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(-) Description

Title :  OPEN-FORM NAVMS SODIUM CHANNEL PORE (WITH C-TERMINAL DOMAIN) AFTER THALLIUM SOAK
 
Authors :  C. Bagneris, C. E. Naylor, B. A. Wallace
Date :  12 Oct 13  (Deposition) - 28 May 14  (Release) - 25 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.66
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  C,D  (2x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Transport Protein, Sodium Channel, Selectivity Filter, Membrane 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: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: C41
    Expression System Vector Type: PLASMID
    Fragment: PORE AND CTD, RESIDUES 130-274
    Organism Scientific: MAGNETOCOCCUS MARINUS MC-1
    Organism Taxid: 156889
    Synonym: NAVMS

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
12CV6Ligand/IonHEGA-10
2NA6Ligand/IonSODIUM ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
12CV4Ligand/IonHEGA-10
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 8)
No.NameCountTypeFull Name
12CV8Ligand/IonHEGA-10
2NA-1Ligand/IonSODIUM ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:193 , ASN A:194 , TRP A:196 , HOH A:2021 , SER B:165 , LYS B:166BINDING SITE FOR RESIDUE 2CV A1201
02AC2SOFTWARETYR A:153 , VAL A:197 , PHE A:198BINDING SITE FOR RESIDUE 2CV A1202
03AC3SOFTWARENA A:1302BINDING SITE FOR RESIDUE NA A1301
04AC4SOFTWARENA A:1301BINDING SITE FOR RESIDUE NA A1302
05AC5SOFTWARESER A:165 , TYR A:169 , PRO B:193 , ASN B:194 , TRP B:196BINDING SITE FOR RESIDUE 2CV B1201
06AC6SOFTWAREALA B:145 , TYR B:153 , ALA B:195 , VAL B:197 , PHE B:198BINDING SITE FOR RESIDUE 2CV B1202
07AC7SOFTWAREPRO C:193 , ASN C:194 , TRP C:196 , HOH C:2022 , SER D:165 , LYS D:166BINDING SITE FOR RESIDUE 2CV C1201
08AC8SOFTWARENA C:1303BINDING SITE FOR RESIDUE NA C1302
09AC9SOFTWARENA C:1302BINDING SITE FOR RESIDUE NA C1303
10BC1SOFTWARESER C:165 , LYS C:166 , PRO D:193 , ASN D:194 , TRP D:196 , HOH D:2022 , HOH D:2023BINDING SITE FOR RESIDUE 2CV D1201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4CBC)

(-) 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:93
 aligned with A0L5S6_MAGMM | A0L5S6 from UniProtKB/TrEMBL  Length:274

    Alignment length:93
                                   139       149       159       169       179       189       199       209       219   
         A0L5S6_MAGMM   130 GVGSVAALLTVVFYIAAVMATNLYGATFPEWFGDLSKSLYTLFQVMTLESWSMGIVRPVMNVHPNAWVFFIPFIMLTTFTVLNLFIGIIVDAM 222
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 4cbc A 130 GVGSVAALLTVVFYIAAVMATNLYGATFPEWFGDLSKSLYTLFQVMTLESWSMGIVRPVMNVHPNAWVFFIPFIMLTTFTVLNLFIGIIVDAM 222
                                   139       149       159       169       179       189       199       209       219   


Chain B from PDB  Type:PROTEIN  Length:93
 aligned with A0L5S6_MAGMM | A0L5S6 from UniProtKB/TrEMBL  Length:274

    Alignment length:93
                                   139       149       159       169       179       189       199       209       219   
         A0L5S6_MAGMM   130 GVGSVAALLTVVFYIAAVMATNLYGATFPEWFGDLSKSLYTLFQVMTLESWSMGIVRPVMNVHPNAWVFFIPFIMLTTFTVLNLFIGIIVDAM 222
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 4cbc B 130 GVGSVAALLTVVFYIAAVMATNLYGATFPEWFGDLSKSLYTLFQVMTLESWSMGIVRPVMNVHPNAWVFFIPFIMLTTFTVLNLFIGIIVDAM 222
                                   139       149       159       169       179       189       199       209       219   


Chain C from PDB  Type:PROTEIN  Length:93
 aligned with A0L5S6_MAGMM | A0L5S6 from UniProtKB/TrEMBL  Length:274

    Alignment length:93
                                   139       149       159       169       179       189       199       209       219   
         A0L5S6_MAGMM   130 GVGSVAALLTVVFYIAAVMATNLYGATFPEWFGDLSKSLYTLFQVMTLESWSMGIVRPVMNVHPNAWVFFIPFIMLTTFTVLNLFIGIIVDAM 222
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 4cbc C 130 GVGSVAALLTVVFYIAAVMATNLYGATFPEWFGDLSKSLYTLFQVMTLESWSMGIVRPVMNVHPNAWVFFIPFIMLTTFTVLNLFIGIIVDAM 222
                                   139       149       159       169       179       189       199       209       219   


Chain D from PDB  Type:PROTEIN  Length:93
 aligned with A0L5S6_MAGMM | A0L5S6 from UniProtKB/TrEMBL  Length:274

    Alignment length:93
                                   139       149       159       169       179       189       199       209       219   
         A0L5S6_MAGMM   130 GVGSVAALLTVVFYIAAVMATNLYGATFPEWFGDLSKSLYTLFQVMTLESWSMGIVRPVMNVHPNAWVFFIPFIMLTTFTVLNLFIGIIVDAM 222
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 4cbc D 130 GVGSVAALLTVVFYIAAVMATNLYGATFPEWFGDLSKSLYTLFQVMTLESWSMGIVRPVMNVHPNAWVFFIPFIMLTTFTVLNLFIGIIVDAM 222
                                   139       149       159       169       179       189       199       209       219
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 4CBC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (A0L5S6_MAGMM | A0L5S6)
molecular function
    GO:0005216    ion channel activity    Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size).
biological process
    GO:0034220    ion transmembrane transport    A process in which an ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0055085    transmembrane transport    The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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

(-) Related Entries Specified in the PDB File

4cal OPEN-FORM NAVMS SODIUM CHANNEL PORE (WITH C-TERMINAL DOMAIN) AND BOUND DRUG
4cbd OPEN-FORM NAVMS SODIUM CHANNEL PORE (WITH C-TERMINAL DOMAIN) AND BOUND DRUG