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(-) Description

Title :  THE CRYSTAL STRUCTURE OF MUNC13-1 C1C2BMUN DOMAIN
 
Authors :  D. R. Tomchick, J. Rizo, J. Xu
Date :  29 Dec 16  (Deposition) - 15 Feb 17  (Release) - 15 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.35
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Alpha Helical, Neurotransmitter Release, Snare Motif, Exocytosis, C1 Domain, C2 Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Xu, M. Camacho, Y. Xu, V. Esser, X. Liu, T. Trimbuch, Y. Z. Pan, C. Ma, D. R. Tomchick, C. Rosenmund, J. Rizo
Mechanistic Insights Into Neurotransmitter Release And Presynaptic Plasticity From The Crystal Structure Of Munc13-1 C1C2Bmun.
Elife V. 6 2017
PubMed-ID: 28177287  |  Reference-DOI: 10.7554/ELIFE.22567
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN UNC-13 HOMOLOG A
    Chains: A, B
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: PFASTBAC
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: C1C2BMUN DOMAIN (UNP RESIDUES 529-1407 AND 1452-1531)
    Gene: UNC13A, UNC13H1
    Mutation: YES
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: MUNC13-1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2ZN4Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:580 , CYS A:583 , HIS A:605 , CYS A:608binding site for residue ZN A 1701
2AC2SOFTWAREHIS A:567 , CYS A:597 , CYS A:600 , CYS A:616binding site for residue ZN A 1702
3AC3SOFTWAREASN A:542 , GLU A:837binding site for residue CL A 1703
4AC4SOFTWAREGLU B:837binding site for residue CL B 1601
5AC5SOFTWARECYS B:580 , CYS B:583 , HIS B:605 , CYS B:608binding site for residue ZN B 1602
6AC6SOFTWAREHIS B:567 , CYS B:597 , CYS B:600 , CYS B:616binding site for residue ZN B 1603

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1B:600 -B:616

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Lys A:858 -Gly A:859
2Arg A:1150 -Val A:1151
3Arg B:1150 -Val B:1151

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5UE8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5UE8)

(-) Exons   (0, 0)

(no "Exon" information available for 5UE8)

(-) 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:847
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh.........eeee.....ee......ee.hhhhheeee.....ee...hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh........eeeeeeeeee........eeeeeee..eeee..........eeeeeeeee.......eeeeeee...eeeeeeee.......eeeeeee.....eeeeeeeee........hhhhhhhhhhhhhhhhhh..........................hhhhhhhhhhh...hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh...hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5ue8 A  541 NNEELKNHVYKKTLQALIYPISCTTPHNFEVWTATTPTYCYECEGLLWGIARQGMRCTECGVKCHEKCQDLLNADCLQRAAEKSSKHGAEDRTQNIIMVLKDRMKIRERNKPEIFELIQEVFAVTKSAHTQQMKAVKQSVLDGTSKWSAKISITVVCAQGLQAGSSDPYVTVQVGKTKKRTKTIYGNLNPVWEENFHFECHNSSDRIKVRVWDESDDFLGQTIIEVRTLSGEMDVWYNLDKSGAIRLHISVEIKGEEKVAPYHVQYTCLHENLFHFVTDVQNNGVVKIPDAKGDDAWKVYYDETAQEIVDEFAMRYGVESIYQAMTHFACLSSKYMCPGVPAVMSTLLANINAYYANVSASDRFAASNFGKERFVKLLDQLHNSLRIDLSMYRNNFPASSPERLQDLKSTVDLLTSITFFRMKVQELQSPPRASQVVKDCVKACLNSTYEYIFNNCHELYGREYQPSIKNLDFWSKLITLIVSIIEEDKNSYTPCLNQFPQELNVGKISAEVMWSLFAQDMKYAMEEHDKHRLCKSADYMNLHFKVKWLYNEYVAELPTFKDRVPEYPAWFEPFVIQWLDENEEVSRDFLHGALERDKKDGFQLFSCSVVDVFSQLNQSFEIIKKLECPDPQIVGHYMRRFAKTISNVLLQYADIVSKDFASYCSKEKEKVPCILMNNTQQLRVQLEKMFEAMGGKELDAEASGTLKELQVKLNNVLDELSHVFATSFQPHIEECVRQMGDILSQVKGVAQDADNVLQPIMDLLDSNLTLFAKICEKTVLKRVLKELWKLVMNTMERTIKQCAVVELALDTIKQYFHAGGVGLKKTFLEKSPDLQSLRYALSLYTQA 1517
                                   550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700  ||   714       724       734       744       754   ||  779       789       799||     816       826       836       846       856       866       876       886       896       906       916     ||932       942       952       962       972       982       992      1002      1012      1022      1032    ||1057      1067      1077      1087      1097      1107      1117      1127      1137      1147      1157      1167      1177      1187  ||  1203      1213      1223      1233      1243      1253      1263      1273      1283      1293      1303      1313      1323      1333      1354      1364      1374      1384      1394      1470      1480      1490      1500      1510       
                                                                                                                                                                                            703|                                               758|                       800|                                                                                                               922|                                                                                                        1037|                                                                                                                                     1190|                                                                                                                                            1341|                                              1403|                                               
                                                                                                                                                                                             708                                                774                        808                                                                                                                929                                                                                                         1053                                                                                                                                      1197                                                                                                                                             1353                                               1470                                               


Chain B from PDB  Type:PROTEIN  Length:838
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.........eeee.....ee......ee.hhhhheeee.....ee...hhhhh..hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh........eeeeeeeeee......eeeeeee..eeee..........eeeeeeee....eeeeeeee..eeeeeeeee.hhh..eeeeeee.......eeeeeeeee...hhhhhhhhhhhhhhhhhh..........................hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5ue8 B  542 NEELKNHVYKKTLQALIYPISCTTPHNFEVWTATTPTYCYECEGLLWGIARQGMRCTECGVKCHEKCQDLLNADCLQRAAEKSSDRTQNIIMVLKDRMKIRERNKPEIFELIQEVFAVTKSAHTQQMKAVKQSVLDGTSKWSAKISITVVCAQGLQSSDPYVTVQVGKTKKRTKTIYGNLNPVWEENFHFNSSDRIKVRVWDEDDFLGQTIIEVRTLSGEMDVWYNLDKRVSGAIRLHISVEIVAPYHVQYTCLHENLFHFVTDVQNNGVVKIPDAKGDDAWKVYYDETAQEIVDEFAMRYGVESIYQAMTHFACLSSKYMCPGVPAVMSTLLANINAYYAHTVSASDRFAASNFGKERFVKLLDQLHNSLRIDLSMYRNNFPASSPERLQDLKSTVDLLTSITFFRMKVQELQSPPRASQVVKDCVKACLNSTYEYIFNNCHELYGREYQQGPSIKNLDFWSKLITLIVSIIEEDKNSYTPCLNQFPQELNVGKISAEVMWSLFAQDMKYAMEEHDKHRLCKSADYMNLHFKVKWLYNEYVAELPTFKDRVPEYPAWFEPFVIQWLDENEEVSRDFLHGALERDKKDGFQQTSEHALFSCSVVDVFSQLNQSFEIIKKLECPDPQIVGHYMRRFAKTISNVLLQYADIVSKDFASYCSKEKEKVPCILMNNTQQLRVQLEKMFEAMGGKELDAEASGTLKELQVKLNNVLDELSHVFATSFQPHIEECVRQMGDILSVAQDADNVLQPIMDLLDSNLTLFAKICEKTVLKRVLKELWKLVMNTMERTIVTPKQCAVVELALDTIKQYFHAGGVGLKKTFLEKSPDLQSLRYALSLYT 1515
                                   551       561       571       581       591       601       611       621   ||  636       646       656       666       676       686       696     ||712       722       732       742|      755  ||   781       791       801|      816  ||   831       841       851       861       871       881       891       901       911       921  ||   936       946       956       966       976       986       996      1006      1016      1026      1036||    1059      1069      1079      1089      1099      1109      1119      1129      1139      1149      1159      1169      1179      1189      1199      1209      1219      1229      1239      1249      1259      1269      1279      1289      1299      1309      1319      1329      1354      1364      1374      1384      1394      1404|     1477      1487      1497      1507        
                                                                                                             625|                                                                    702|                              742|         758|                       801|         819|                                                                                                924|                                                                                                       1037|                                                                                                                                                                                                                                                                                          1337|                                               1404|                                               
                                                                                                              631                                                                     709                               746          775                        807          825                                                                                                 930                                                                                                        1051                                                                                                                                                                                                                                                                                           1353                                                1468
   Legend:   → Mismatch (orange background)
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    → 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 5UE8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5UE8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5UE8)

(-) Gene Ontology  (26, 26)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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        UN13A_RAT | Q62768: 1y8f 2cjs 2cjt 2kdu 3kwt 3kwu 3swh 4y21 5uf7

(-) Related Entries Specified in the PDB File

5uf7