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(-) Description

Title :  CRYSTAL STRUCTURE OF THE QUINTUPLE MUTANT OF THE SYNAPTOTAGMIN-1 C2B DOMAIN
 
Authors :  Q. Zhou, M. Zhao, A. T. Brunger
Date :  02 Jul 15  (Deposition) - 12 Aug 15  (Release) - 16 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  A,B,C,D  (1x)
Keywords :  Synaptotagmin1, C2B Domain, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. Zhou, Y. Lai, T. Bacaj, M. Zhao, A. Y. Lyubimov, M. Uervirojnangkoorn, O. B. Zeldin, A. S. Brewster, N. K. Sauter, A. E. Cohen, S. M. Soltis, R. Alonso-Mori, M. Chollet, H. T. Lemke, R. A. Pfuetzner, U. B. Choi, W. I. Weis, J. Diao, T. C. Sudhof, A. T. Brunger
Architecture Of The Synaptotagmin-Snare Machinery For Neuronal Exocytosis.
Nature V. 525 62 2015
PubMed-ID: 26280336  |  Reference-DOI: 10.1038/NATURE14975

(-) Compounds

Molecule 1 - SYNAPTOTAGMIN-1
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P-1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 271-421
    Gene: SYT1
    Mutation: YES
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: SYNAPTOTAGMIN I,SYTI,P65

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D
Biological Unit 5 (1x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 49)

Asymmetric Unit (2, 49)
No.NameCountTypeFull Name
1GOL27Ligand/IonGLYCEROL
2SO422Ligand/IonSULFATE ION
Biological Unit 1 (2, 11)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL
2SO45Ligand/IonSULFATE ION
Biological Unit 2 (2, 15)
No.NameCountTypeFull Name
1GOL7Ligand/IonGLYCEROL
2SO48Ligand/IonSULFATE ION
Biological Unit 3 (2, 9)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL
2SO43Ligand/IonSULFATE ION
Biological Unit 4 (2, 14)
No.NameCountTypeFull Name
1GOL8Ligand/IonGLYCEROL
2SO46Ligand/IonSULFATE ION
Biological Unit 5 (2, 49)
No.NameCountTypeFull Name
1GOL27Ligand/IonGLYCEROL
2SO422Ligand/IonSULFATE ION

(-) Sites  (49, 49)

Asymmetric Unit (49, 49)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:383 , GLY A:384 , HOH A:616 , HOH A:765 , LEU C:294 , ASN C:340 , SO4 C:507 , HOH C:729 , ALA D:395 , ASN D:396binding site for residue GOL A 501
02AC2SOFTWARETYR A:311 , LYS A:327 , THR A:328 , ILE A:330 , SO4 A:508 , HOH A:608 , HOH A:651binding site for residue GOL A 502
03AC3SOFTWARETHR A:334 , LEU A:335 , ASN A:336 , HOH A:609 , HOH A:641 , HOH A:696 , HOH D:642 , HOH D:695binding site for residue GOL A 503
04AC4SOFTWAREVAL A:376 , PHE A:377 , SER A:382 , THR A:383 , GLU A:386 , MET A:416binding site for residue GOL A 504
05AC5SOFTWAREARG A:322 , LYS A:325 , SO4 A:507 , HOH A:723binding site for residue GOL A 505
06AC6SOFTWAREALA A:399 , PRO A:400 , HOH A:615 , HOH A:714 , ARG B:388 , SER B:391 , ASP B:392 , SO4 B:510 , HOH B:717 , HOH C:650binding site for residue GOL A 506
07AC7SOFTWARELYS A:313 , HIS A:315 , ARG A:322 , LYS A:325 , GOL A:505 , HOH A:612binding site for residue SO4 A 507
08AC8SOFTWARETYR A:311 , LYS A:313 , LYS A:325 , LYS A:327 , ASN A:370 , GOL A:502 , HOH A:607binding site for residue SO4 A 508
09AC9SOFTWARETRP A:338 , ASN A:340 , HOH A:680 , GOL C:504 , LYS D:354 , LYS D:420binding site for residue SO4 A 509
10AD1SOFTWAREARG A:322binding site for residue SO4 A 510
11AD2SOFTWARELYS A:300 , HOH A:604 , ILE B:330 , TYR B:364binding site for residue SO4 A 511
12AD3SOFTWARELYS A:369 , LYS B:326 , HOH B:623 , HOH B:646binding site for residue GOL B 501
13AD4SOFTWARELYS B:327 , THR B:328 , ILE B:330 , SO4 B:512 , HOH B:604 , HOH B:622binding site for residue GOL B 502
14AD5SOFTWAREASN B:340 , SER B:342 , HOH B:614 , HOH B:698 , HOH B:720 , HOH B:734 , ALA C:395 , GOL D:505binding site for residue GOL B 503
15AD6SOFTWARELYS B:324 , LYS B:326 , SER B:344 , PHE B:345 , GLU B:346 , HOH B:719 , HOH B:737binding site for residue GOL B 504
16AD7SOFTWARETHR B:329 , ILE B:330 , HOH B:622 , HOH B:627binding site for residue GOL B 505
17AD8SOFTWAREARG B:388 , SO4 B:513 , HOH B:611 , HOH B:631 , HOH B:652 , HOH B:727binding site for residue GOL B 506
18AD9SOFTWARETRP B:338 , ASN B:340 , HOH B:724 , PRO C:397binding site for residue GOL B 507
19AE1SOFTWAREHOH A:603 , HOH A:624 , LYS B:313 , HIS B:315 , ARG B:322 , LYS B:325 , HOH B:742binding site for residue SO4 B 508
20AE2SOFTWARELYS B:321 , ARG B:322 , LYS B:421 , HOH B:741binding site for residue SO4 B 509
21AE3SOFTWAREGOL A:506 , ARG B:388 , GLN B:403 , HOH B:608 , HOH B:631 , HOH B:658 , HOH B:670 , TYR C:380 , HOH C:673binding site for residue SO4 B 510
22AE4SOFTWARETHR B:334 , LEU B:335 , ASN B:336binding site for residue SO4 B 511
23AE5SOFTWAREASP A:303 , VAL A:304 , HOH A:603 , TYR B:311 , LYS B:313 , LYS B:325 , LYS B:327 , GOL B:502 , HOH B:604binding site for residue SO4 B 512
24AE6SOFTWAREGLY B:384 , ARG B:388 , GOL B:506 , HOH B:620 , GOL D:502 , HOH D:607binding site for residue SO4 B 513
25AE7SOFTWAREGLY B:368 , LYS B:369 , HOH B:628binding site for residue SO4 B 514
26AE8SOFTWARELYS B:331 , LYS B:332 , HOH B:627 , HOH B:630 , HOH B:707 , HOH B:728binding site for residue SO4 B 515
27AE9SOFTWAREVAL C:376 , PHE C:377 , SER C:382 , THR C:383 , GLU C:386 , HOH C:603binding site for residue GOL C 501
28AF1SOFTWAREHOH B:606 , THR C:334 , LEU C:335 , ASN C:336 , HOH C:605binding site for residue GOL C 502
29AF2SOFTWARELYS C:331 , LYS C:332 , HOH C:602 , HOH C:634 , HOH C:639 , HOH C:642binding site for residue GOL C 503
30AF3SOFTWARELEU A:294 , ASN A:340 , SO4 A:509 , HOH A:742 , HOH A:752 , ALA B:395 , ASN B:396 , THR C:383 , GLY C:384binding site for residue GOL C 504
31AF4SOFTWAREARG C:322 , LEU C:323 , LYS C:324 , LYS C:325binding site for residue GOL C 505
32AF5SOFTWARETYR C:311 , LYS C:313 , ASN C:370 , HOH C:641 , ILE D:367 , GLY D:368binding site for residue GOL C 506
33AF6SOFTWAREGOL A:501 , HOH A:778 , LYS B:354 , LYS B:420 , TRP C:338 , ASN C:340 , HOH C:606binding site for residue SO4 C 507
34AF7SOFTWARELYS C:313 , HIS C:315binding site for residue SO4 C 508
35AF8SOFTWARELYS C:321 , ARG C:322binding site for residue SO4 C 509
36AF9SOFTWARELYS D:327 , THR D:328 , ILE D:330 , ASN D:370 , HOH D:715binding site for residue GOL D 501
37AG1SOFTWAREALA A:395 , THR B:383 , GLY B:384 , SO4 B:513 , HOH B:702 , GOL D:504 , GOL D:508 , HOH D:607 , HOH D:719binding site for residue GOL D 502
38AG2SOFTWAREALA B:286 , GLU D:412 , MET D:416 , HOH D:616 , HOH D:767binding site for residue GOL D 503
39AG3SOFTWAREALA A:395 , HOH A:795 , VAL D:292 , ASN D:340 , SER D:342 , GOL D:502 , HOH D:669 , HOH D:676binding site for residue GOL D 504
40AG4SOFTWAREGOL B:503 , HOH B:698 , THR D:383 , HOH D:627 , HOH D:646 , HOH D:660 , HOH D:661 , HOH D:746 , HOH D:751binding site for residue GOL D 505
41AG5SOFTWARETRP D:338 , ASN D:340binding site for residue GOL D 506
42AG6SOFTWARETYR A:380 , ASN A:381 , SER A:382 , HOH A:737 , ASP D:392 , HOH D:636 , HOH D:683 , HOH D:690 , HOH D:699 , HOH D:783binding site for residue GOL D 507
43AG7SOFTWAREHOH A:635 , HOH A:795 , THR B:383 , GOL D:502 , HOH D:633 , HOH D:640 , HOH D:665 , HOH D:669binding site for residue GOL D 508
44AG8SOFTWARETYR A:380 , ARG D:388 , GLN D:403 , HOH D:602 , HOH D:636 , HOH D:658 , HOH D:711 , HOH D:738binding site for residue SO4 D 509
45AG9SOFTWARELYS D:313 , HIS D:315 , ARG D:322 , LYS D:325binding site for residue SO4 D 510
46AH1SOFTWARETYR D:311 , LYS D:313 , LYS D:325 , LYS D:327 , ASN D:370 , HOH D:612binding site for residue SO4 D 511
47AH2SOFTWARETHR D:334 , LEU D:335 , ASN D:336binding site for residue SO4 D 512
48AH3SOFTWARELYS D:321 , ARG D:322 , LYS D:421binding site for residue SO4 D 513
49AH4SOFTWAREGLY D:384 , ARG D:388 , HOH D:608 , HOH D:661 , HOH D:667 , HOH D:689binding site for residue SO4 D 514

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5CCJ)

(-) 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:148
                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee....eeeeeeeeee............eeeeeeeee..eeeeeee..........eeeeeeeee.hhhhhh.eeeeeeeee.......eeeeeeeee...hhhhhhhhhhhhhh....eeeeee..hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ccj A 271 EKLGDICFSLAYVPTAGKLTVVILAAKNLKKMDVGGLSDPYVKIHLMQNGKRLKKKKTTIKKNTLNPWYNESFSFEVPFEQIQKVQVVVTVLDYDKIGKNDAIGKVFVGYNSTGAELRHWSDMLANPAAPIAQWHTLQVEEEVDAMLA 418
                                   280       290       300       310       320       330       340       350       360       370       380       390       400       410        


Chain B from PDB  Type:PROTEIN  Length:151
                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee....eeeeeeeeee............eeeeeeeee..eeeeeee..........eeeeeeeee.hhhhh..eeeeeeeee.......eeeeeeeee...hhhhhhhhhhhhhh....eeeeee..hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ccj B 271 EKLGDICFSLAYVPTAGKLTVVILAAKNLKKMDVGGLSDPYVKIHLMQNGKRLKKKKTTIKKNTLNPWYNESFSFEVPFEQIQKVQVVVTVLDYDKIGKNDAIGKVFVGYNSTGAELRHWSDMLANPAAPIAQWHTLQVEEEVDAMLAVKK 421
                                   280       290       300       310       320       330       340       350       360       370       380       390       400       410       420 


Chain C from PDB  Type:PROTEIN  Length:148
                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee....eeeeeeeeee............eeeeeeeee..eeeeeee..........eeeeeeeee.hhhhhh.eeeeeeeee.......eeeeeeeee...hhhhhhhhhhhhhh....eeeeee..hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ccj C 271 EKLGDICFSLAYVPTAGKLTVVILAAKNLKKMDVGGLSDPYVKIHLMQNGKRLKKKKTTIKKNTLNPWYNESFSFEVPFEQIQKVQVVVTVLDYDKIGKNDAIGKVFVGYNSTGAELRHWSDMLANPAAPIAQWHTLQVEEEVDAMLA 418
                                   280       290       300       310       320       330       340       350       360       370       380       390       400       410        


Chain D from PDB  Type:PROTEIN  Length:152
                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeee....eeeeeeeeee............eeeeeeeee..eeeeeee..........eeeeeeeee.hhhhh..eeeeeeeee.......eeeeeeeee...hhhhhhhhhhhhhh....eeeeee..hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ccj D 270 SEKLGDICFSLAYVPTAGKLTVVILAAKNLKKMDVGGLSDPYVKIHLMQNGKRLKKKKTTIKKNTLNPWYNESFSFEVPFEQIQKVQVVVTVLDYDKIGKNDAIGKVFVGYNSTGAELRHWSDMLANPAAPIAQWHTLQVEEEVDAMLAVKK 421
                                   279       289       299       309       319       329       339       349       359       369       379       389       399       409       419
   Legend:   → Mismatch (orange background)
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  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 5CCJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (56, 56)

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  SYT1_RAT | P21707
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 Related Entries

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

UniProtKB/Swiss-Prot
        SYT1_RAT | P21707: 1byn 1k5w 1rsy 1tjm 1tjx 1uov 1uow 2yoa 4wee 5ccg 5cch 5cci 5kj7 5kj8

(-) Related Entries Specified in the PDB File

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