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(-) Description

Title :  NAVMS VOLTAGE-GATED SODIUM CHANNEL PORE AND C-TERMINAL DOMAIN
 
Authors :  C. E. Naylor, C. Bagneris, B. A. Wallace
Date :  11 Jun 15  (Deposition) - 24 Feb 16  (Release) - 27 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Transport Protein, Selectivity Filter, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. E. Naylor, C. Bagneris, P. G. Decaen, A. Sula, A. Scaglione, D. E. Clapham, B. A. Wallace
Molecular Basis Of Ion Permeability In A Voltage-Gated Sodium Channel.
Embo J. V. 35 820 2016
PubMed-ID: 26873592  |  Reference-DOI: 10.15252/EMBJ.201593285
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ION TRANSPORT PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Taxid: 469008
    Expression System Variant: C41
    Expression System Vector Type: PLASMID
    Fragment: NAVMS PORE AND C-TERMINAL DOMAIN, UNP RESIDUES 130-274
    Gene: MMC1_0798
    Organism Scientific: MAGNETOCOCCUS MARINUS MC-1
    Organism Taxid: 156889
    Other Details: C-TERMINAL IS NOT VISIBLE IN THE ELECTRON DENSITY
    Synonym: NAVMS

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric/Biological Unit (3, 13)
No.NameCountTypeFull Name
112P3Ligand/IonDODECAETHYLENE GLYCOL
22CV4Ligand/IonHEGA-10
3NA6Ligand/IonSODIUM ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:153 , HIS A:192 , ASN A:194 , ALA A:195 , HOH A:406 , HOH A:422binding site for residue 12P A 301
02AC2SOFTWARENA A:303binding site for residue NA A 302
03AC3SOFTWARENA A:302 , HOH A:443binding site for residue NA A 303
04AC4SOFTWAREHOH A:440 , HOH A:443 , HOH B:417 , HOH B:452binding site for residue NA A 304
05AC5SOFTWAREMET A:189 , PRO A:193 , TRP A:196 , GLU B:159 , SER B:165 , LYS B:166 , TYR B:169 , HOH B:406 , HOH B:415binding site for residue 2CV B 301
06AC6SOFTWARESER A:165 , LYS A:166 , MET B:189 , PRO B:193 , TRP B:196 , HOH B:404 , HOH B:409 , HOH B:418binding site for residue 2CV B 302
07AC7SOFTWARETYR B:153 , HIS B:192 , VAL B:197 , PHE B:198 , HOH B:402binding site for residue 12P B 303
08AC8SOFTWARETYR C:153 , ALA C:195 , VAL C:197 , PHE C:198binding site for residue 12P C 301
09AC9SOFTWAREHOH C:417 , NA D:303 , HOH D:415binding site for residue NA C 302
10AD1SOFTWAREHOH C:423 , HOH C:435 , HOH C:437 , HOH D:435binding site for residue NA C 303
11AD2SOFTWAREARG C:186 , MET C:189 , PRO C:193 , ASN C:194 , TRP C:196 , HOH C:401 , PHE D:142 , GLU D:159 , SER D:165 , LYS D:166 , TYR D:169 , HOH D:402 , HOH D:411 , HOH D:414binding site for residue 2CV D 301
12AD3SOFTWAREGLU C:159 , SER C:165 , LYS C:166 , TYR C:169 , ARG D:186 , MET D:189 , PRO D:193 , ASN D:194 , TRP D:196 , HOH D:409 , HOH D:412 , HOH D:416 , HOH D:419binding site for residue 2CV D 302
13AD4SOFTWARENA C:302 , HOH C:417 , HOH D:415binding site for residue NA D 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5BZB)

(-) 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:92
                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.......hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 5bzb A 131 VGSVAALLTVVFYIAAVMATNLYGATFPEWFGDLSKSLYTLFQVMTLESWSMGIVRPVMNVHPNAWVFFIPFIMLTTFTVLNLFIGIIVDAM 222
                                   140       150       160       170       180       190       200       210       220  


Chain B from PDB  Type:PROTEIN  Length:90
                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.......hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 5bzb B 131 VGSVAALLTVVFYIAAVMATNLYGATFPEWFGDLSKSLYTLFQVMTLESWSMGIVRPVMNVHPNAWVFFIPFIMLTTFTVLNLFIGIIVD 220
                                   140       150       160       170       180       190       200       210       220


Chain C from PDB  Type:PROTEIN  Length:91
                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.......hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 5bzb C 130 GVGSVAALLTVVFYIAAVMATNLYGATFPEWFGDLSKSLYTLFQVMTLESWSMGIVRPVMNVHPNAWVFFIPFIMLTTFTVLNLFIGIIVD 220
                                   139       149       159       169       179       189       199       209       219 


Chain D from PDB  Type:PROTEIN  Length:91
                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.......hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 5bzb D 130 GVGSVAALLTVVFYIAAVMATNLYGATFPEWFGDLSKSLYTLFQVMTLESWSMGIVRPVMNVHPNAWVFFIPFIMLTTFTVLNLFIGIIVD 220
                                   139       149       159       169       179       189       199       209       219
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  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 5BZB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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        A0L5S6_MAGMM | A0L5S6: 3zjz 4cbc 4f4l 4oxs 4p2z 4p30 4p9o 4p9p 4pa3 4pa4 4pa6 4pa7 4pa9 4x88 4x89 4x8a 5hvd 5hvx

(-) Related Entries Specified in the PDB File

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