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(-) Description

Title :  PARALLEL HOMODIMER STRUCTURES OF VOLTAGE-GATED SODIUM CHANNEL BETA4 FOR CELL-CELL ADHESION
 
Authors :  H. Shimizu, S. Yokoyama
Date :  15 Mar 17  (Deposition) - 05 Jul 17  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ig, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Shimizu, A. Tosaki, N. Ohsawa, Y. Ishizuka-Katsura, S. Shoji, H. Miyazaki, F. Oyama, T. Terada, M. Shirouzu, S. Sekine, N. Nukina, S. Yokoyama
Parallel Homodimer Structures Of The Extracellular Domains Of The Voltage-Gated Sodium Channel Beta-4 Subunit Explain Its Role In Cell-Cell Adhesion
J. Biol. Chem. 2017
PubMed: search  |  Reference-DOI: 10.1074/JBC.M117.786509

(-) Compounds

Molecule 1 - SODIUM CHANNEL SUBUNIT BETA-4
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI K-12
    Expression System Strain: K-12
    Expression System Taxid: 83333
    Fragment: UNP RESIDUES 30-152
    Gene: SCN4B
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2P332Ligand/Ion3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
3PG43Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:48 , HIS A:65 , PHE A:66 , ARG A:67 , GLY A:82 , THR A:83 , HIS A:132 , HOH A:304binding site for residue P33 A 201
2AC2SOFTWARETYR A:70 , LYS A:77 , LEU A:79 , ASP A:97 , ASP A:98 , ARG A:100 , SER A:124 , ASP A:125 , TYR A:129binding site for residue PG4 A 202
3AC3SOFTWARETHR A:39 , ASP A:40 , THR B:39 , ASP B:40binding site for residue PG4 A 203
4AC4SOFTWAREGLY A:46 , THR A:47 , GLU A:48 , ASP A:120 , LYS A:128 , THR A:130 , HIS A:132binding site for residue GOL A 204
5AC5SOFTWAREGLU B:48 , HIS B:65 , PHE B:66 , ARG B:67 , GLU B:81 , GLY B:82 , HIS B:132 , HOH B:306binding site for residue P33 B 201
6AC6SOFTWARETYR B:70 , LYS B:77 , LEU B:79 , ASP B:97 , ASP B:98 , ARG B:100 , ILE B:101 , SER B:124 , ASP B:125 , TYR B:129binding site for residue PG4 B 202
7AC7SOFTWAREGLY B:46 , THR B:47 , GLU B:48 , ARG B:119 , ASP B:120 , LYS B:128 , THR B:130 , HIS B:132binding site for residue GOL B 203

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:58 -B:58

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5XAW)

(-) 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:112
                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eeeeee.....eee..eeee....eeeeeeeeeee..eeeeeeeeeeee....eeeeee....eee.....eee...hhhhheeeeeeee...eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 5xaw A  30 SLEVSVGKATDIYAVNGTEILLPCTFSSCFGFEDLHFRWTYNSSDAFKILIEGTVKNEKSDPKVTLKDDDRITLVNNISIVLRDLEFSDTGKYTCHVKNPLQHHATIFLQVV 152
                                    39        49        59        69        79        89        99    || 116       126       136|      150  
                                                                                                    104|                     136|           
                                                                                                     112                      141           


Chain B from PDB  Type:PROTEIN  Length:110
                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eeeeeee....eee..eee.....eeeeeeeeeee..eeeeeeeeeeee....eeeeee....eee.....eee...hhhhheeeeeeee..eeeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 5xaw B  30 SLEVSVGKATDIYAVNGTEILLPCTFSSCFGFEDLHFRWTYNSSDAFKILIEGTVKNEKSDPKVTLKDDDRITLVNNISIVLRDLEFSDTGKYTCHVKNQHHATIFLQVV 152
                                    39        49        59        69        79        89        99    || 116       126       142       152
                                                                                                    104|                    135|          
                                                                                                     112                     142
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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 5XAW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (26, 26)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        SCN4B_HUMAN | Q8IWT1: 4mz2 4mz3

(-) Related Entries Specified in the PDB File

5xax