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(-) Description

Title :  STRUCTURE OF THE CA2+-BOUND RABPHILIN3A C2B- SNAP25 COMPLEX (C2 SPACE GROUP)
 
Authors :  C. Ferrer-Orta, N. Verdaguer
Date :  09 Aug 16  (Deposition) - 21 Jun 17  (Release) - 21 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G
Keywords :  Membrane Fusion, Snare Complex, Pip2, C2 Domain, Exocytosis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Ferrer-Orta, T. Coronado-Parra, M. D. Perez-Sanchez, C. Silva, D. Lopez-Martinez, J. Baltanas-Copado, J. C. Gomez-Fernandez, S. Corbalan-Garcia, N. Verdaguer
The Rabphilin 3A-Snap25 Interaction: A New Piece To The Synaptic Puzzle
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - RABPHILIN-3A
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Taxid: 511693
    Expression System Vector: PET28A
    Expression System Vector Type: PLASMID
    Gene: RPH3A
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: EXOPHILIN-1
 
Molecule 2 - SYNAPTOSOMAL-ASSOCIATED PROTEIN 25
    Chains: D, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Taxid: 511693
    Expression System Vector: PET28
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL HELIX
    Gene: SNAP25, SNAP
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: SNAP-25,SUPER PROTEIN,SUP,SYNAPTOSOMAL-ASSOCIATED 25 KDA PROTEIN,SNAP-25,SUPER PROTEIN,SUP,SYNAPTOSOMAL-ASSOCIATED 25 KDA PROTEIN
 
Molecule 3 - SYNAPTOSOMAL-ASSOCIATED PROTEIN 25
    Chains: E, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Taxid: 511693
    Expression System Vector: PET28
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL HELIX
    Gene: SNAP25, SNAP
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: SNAP-25,SUPER PROTEIN,SUP,SYNAPTOSOMAL-ASSOCIATED 25 KDA PROTEIN,SNAP-25,SUPER PROTEIN,SUP,SYNAPTOSOMAL-ASSOCIATED 25 KDA PROTEIN

 Structural Features

(-) Chains, Units

  1234567
Asymmetric/Biological Unit : ABCDEFG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 44)

Asymmetric/Biological Unit (4, 44)
No.NameCountTypeFull Name
1CA6Ligand/IonCALCIUM ION
2GOL9Ligand/IonGLYCEROL
3SO410Ligand/IonSULFATE ION
4UNK19Mod. Amino Acid

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:571 , ASP A:577 , ASP A:631 , TYR A:632 , ASP A:633 , SO4 A:703binding site for residue CA A 701
02AC2SOFTWAREMET A:570 , ASP A:571 , ASP A:631 , ASP A:633 , ASP A:639binding site for residue CA A 702
03AC3SOFTWAREASP A:571 , ASP A:577 , ASP A:633 , ILE A:634 , CA A:701binding site for residue SO4 A 703
04AC4SOFTWAREGLN A:554 , ILE A:558 , PHE A:611 , PHE A:612 , SO4 A:705 , ARG D:16 , GLN D:20binding site for residue SO4 A 704
05AC5SOFTWAREHIS A:594 , PHE A:612 , SO4 A:704 , ARG D:16binding site for residue SO4 A 705
06AC6SOFTWAREHIS A:617 , GLU D:55binding site for residue SO4 A 706
07AC7SOFTWAREASN A:677binding site for residue GOL A 707
08AC8SOFTWAREGLU A:653 , ARG A:671 , TRP A:672binding site for residue GOL A 708
09AC9SOFTWAREASP B:571 , ASP B:577 , ASP B:631 , TYR B:632 , ASP B:633binding site for residue CA B 701
10AD1SOFTWAREMET B:570 , ASP B:571 , ASP B:631 , ASP B:633 , ASP B:639binding site for residue CA B 702
11AD2SOFTWARETHR B:602 , LEU B:603 , ASN B:604binding site for residue SO4 B 703
12AD3SOFTWARESER B:637 , ASN B:638binding site for residue SO4 B 704
13AD4SOFTWAREASN A:677binding site for residue GOL B 705
14AD5SOFTWAREASP C:571 , ASP C:577 , ASP C:631 , TYR C:632 , ASP C:633 , CA C:702 , SO4 C:703binding site for residue CA C 701
15AD6SOFTWAREMET C:570 , ASP C:571 , ASP C:631 , ASP C:633 , ASP C:639 , CA C:701binding site for residue CA C 702
16AD7SOFTWAREASP C:571 , ASP C:577 , TYR C:632 , ASP C:633 , ILE C:634 , CA C:701binding site for residue SO4 C 703
17AD8SOFTWAREASN E:159 , MET E:163binding site for residue SO4 E 301
18AD9SOFTWAREASP F:51 , GLY F:54 , GLU F:55 , GLU G:170 , SO4 G:301binding site for residue SO4 F 101
19AE1SOFTWAREGOL F:103binding site for residue GOL F 102
20AE2SOFTWAREGOL F:102binding site for residue GOL F 103
21AE3SOFTWAREASP F:58 , SO4 F:101 , THR G:173binding site for residue SO4 G 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5LOB)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5LOB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5LOB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5LOB)

(-) Exons   (0, 0)

(no "Exon" information available for 5LOB)

(-) Sequences/Alignments

Asymmetric/Biological 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:138
                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeee....eeeeeeeeee............eeeeeee........eee..........eeeeeeee...........eeeeeee.......eeeeeeee.....hhhhhhhhhhhhh....eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5lob A 540 ERGKILVSLMYSTQQGGLIVGIIRCVHLAAMDANGYSDPFVKLWLKPDMGKKAKHKTQIKKKTLNPEFNEEFFYDIKHSDLAKKSLDISVWDYDIGKSNDYIGGCQLGISAKGERLKHWYECLKNKDKKIERWHQLQN 677
                                   549       559       569       579       589       599       609       619       629       639       649       659       669        


Chain B from PDB  Type:PROTEIN  Length:139
                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee....eeeeeeeeee............eeeeeee........eee..........eeeeeeeee.........eeeeeeee.......eeeeeeeee....hhhhhhhhhhhhh....eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lob B 539 EERGKILVSLMYSTQQGGLIVGIIRCVHLAAMDANGYSDPFVKLWLKPDMGKKAKHKTQIKKKTLNPEFNEEFFYDIKHSDLAKKSLDISVWDYDIGKSNDYIGGCQLGISAKGERLKHWYECLKNKDKKIERWHQLQN 677
                                   548       558       568       578       588       598       608       618       628       638       648       658       668         


Chain C from PDB  Type:PROTEIN  Length:138
                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeee....eeeeeeeeee............eeeeeee........eee..........eeeeeeee..........eeeeeeee.......eeeeeeeee....hhhhhhhhhhhhh....eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5lob C 540 ERGKILVSLMYSTQQGGLIVGIIRCVHLAAMDANGYSDPFVKLWLKPDMGKKAKHKTQIKKKTLNPEFNEEFFYDIKHSDLAKKSLDISVWDYDIGKSNDYIGGCQLGISAKGERLKHWYECLKNKDKKIERWHQLQN 677
                                   549       559       569       579       589       599       609       619       629       639       649       659       669        


Chain D from PDB  Type:PROTEIN  Length:85
                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 5lob D  -4 GGQQMGRGSEFMRNELEEMQRRADQLADESLESTRRMLQLVEESKDAGIRTLVMLDEQGEQLDRVEEGMNHINQDMKEAEKNLKD  80
                                     5        15        25        35        45        55        65        75     


Chain E from PDB  Type:PROTEIN  Length:66
                                                                                                  
               SCOP domains ------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                 5lob E 138 SEFARENEMDENLEQVSGIIGNLRHMALDMGNEIDTQNRQIDRIMEKADSNKTRIDEANQRATKML 203
                                   147       157       167       177       187       197      


Chain F from PDB  Type:PROTEIN  Length:88
                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 5lob F -17 xxxxxMGRGSEFMRNELEEMQRRADQLADESLESTRRMLQLVEESKDAGIRTLVMLDEQGEQLDRVEEGMNHINQDMKEAEKNLKDLG  82
                            ||||||   4        14        24        34        44        54        64        74        
                          -17-UNK|                                                                                  
                           -16-UNK                                                                                  
                            -15-UNK                                                                                 
                             -14-UNK                                                                                
                              -13-UNK                                                                               
                                 0                                                                                  


Chain G from PDB  Type:PROTEIN  Length:71
                                                                                                       
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                 5lob G 108 xxxxxxxxxxxxxxARENEMDENLEQVSGIIGNLRHMALDMGNEIDTQNRQIDRIMEKADSNKTRIDEANQ 197
                            |||||||117|||||  146       156       166       176       186       196 
                          108-UNK||117-UNK|                                                        
                           109-UNK||118-UNK                                                        
                            110-UNK||119-UNK                                                       
                             111-UNK| 120-UNK                                                      
                              112-UNK  121-UNK                                                     
                               113-UNK  141                                                        
                                114-UNK                                                            
                                 115-UNK                                                           
                                  116-UNK
   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 5LOB)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5LOB)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5LOB)

(-) Gene Ontology  (75, 83)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/Swiss-Prot
        RP3A_RAT | P47709: 1zbd 2chd 2cm5 2cm6 3rpb 4lt7 4np9 4ns0 5lo8 5low
        SNP25_RAT | P60881: 1jth 1n7s 1sfc 1uee 1urq 3hd7 3ipd 3j96 3j97 3j98 3j99 5ccg 5cch 5cci 5kj7 5kj8 5low

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