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(-) Description

Title :  CRYSTAL STRUCTURE OF THE NAVAB VOLTAGE-GATED SODIUM CHANNEL IN A CLOSED CONFORMATION
 
Authors :  M. J. Lenaeus, W. A. Catterall
Date :  28 Mar 17  (Deposition) - 05 Apr 17  (Release) - 19 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Voltage-Gated Sodium Channel, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Lenaeus, T. M. Gamal El-Din, C. Ing, K. Ramanadane, R. Pomes, N. Zheng, W. A. Catterall
Structures Of Closed And Open States Of A Voltage-Gated Sodium Channel.
Proc. Natl. Acad. Sci. V. 114 E3051 2017 U. S. A.
PubMed-ID: 28348242  |  Reference-DOI: 10.1073/PNAS.1700761114

(-) Compounds

Molecule 1 - ION TRANSPORT PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Mutation: YES
    Organism Scientific: ARCOBACTER BUTZLERI
    Organism Taxid: 28197

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 26)

Asymmetric/Biological Unit (4, 26)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2CPS8Ligand/Ion3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
3PO44Ligand/IonPHOSPHATE ION
4PX413Ligand/Ion1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

(-) Sites  (25, 25)

Asymmetric Unit (25, 25)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:1129 , ILE A:1216 , ASP A:1219 , ILE A:1223 , HOH A:1405 , ILE D:2119binding site for residue CPS A 1301
02AC2SOFTWARESER A:1125 , VAL A:1126 , ALA A:1220 , VAL B:2218 , ASP B:2219binding site for residue CPS A 1302
03AC3SOFTWAREMET A:1188 , PRO A:1192 , TRP A:1195 , HOH A:1401 , MET D:2137 , THR D:2162 , GLY D:2164 , GLU D:2165 , PHE D:2167 , TYR D:2168binding site for residue PX4 A 1303
04AC4SOFTWAREGLY A:1030 , SER A:1034 , THR B:2162 , GLY B:2164 , PX4 B:2306binding site for residue PX4 A 1304
05AC5SOFTWAREPHE A:1144 , ARG A:1155 , TYR A:1191 , TYR A:1193 , HOH A:1402 , ILE D:2097binding site for residue PX4 A 1305
06AC6SOFTWARETRP A:1076 , SER A:1121binding site for residue PO4 A 1306
07AC7SOFTWAREILE A:1119 , GLY B:2129 , ILE B:2216 , ASP B:2219 , ALA B:2220 , ILE B:2223 , HOH B:2404binding site for residue CPS B 2301
08AC8SOFTWAREALA B:2122 , SER B:2125 , VAL B:2126 , ILE B:2223 , LEU B:2224binding site for residue CPS B 2302
09AC9SOFTWAREILE A:1097 , LEU B:2151 , PHE B:2152 , ARG B:2155 , TYR B:2191 , VAL B:2196 , HOH B:2405binding site for residue PX4 B 2303
10AD1SOFTWAREMET A:1137 , PHE A:1141 , GLY A:1164 , PHE A:1167 , TYR A:1168 , MET B:2188 , PRO B:2192 , TRP B:2195 , PX4 D:2303binding site for residue PX4 B 2304
11AD2SOFTWAREGLY B:2030 , LEU B:2031 , SER B:2034 , THR B:2036 , TYR C:1142 , THR C:1162 , GLY C:1164binding site for residue PX4 B 2305
12AD3SOFTWAREPX4 A:1304 , MET B:2137 , PHE B:2141 , GLY B:2164 , GLU B:2165 , HOH B:2403 , MET C:1188 , PRO C:1192binding site for residue PX4 B 2306
13AD4SOFTWARESER C:1125 , VAL C:1126 , ALA C:1220 , VAL D:2218 , ASP D:2219binding site for residue CPS C 1301
14AD5SOFTWAREILE B:2119 , GLY C:1129 , ILE C:1216 , ASP C:1219binding site for residue CPS C 1302
15AD6SOFTWAREGLY C:1030 , LEU C:1031 , SER C:1034 , THR D:2162 , LEU D:2163binding site for residue PX4 C 1303
16AD7SOFTWAREGLY C:1164 , GLU C:1165 , PHE C:1167 , TYR C:1168 , MET D:2188 , TRP D:2195binding site for residue PX4 C 1304
17AD8SOFTWAREILE B:2097 , PHE C:1144 , LEU C:1151 , PHE C:1152 , VAL C:1190 , TYR C:1191 , TYR C:1193 , HOH C:1404binding site for residue PX4 C 1305
18AD9SOFTWARESER C:1121binding site for residue PO4 C 1306
19AE1SOFTWAREHIS A:1239 , HIS B:2239 , HIS C:1239 , HIS D:2239binding site for residue CL C 1307
20AE2SOFTWAREILE C:1119 , GLY D:2129 , ASP D:2219 , ALA D:2220 , ILE D:2223binding site for residue CPS D 2301
21AE3SOFTWAREASP A:1219 , ALA D:2122 , SER D:2125 , VAL D:2126 , ILE D:2223binding site for residue CPS D 2302
22AE4SOFTWARETHR A:1162 , GLY A:1164 , PX4 B:2304 , GLY D:2030 , LEU D:2031 , SER D:2034binding site for residue PX4 D 2303
23AE5SOFTWAREILE C:1097 , LEU D:2151 , TYR D:2191 , TYR D:2193 , VAL D:2196binding site for residue PX4 D 2304
24AE6SOFTWAREPRO D:2075 , TRP D:2076 , PHE D:2079 , SER D:2121 , ILE D:2124binding site for residue PX4 D 2305
25AE7SOFTWAREGLN C:1115 , SER D:2132binding site for residue PO4 D 2306

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5VB2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5VB2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5VB2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5VB2)

(-) Exons   (0, 0)

(no "Exon" information available for 5VB2)

(-) 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:262
                                                                                                                                                                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5vb2 A 1000 HMYLRITNIVESSFFTKFIIYLIVLNGITMGLETSKTFMQSFGVYTTLFNQIVITIFTIEIILRIYVHRISFFKDPWSLFDFFVVAISLVPTEILRVLRVLRLFRLVTAVPQMRKIVSALISVIPGMLSVIALMTLFFYIFAIMATQLFGERFPEWFGTLGESFYTLFQVMTLESWSMGIVRPLMEVYPYAWVFFIPFIFVVFFVMINLYVAIIVDAMAILNQKEEQHIIDEVQSHEDNINNEIIKLREEIVELKELIKTSL 1265
                                  1009      1019      1029      1039      1049      1059      1069      1079      1089 ||   1103      1113      1123      1133      1143      1153      1163      1173      1183      1193      1203      1213      1223      1233      1243      1253      1263  
                                                                                                                    1091|                                                                                                                                                                         
                                                                                                                     1096                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:259
                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5vb2 B 2001 MYLRITNIVESSFFTKFIIYLIVLNGITMGLETSKTFMQSFGVYTTLFNQIVITIFTIEIILRIYVHRISFFKDPWSLFDFFVVAISLVPTSSFEILRVLRVLRLFRLVTAVPQMRKIVSALISVIPGMLSVIALMTLFFYIFAIMATQLFGERFPEWFGTLGESFYTLFQVMTLESWSMGIVRPLMEVYPYAWVFFIPFIFVVFFVMINLYVAIIVDAMAILNQKEEQHIIDEVQSHEDNINNEIIKLREEIVELKEL 2260
                                  2010      2020      2030      2040      2050      2060      2070      2080      2090  ||  2101      2111      2121      2131      2141      2151      2161      2171      2181      2191      2201      2211      2221      2231      2241      2251         
                                                                                                                     2093|                                                                                                                                                                     
                                                                                                                      2095                                                                                                                                                                     


Chain C from PDB  Type:PROTEIN  Length:261
                                                                                                                                                                                                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5vb2 C 1002 YLRITNIVESSFFTKFIIYLIVLNGITMGLETSKTFMQSFGVYTTLFNQIVITIFTIEIILRIYVHRISFFKDPWSLFDFFVVAISLVPTSFEILRVLRVLRLFRLVTAVPQMRKIVSALISVIPGMLSVIALMTLFFYIFAIMATQLFGERFPEWFGTLGESFYTLFQVMTLESWSMGIVRPLMEVYPYAWVFFIPFIFVVFFVMINLYVAIIVDAMAILNQKEEQHIIDEVQSHEDNINNEIIKLREEIVELKELIKTS 1264
                                  1011      1021      1031      1041      1051      1061      1071      1081      1091||    1103      1113      1123      1133      1143      1153      1163      1173      1183      1193      1203      1213      1223      1233      1243      1253      1263 
                                                                                                                   1092|                                                                                                                                                                         
                                                                                                                    1095                                                                                                                                                                         


Chain D from PDB  Type:PROTEIN  Length:268
                                                                                                                                                                                                                                                                                                             
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5vb2 D 1995 VPRGSHMYLRITNIVESSFFTKFIIYLIVLNGITMGLETSKTFMQSFGVYTTLFNQIVITIFTIEIILRIYVHRISFFKDPWSLFDFFVVAISLVPTSSGFEILRVLRVLRLFRLVTAVPQMRKIVSALISVIPGMLSVIALMTLFFYIFAIMATQLFGERFPEWFGTLGESFYTLFQVMTLESWSMGIVRPLMEVYPYAWVFFIPFIFVVFFVMINLYVAIIVDAMAILNQKEEQHIIDEVQSHEDNINNEIIKLREEIVELKELIK 2262
                                  2004      2014      2024      2034      2044      2054      2064      2074      2084      2094      2104      2114      2124      2134      2144      2154      2164      2174      2184      2194      2204      2214      2224      2234      2244      2254
   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 5VB2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5VB2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5VB2)

(-) Gene Ontology  (7, 7)

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

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        A8EVM5_ARCB4 | A8EVM5: 3rvy 3rvz 3rw0 4ekw 4ms2 4mtf 4mtg 4mto 4mvm 4mvo 4mvq 4mvr 4mvs 4mvu 4mvz 4mw3 4mw8 5ek0 5klb 5klg 5kls 5kmd 5kmf 5kmh 5vb8

(-) Related Entries Specified in the PDB File

5vb8