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(-) Description

Title :  OPEN-FORM NAVMS SODIUM CHANNEL PORE (WITH C-TERMINAL DOMAIN)
 
Authors :  C. Bagneris, C. E. Naylor, B. A. Wallace
Date :  21 Jan 13  (Deposition) - 02 Oct 13  (Release) - 02 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.92
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  C,D  (2x)
Keywords :  Transport Protein, Selectivity Filter, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Bagneris, P. G. Decaen, B. A. Hall, C. E. Naylor, D. E. Clapham, C. W. M. Kay, B. A. Wallace
Role Of The C-Terminal Domain In The Structure And Function Of Tetrameric Sodium Channels.
Nat. Commun. V. 4 2465 2013
PubMed-ID: 24051986  |  Reference-DOI: 10.1038/NCOMMS3465
(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 Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: C41
    Expression System Vector: PET15B
    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): AB  
Biological Unit 2 (2x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
112P3Ligand/IonDODECAETHYLENE GLYCOL
22CV4Ligand/IonHEGA-10
3NA5Ligand/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  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:40 , LYS A:41 , TYR A:44 , HOH A:3033 , PRO B:68 , TRP B:71BINDING SITE FOR RESIDUE 2CV A1100
02AC2SOFTWARETYR A:28 , HIS A:67 , PRO A:68 , ASN A:69 , ALA A:70 , VAL A:72BINDING SITE FOR RESIDUE 12P A1200
03AC3SOFTWAREGLU A:53 , GLU B:53 , SER B:54BINDING SITE FOR RESIDUE NA A1400
04AC4SOFTWARETHR B:51BINDING SITE FOR RESIDUE NA A1402
05AC5SOFTWAREPRO A:68 , TRP A:71 , ASP B:38 , SER B:40 , LYS B:41 , TYR B:44 , HOH B:3027BINDING SITE FOR RESIDUE 2CV B1100
06AC6SOFTWAREALA B:20 , TYR B:28 , HIS B:67 , ASN B:69BINDING SITE FOR RESIDUE 12P B1200
07AC7SOFTWAREGLU C:34 , SER C:40 , LYS C:41 , TYR C:44 , HOH C:3017 , HOH C:3038 , PRO D:68 , ASN D:69 , TRP D:71 , HOH D:3033BINDING SITE FOR RESIDUE 2CV C1100
08AC8SOFTWARELEU C:12 , VAL C:15 , VAL C:16 , ILE C:19 , ALA C:20 , MET C:23 , TYR C:28 , HIS C:67 , ASN C:69 , ALA C:70 , PHE C:73BINDING SITE FOR RESIDUE 12P C1200
09AC9SOFTWARETHR C:51BINDING SITE FOR RESIDUE NA C1401
10BC1SOFTWAREMET C:64 , PRO C:68 , ASN C:69 , TRP C:71 , PHE D:17 , GLU D:34 , SER D:40 , LYS D:41 , TYR D:44 , HOH D:3042BINDING SITE FOR RESIDUE 2CV D1100

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ZJZ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3ZJZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ZJZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ZJZ)

(-) Exons   (0, 0)

(no "Exon" information available for 3ZJZ)

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

    Alignment length:92
                                   140       150       160       170       180       190       200       210       220  
         A0L5S6_MAGMM   131 VGSVAALLTVVFYIAAVMATNLYGATFPEWFGDLSKSLYTLFQVMTLESWSMGIVRPVMNVHPNAWVFFIPFIMLTTFTVLNLFIGIIVDAM 222
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 3zjz A   6 VGSVAALLTVVFYIAAVMATNLYGATFPEWFGDLSKSLYTLFQVMTLESWSMGIVRPVMNVHPNAWVFFIPFIMLTTFTVLNLFIGIIVDAM  97
                                    15        25        35        45        55        65        75        85        95  


Chain B from PDB  Type:PROTEIN  Length:92
 aligned with A0L5S6_MAGMM | A0L5S6 from UniProtKB/TrEMBL  Length:274

    Alignment length:92
                                   140       150       160       170       180       190       200       210       220  
         A0L5S6_MAGMM   131 VGSVAALLTVVFYIAAVMATNLYGATFPEWFGDLSKSLYTLFQVMTLESWSMGIVRPVMNVHPNAWVFFIPFIMLTTFTVLNLFIGIIVDAM 222
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 3zjz B   6 VGSVAALLTVVFYIAAVMATNLYGATFPEWFGDLSKSLYTLFQVMTLESWSMGIVRPVMNVHPNAWVFFIPFIMLTTFTVLNLFIGIIVDAM  97
                                    15        25        35        45        55        65        75        85        95  


Chain C from PDB  Type:PROTEIN  Length:91
 aligned with A0L5S6_MAGMM | A0L5S6 from UniProtKB/TrEMBL  Length:274

    Alignment length:91
                                   139       149       159       169       179       189       199       209       219 
         A0L5S6_MAGMM   130 GVGSVAALLTVVFYIAAVMATNLYGATFPEWFGDLSKSLYTLFQVMTLESWSMGIVRPVMNVHPNAWVFFIPFIMLTTFTVLNLFIGIIVD 220
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 3zjz C   5 GVGSVAALLTVVFYIAAVMATNLYGATFPEWFGDLSKSLYTLFQVMTLESWSMGIVRPVMNVHPNAWVFFIPFIMLTTFTVLNLFIGIIVD  95
                                    14        24        34        44        54        64        74        84        94 


Chain D from PDB  Type:PROTEIN  Length:91
 aligned with A0L5S6_MAGMM | A0L5S6 from UniProtKB/TrEMBL  Length:274

    Alignment length:91
                                   139       149       159       169       179       189       199       209       219 
         A0L5S6_MAGMM   130 GVGSVAALLTVVFYIAAVMATNLYGATFPEWFGDLSKSLYTLFQVMTLESWSMGIVRPVMNVHPNAWVFFIPFIMLTTFTVLNLFIGIIVD 220
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 3zjz D   5 GVGSVAALLTVVFYIAAVMATNLYGATFPEWFGDLSKSLYTLFQVMTLESWSMGIVRPVMNVHPNAWVFFIPFIMLTTFTVLNLFIGIIVD  95
                                    14        24        34        44        54        64        74        84        94
   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 3ZJZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ZJZ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZJZ)

(-) 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: 4cbc 4f4l 4oxs 4p2z 4p30 4p9o 4p9p 4pa3 4pa4 4pa6 4pa7 4pa9 4x88 4x89 4x8a 5bzb 5hvd 5hvx

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