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(-) Description

Title :  DYNAMIC BINDING MODE OF A SYNAPTOTAGMIN-1-SNARE COMPLEX IN SOLUTION
 
Authors :  K. Brewer, T. Bacaj, A. Cavalli, C. Camilloni, J. Swarbrick, J. Liu, A. Z P. Zhou, N. Barlow, J. Xu, A. Seven, E. Prinslow, R. Voleti, D. Haussing A. Bonvin, D. Tomchick, M. Vendruscolo, B. Graham, T. Sudhof, J. Rizo
Date :  21 Apr 15  (Deposition) - 03 Jun 15  (Release) - 22 Jul 15  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B,C,D,E  (5x)
NMR Structure *:  A,B,C,D,E  (1x)
Keywords :  Synaptotagmin-1, C2B Domain, Syntaxin-1A, Synaptobrevin-2, Snap-25, Snap-25A, Snare Complex, Exocytosis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. D. Brewer, T. Bacaj, A. Cavalli, C. Camilloni, J. D. Swarbrick, J. Liu, A. Zhou, P. Zhou, N. Barlow, J. Xu, A. B. Seven, E. A. Prinslow, R. Voleti, D. Haussinger, A. M. Bonvin, D. R. Tomchick, M. Vendruscolo B. Graham, T. C. Sudhof, J. Rizo
Dynamic Binding Mode Of A Synaptotagmin-1-Snare Complex In Solution.
Nat. Struct. Mol. Biol. V. 22 555 2015
PubMed-ID: 26030874  |  Reference-DOI: 10.1038/NSMB.3035

(-) Compounds

Molecule 1 - VESICLE-ASSOCIATED MEMBRANE PROTEIN 2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-KT
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 25-93
    Gene: SYB2, VAMP2
    Organism Common: BROWN RAT,RAT,RATS
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: VAMP-2, SYNAPTOBREVIN-2
 
Molecule 2 - SYNTAXIN-1A
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-KT
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 188-259
    Gene: SAP, STX1A
    Organism Common: BROWN RAT,RAT,RATS
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: NEURON-SPECIFIC ANTIGEN HPC-1, SYNAPTOTAGMIN-ASSOCIATED 35 KDA PROTEIN, P35A
 
Molecule 3 - SYNAPTOSOMAL-ASSOCIATED PROTEIN 25
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-KT
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DOMAIN (UNP RESIDUES 7-83)
    Gene: SNAP, SNAP25, SNAP-25A
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SNAP-25, SNAP-25A, SUPER PROTEIN, SUP, SYNAPTOSOMAL- ASSOCIATED 25 KDA PROTEIN
 
Molecule 4 - SYNAPTOSOMAL-ASSOCIATED PROTEIN 25
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-KT
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN (UNP RESIDUES 131-204)
    Gene: SNAP, SNAP25, SNAP-25A
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SNAP-25, SNAP-25A, SUPER PROTEIN, SUP, SYNAPTOSOMAL- ASSOCIATED 25 KDA PROTEIN
 
Molecule 5 - SYNAPTOTAGMIN-1
    Chains: E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-KT
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: C2B DOMAIN (UNP RESIDUES 272-419)
    Gene: SVP65, SYT, SYT1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SYNAPTOTAGMIN I, SYTI, P65

 Structural Features

(-) Chains, Units

  12345
NMR Structure (5x): ABCDE
NMR Structure * (1x): ABCDE

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2N1T)

(-) Sites  (0, 0)

(no "Site" information available for 2N1T)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2N1T)

(-) Cis Peptide Bonds  (1, 1)

NMR Structure
No.Residues
1Leu E:307 -Ser E:308

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2N1T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2N1T)

(-) Exons   (0, 0)

(no "Exon" information available for 2N1T)

(-) 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:69
                                                                                                     
               SCOP domains --------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                 2n1t A  25 NLTSNRRLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKLKRKYWWKNL  93
                                    34        44        54        64        74        84         


Chain B from PDB  Type:PROTEIN  Length:72
                                                                                                        
               SCOP domains ------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                 2n1t B 188 SKQALSEIETRHSEIIKLENSIRELHDMFMDMAMLVESQGEMIDRIEYNVEHAVDYVERAVSDTKKAVKYQS 259
                                   197       207       217       227       237       247       257  


Chain C from PDB  Type:PROTEIN  Length:77
                                                                                                             
               SCOP domains ----------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                 2n1t C   7 MRNELEEMQRRADQLADESLESTRRMLQLVEESKDAGIRTLVMLDEQGEQLDRVEEGMNHINQDMKEAEKNLKDLGK  83
                                    16        26        36        46        56        66        76       


Chain D from PDB  Type:PROTEIN  Length:74
                                                                                                          
               SCOP domains -------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 2n1t D 131 GGFIRRVTNDARENEMDENLEQVSGIIGNLRHMALDMGNEIDTQNRQIDRIMEKADSNKTRIDEANQRATKMLG 204
                                   140       150       160       170       180       190       200    


Chain E from PDB  Type:PROTEIN  Length:156
                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhh....eeeeeeee.....eeeeeeeeee.............eeeeeeee..eeeeeee..........eeeeeeeee.hhhhhh.eeeeeeee.........eeeeeeee...hhhhhhhhhhhhhh......eeee..hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2n1t E 263 SGGGGGILEKLGDICFSLRYVPTAGKLTVVILEAKNLKKMDVGGLSDPYVKIHLMQNGKRLKKKKTTIKKNTLNPYYNESFSFEVPFEQIQKVQVVVTVLDYDKIGKNDAIGKVFVGYNSTGAELRHWSDMLANPRRPIAQWHTLQVEEEVDAMLA 418
                                   272       282       292       302       312       322       332       342       352       362       372       382       392       402       412
   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 2N1T)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2N1T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2N1T)

(-) Gene Ontology  (130, 208)

NMR Structure(hide GO term definitions)

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  Sites
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  Cis Peptide Bonds
    Leu E:307 - Ser E:308   [ RasMol ]  
 

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  STX1A_RAT | P32851
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  SYT1_HUMAN | P21579
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  VAMP2_RAT | P63045
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 Related Entries

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

UniProtKB/Swiss-Prot
        SNP25_HUMAN | P60880: 1kil 1uee 1urq 1xtg 3dda 3ddb 3rk2 3rk3 3rl0 3zur
        STX1A_RAT | P32851: 1br0 1ez3 1hvv 1jth 1kil 1n7s 1sfc 1urq 2bu0 2m8r 3c98 3hd7 3ipd 3j96 3j97 3j98 3j99 3rk2 3rk3 3rl0 4jeh 4jeu 5ccg 5cch 5cci 5kj7 5kj8
        SYT1_HUMAN | P21579: 2k45 2k4a 2k8m 2ki6 2lha 2r83 3f00 3f01 3f04 3f05 4isq 4v11
        VAMP2_RAT | P63045: 1kil 1n7s 1sfc 2bu0 2kog 3hd7 3ipd 3j96 3j97 3j98 3j99 5ccg 5cch 5cci

(-) Related Entries Specified in the PDB File

5194 SYNAPTOTAGMIN-1 C2B DOMAIN
6235 SNARE COMPLEX
1sfc CRYSTAL STRUCTURE OF A SNARE COMPLEX, ONE OF THE STARTING STRUCTURES FOR THE MD SIMULATIONS IN THIS STUDY.
1uow CRYSTAL STRUCTURE OF SYNAPTOTAGMIN-1 C2B DOMAIN, ONE OF THE STARTING STRUCTURES FOR THE MD SIMULATIONS IN THIS STUDY.