                                                                                                                                                                                  329   335 |    344                                                                         
                                                                                                                                                                                                                                                          337                                                                                

   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  (2, 4)

Asymmetric Unit

(-) CATH Domains  (3, 6)

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

(-) Pfam Domains  (2, 4)

Asymmetric Unit

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SYN1_RAT | P09951)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    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:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
biological process
    GO:0007269    neurotransmitter secretion    The regulated release of neurotransmitter from the presynapse into the synaptic cleft via calcium regualated exocytosis during synaptic transmission.
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: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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0030425    dendrite    A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
    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:0043209    myelin sheath    An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.
    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: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: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:0000795    synaptonemal complex    A proteinaceous scaffold found between homologous chromosomes during meiosis. It consists of 2 lateral elements and a central element, all running parallel to each other. Transverse filaments connect the lateral elements to the central element.
    GO:0043195    terminal bouton    Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal bouton is a specialized region of it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SYN1_RAT | P099511pk8

(-) Related Entries Specified in the PDB File

1aux BOVINE SYNAPSIN I C DOMAIN COMPLEXED TO CA.ATP-GAMMA-S
1pk8 FORM 2 OF SAME STRUCTURE