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(-) Description

Title :  STRUCTURE OF NAVMS PORE AND C-TERMINAL DOMAIN CRYSTALLISED IN PRESENCE OF CHANNEL BLOCKING COMPOUND
 
Authors :  C. E. Naylor, C. Bagneris, B. A. Wallace
Date :  07 Apr 14  (Deposition) - 04 Jun 14  (Release) - 06 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.02
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  C,D  (2x)
Keywords :  Channel Blocking Compound, Sodium Channel, Pore, Membrane Protein, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Bagneris, P. G. Decaen, C. E. Naylor, D. C. Pryde, I. Nobeli, D. E. Clapham, B. A. Wallace
Prokaryotic Navms Channel As A Structural And Functional Model For Eukaryotic Sodium Channel Antagonism.
Proc. Natl. Acad. Sci. Usa V. 111 8428 2014
PubMed-ID: 24850863  |  Reference-DOI: 10.1073/PNAS.1406855111
(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
    Expression System Plasmid: PET15B
    Expression System Strain: C41
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MMC1_0798
    Organism Scientific: MAGNETOCOCCUS SP.
    Organism Taxid: 156889
    Other Details: PORE AND C-TERMINAL DOMAIN
    Strain: MC-1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (2x): AB  
Biological Unit 2 (2x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
112P3Ligand/IonDODECAETHYLENE GLYCOL
22CV4Ligand/IonHEGA-10
3NA7Ligand/IonSODIUM ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
112P4Ligand/IonDODECAETHYLENE GLYCOL
22CV4Ligand/IonHEGA-10
3NA-1Ligand/IonSODIUM ION
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
112P2Ligand/IonDODECAETHYLENE GLYCOL
22CV4Ligand/IonHEGA-10
3NA-1Ligand/IonSODIUM ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:193 , ASN A:194 , TRP A:196 , SER B:165 , LYS B:166 , PHE B:172binding site for residue 2CV A 301
02AC2SOFTWAREILE A:144 , ALA A:145 , MET A:148 , TYR A:153 , ASN A:194 , VAL A:197 , PHE A:198binding site for residue 12P A 302
03AC3SOFTWAREHOH A:402 , NA B:304binding site for residue NA A 303
04AC4SOFTWARESER A:165 , LYS A:166 , PRO B:193 , ASN B:194 , TRP B:196binding site for residue 2CV B 301
05AC5SOFTWARETYR B:153 , VAL B:197binding site for residue 12P B 302
06AC6SOFTWARENA B:304 , NA B:305binding site for residue NA B 303
07AC7SOFTWARENA A:303 , NA B:303binding site for residue NA B 304
08AC8SOFTWARENA B:303binding site for residue NA B 305
09AC9SOFTWAREPRO C:193 , ASN C:194 , TRP C:196 , PHE D:142 , SER D:165binding site for residue 2CV C 301
10AD1SOFTWARETYR C:153 , HIS C:192 , ASN C:194 , PHE C:198binding site for residue 12P C 302
11AD2SOFTWARENA D:302binding site for residue NA C 303
12AD3SOFTWAREPHE C:142 , SER C:165 , PRO D:193 , ASN D:194 , TRP D:196binding site for residue 2CV D 301
13AD4SOFTWARENA C:303binding site for residue NA D 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4PA7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4PA7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PA7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PA7)

(-) Exons   (0, 0)

(no "Exon" information available for 4PA7)

(-) 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:92
                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh......hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 4pa7 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..hhhhhhhhhhhhhhhhhhhhh......hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 4pa7 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..hhhhhhhhhhhhhhhhhhhhh......hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 4pa7 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..hhhhhhhhhhhhhhhhhhhhh......hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 4pa7 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 4PA7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PA7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PA7)

(-) Gene Ontology  (7, 7)

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 Related Entries

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

(-) Related Entries Specified in the PDB File

4cbc WILD-TYPE APO CHANNEL
4p2z MUTANT T207A/F214A CHANNEL
4p90 CHANNEL IN PRESENCE OF CHANNEL BLOCKING COMPOUND