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(-) Description

Title :  STRUCTURE OF THE CA2+-BOUND RABPHILIN 3A C2B DOMAIN SNAP25 COMPLEX (P21 SPACE GROUP)
 
Authors :  N. Verdaguer, C. Ferrer-Orta
Date :  10 Aug 16  (Deposition) - 21 Jun 17  (Release) - 21 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L,M,N
Biol. Unit 1:  A,B,C,D,E,F,G  (1x)
Biol. Unit 2:  H,I,J,K,L,M,N  (1x)
Keywords :  Membrane Fusion, Calcium, C2 Domain, Exocytosis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Ferrer-Orta, T. Coronada-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, H, I, J
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Taxid: 511693
    Expression System Vector: PET28
    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, K, M
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Taxid: 511693
    Expression System Vector: PET28
    Expression System Vector Type: PLASMID
    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
 
Molecule 3 - SYNAPTOSOMAL-ASSOCIATED PROTEIN 25
    Chains: E, G, L, N
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Taxid: 511693
    Expression System Vector: PET28
    Expression System Vector Type: PLASMID
    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

 Structural Features

(-) Chains, Units

  1234567891011121314
Asymmetric Unit : ABCDEFGHIJKLMN
Biological Unit 1 (1x): ABCDEFG       
Biological Unit 2 (1x):        HIJKLMN

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 19)

Asymmetric Unit (2, 19)
No.NameCountTypeFull Name
1CA12Ligand/IonCALCIUM ION
2GOL7Ligand/IonGLYCEROL
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GOL3Ligand/IonGLYCEROL
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GOL4Ligand/IonGLYCEROL

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:554 , GLU A:610 , GLN K:20binding site for residue GOL A 701
02AC2SOFTWAREASP A:571 , ASP A:577 , ASP A:631 , TYR A:632 , ASP A:633binding site for residue CA A 702
03AC3SOFTWAREMET A:570 , ASP A:571 , ASP A:631 , ASP A:633 , ASP A:639binding site for residue CA A 703
04AC4SOFTWARELYS B:616 , LEU H:545 , GLU H:670binding site for residue GOL B 701
05AC5SOFTWAREMET B:570 , ASP B:571 , ASP B:631 , ASP B:633 , ASP B:639 , CA B:703 , HOH B:806binding site for residue CA B 702
06AC6SOFTWAREASP B:571 , ASP B:577 , ASP B:631 , TYR B:632 , ASP B:633 , CA B:702 , HOH J:804binding site for residue CA B 703
07AC7SOFTWARETRP C:672binding site for residue GOL C 701
08AC8SOFTWAREMET C:570 , ASP C:571 , ASP C:631 , ASP C:633 , ASP C:639 , HOH C:806binding site for residue CA C 702
09AC9SOFTWAREASP C:571 , ASP C:577 , ASP C:631 , TYR C:632 , ASP C:633 , HOH C:805binding site for residue CA C 703
10AD1SOFTWAREASP H:571 , ASP H:577 , ASP H:631 , TYR H:632 , ASP H:633 , HOH H:802binding site for residue CA H 701
11AD2SOFTWAREHOH G:301 , MET H:570 , ASP H:633 , ASP H:639 , HOH H:803binding site for residue CA H 702
12AD3SOFTWAREASP C:614 , ASP I:571 , ASP I:577 , ASP I:631 , TYR I:632 , ASP I:633binding site for residue CA I 701
13AD4SOFTWAREMET I:570 , ASP I:571 , ASP I:631 , ASP I:633 , ASP I:639binding site for residue CA I 702
14AD5SOFTWAREMET J:570 , ASP J:571 , ASP J:633 , ASP J:639 , HOH J:809binding site for residue CA J 701
15AD6SOFTWAREASP J:571 , ASP J:577 , ASP J:631 , TYR J:632 , ASP J:633binding site for residue CA J 702
16AD7SOFTWAREHIS H:617 , ARG K:59binding site for residue GOL K 101
17AD8SOFTWAREGLY C:635 , ASP M:19 , ASP M:23 , GLU N:143binding site for residue GOL M 101
18AD9SOFTWARETHR N:190 , ASP N:193 , GLN N:197binding site for residue GOL N 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Lys A:585 -Pro A:586
2Lys B:585 -Pro B:586
3Lys C:585 -Pro C:586
4Lys H:585 -Pro H:586
5Lys I:585 -Pro I:586
6Lys J:585 -Pro J:586

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5LOW)

(-) 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:142
                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee.ee....ee..eeeeee............eeeeeeee.......ee..............ee..ee.hhhhhhh.eeeeeeee.......eeeeeeeee...hhhhhhhhhhhhhh....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5low A 537 DIEERGKILVSLMYSTQQGGLIVGIIRCVHLAAMDANGYSDPFVKLWLKPDMGKKAKHKTQIKKKTLNPEFNEEFFYDIKHSDLAKKSLDISVWDYDIGKSNDYIGGCQLGISAKGERLKHWYECLKNKDKKIERWHQLQNE 678
                                   546       556       566       576       586       596       606       616       626       636       646       656       666       676  


Chain B from PDB  Type:PROTEIN  Length:144
                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeeeee....eeeeeeeeee............eeeeeeee.......eee.............eeeee..hhhhhh..ee..eeee.......eeeee..ee....hhhhhhhhhhhhh....eeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5low B 537 DIEERGKILVSLMYSTQQGGLIVGIIRCVHLAAMDANGYSDPFVKLWLKPDMGKKAKHKTQIKKKTLNPEFNEEFFYDIKHSDLAKKSLDISVWDYDIGKSNDYIGGCQLGISAKGERLKHWYECLKNKDKKIERWHQLQNENH 680
                                   546       556       566       576       586       596       606       616       626       636       646       656       666       676    


Chain C from PDB  Type:PROTEIN  Length:144
                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeeeee....eeeeeeeeee............eeeeeeee.......eee..........eeeeeeeee.hhhhhh..eeeeeeee.......eeeeeeeee....hhhhhhhhhhhhh....eeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5low C 537 DIEERGKILVSLMYSTQQGGLIVGIIRCVHLAAMDANGYSDPFVKLWLKPDMGKKAKHKTQIKKKTLNPEFNEEFFYDIKHSDLAKKSLDISVWDYDIGKSNDYIGGCQLGISAKGERLKHWYECLKNKDKKIERWHQLQNENH 680
                                   546       556       566       576       586       596       606       616       626       636       646       656       666       676    


Chain D from PDB  Type:PROTEIN  Length:68
                                                                                                    
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 5low D   5 EFMRNELEEMQRRADQLADESLESTRRMLQLVEESKDAGIRTLVMLDEQGEQLDRVEEGMNHINQDMK  72
                                    14        24        34        44        54        64        


Chain E from PDB  Type:PROTEIN  Length:56
                                                                                        
               SCOP domains -------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                 5low E 142 RENEMDENLEQVSGIIGNLRHMALDMGNEIDTQNRQIDRIMEKADSNKTRIDEANQ 197
                                   151       161       171       181       191      


Chain F from PDB  Type:PROTEIN  Length:68
                                                                                                    
               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
                 5low F  15 QRRADQLADESLESTRRMLQLVEESKDAGIRTLVMLDEQGEQLDRVEEGMNHINQDMKEAEKNLKDLG  82
                                    24        34        44        54        64        74        


Chain G from PDB  Type:PROTEIN  Length:60
                                                                                            
               SCOP domains ------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------ Transcript
                 5low G 140 FARENEMDENLEQVSGIIGNLRHMALDMGNEIDTQNRQIDRIMEKADSNKTRIDEANQRA 199
                                   149       159       169       179       189       199


Chain H from PDB  Type:PROTEIN  Length:140
                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee....eeeeeeeeee.............eeeeeee.......eee..........eeeeeeeee...hhhhh.eeeeeee.........eeeeeeee....hhhhhhhhhhhhh....eeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5low H 540 ERGKILVSLMYSTQQGGLIVGIIRCVHLAAMDANGYSDPFVKLWLKPDMGKKAKHKTQIKKKTLNPEFNEEFFYDIKHSDLAKKSLDISVWDYDIGKSNDYIGGCQLGISAKGERLKHWYECLKNKDKKIERWHQLQNEN 679
                                   549       559       569       579       589       599       609       619       629       639       649       659       669       679


Chain I from PDB  Type:PROTEIN  Length:145
                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeee....eeeeeeee..............eeeeeeee.......eee.............eeeeee.hhhhhh..eeeeeeee.......eeeeeeee.....hhhhhhhhhhhhh....eeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5low I 536 GDIEERGKILVSLMYSTQQGGLIVGIIRCVHLAAMDANGYSDPFVKLWLKPDMGKKAKHKTQIKKKTLNPEFNEEFFYDIKHSDLAKKSLDISVWDYDIGKSNDYIGGCQLGISAKGERLKHWYECLKNKDKKIERWHQLQNENH 680
                                   545       555       565       575       585       595       605       615       625       635       645       655       665       675     


Chain J from PDB  Type:PROTEIN  Length:140
                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeee....eeeeeeeeee............eeeeeeee.......eee..........eeeeeeeee...hhhhh.eeeeeeee.......eeeee..ee....hhhhhhhhhhhhh....eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5low J 537 DIEERGKILVSLMYSTQQGGLIVGIIRCVHLAAMDANGYSDPFVKLWLKPDMGKKAKHKTQIKKKTLNPEFNEEFFYDIKHSDLAKKSLDISVWDYDIGKSNDYIGGCQLGISAKGERLKHWYECLKNKDKKIERWHQLQ 676
                                   546       556       566       576       586       596       606       616       626       636       646       656       666       676


Chain K from PDB  Type:PROTEIN  Length:72
                                                                                                        
               SCOP domains ------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                 5low K   3 GSEFMRNELEEMQRRADQLADESLESTRRMLQLVEESKDAGIRTLVMLDEQGEQLDRVEEGMNHINQDMKEA  74
                                    12        22        32        42        52        62        72  


Chain L from PDB  Type:PROTEIN  Length:63
                                                                                               
               SCOP domains --------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                 5low L 141 ARENEMDENLEQVSGIIGNLRHMALDMGNEIDTQNRQIDRIMEKADSNKTRIDEANQRATKML 203
                                   150       160       170       180       190       200   


Chain M from PDB  Type:PROTEIN  Length:72
                                                                                                        
               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
                 5low M  11 LEEMQRRADQLADESLESTRRMLQLVEESKDAGIRTLVMLDEQGEQLDRVEEGMNHINQDMKEAEKNLKDLG  82
                                    20        30        40        50        60        70        80  


Chain N from PDB  Type:PROTEIN  Length:60
                                                                                            
               SCOP domains ------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------ Transcript
                 5low N 139 EFARENEMDENLEQVSGIIGNLRHMALDMGNEIDTQNRQIDRIMEKADSNKTRIDEANQR 198
                                   148       158       168       178       188       198
   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 5LOW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (75, 83)

Asymmetric Unit(hide GO term definitions)

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  5low
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  RP3A_RAT | P47709
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  SNP25_RAT | P60881
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5LOW)