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(-) Description

Title :  STRUCTURE AND FUNCTION OF THE DIVALENT ANION/NA+ SYMPORTER FROM VIBRIO CHOLERAE AND A HUMANIZED VARIANT
 
Authors :  M. Lu
Date :  24 Jan 17  (Deposition) - 17 May 17  (Release) - 17 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.78
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Nie, S. Stark, J. Symersky, R. S. Kaplan, M. Lu
Structure And Function Of The Divalent Anion/Na(+) Symporte From Vibrio Cholerae And A Humanized Variant.
Nat Commun V. 8 15009 2017
PubMed-ID: 28436435  |  Reference-DOI: 10.1038/NCOMMS15009

(-) Compounds

Molecule 1 - TRANSPORTER, NADC FAMILY
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: VC_A0025
    Organism Scientific: VIBRIO CHOLERAE SEROTYPE O1 (STRAIN ATCC 39315 / EL TOR INABA N16961)
    Organism Taxid: 243277
    Strain: ATCC 39315 / EL TOR INABA N16961

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1CIT4Ligand/IonCITRIC ACID
2NA8Ligand/IonSODIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CIT2Ligand/IonCITRIC ACID
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CIT2Ligand/IonCITRIC ACID
2NA-1Ligand/IonSODIUM ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:146 , SER A:150 , ASN A:151 , GLY A:193 , GLY A:199binding site for residue NA A 501
02AC2SOFTWARETHR A:373 , THR A:376 , SER A:377 , ASN A:378 , ALA A:420binding site for residue NA A 502
03AC3SOFTWAREASN A:151 , THR A:152 , THR A:200 , GLY A:201 , PRO A:202 , ILE A:322 , SER A:377 , ASN A:378 , VAL A:379 , THR A:421 , PRO A:422binding site for residue CIT A 503
04AC4SOFTWARESER B:146 , SER B:150 , ASN B:151 , GLY B:193 , GLY B:199binding site for residue NA B 501
05AC5SOFTWARETHR B:373 , THR B:376 , SER B:377 , ASN B:378 , ALA B:420binding site for residue NA B 502
06AC6SOFTWAREASN B:151 , THR B:152 , THR B:200 , GLY B:201 , PRO B:202 , ILE B:322 , SER B:377 , ASN B:378 , VAL B:379 , THR B:421 , PRO B:422binding site for residue CIT B 503
07AC7SOFTWARESER C:146 , SER C:150 , ASN C:151 , GLY C:193 , GLY C:199binding site for residue NA C 501
08AC8SOFTWARETHR C:373 , THR C:376 , SER C:377 , ASN C:378 , ALA C:420binding site for residue NA C 502
09AC9SOFTWAREASN C:151 , THR C:152 , THR C:200 , GLY C:201 , PRO C:202 , ILE C:322 , SER C:377 , ASN C:378 , VAL C:379 , THR C:421 , PRO C:422binding site for residue CIT C 503
10AD1SOFTWARESER D:146 , SER D:150 , ASN D:151 , GLY D:193 , GLY D:199binding site for residue NA D 501
11AD2SOFTWARETHR D:373 , THR D:376 , SER D:377 , ASN D:378 , ALA D:420binding site for residue NA D 502
12AD3SOFTWAREASN D:151 , THR D:152 , THR D:200 , GLY D:201 , PRO D:202 , ILE D:322 , SER D:377 , ASN D:378 , VAL D:379 , THR D:421 , PRO D:422binding site for residue CIT D 503

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5ULD)

(-) 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:445
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh........hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uld A  18 LHRNSLIVLADVALFLALYHFLPFEHNVVLGISMLAFIAVLWLTEALHVTVTAILVPVMAVFFGIFETQAALNNFANSIIFLFLGGFALAAAMHHQGLDKVIADKVLAMAQGKMSVAVFMLFGVTALLSMWISNTATAAMMLPLVLGVLSKVDADKQRSTYVFVLLGVAYSASIGGIATLVGTGPNAIAAAEVGLSFTDWMKFGLPTAMMMLPMAIAILYFLLKPTLNGMFELDRAPVNWDKGKVVTLGIFGLTVFLWIFSSPINAALGGFKSFDTLVALGAILMLSFARVVHWKEIQKTADWGILLLFGGGLCLSNVLKQTGTSVFLANALSDMVSHMGIFVVILVVATFVVFLTEFTSNVATTTLLIPVFATVAEAFGMSPVLLSVLIAVAASCAFMLPVATPPNAIVFASGHIKQSEMMRVGLYLNIACIGLLTAIAMLFWQ 462
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457     


Chain B from PDB  Type:PROTEIN  Length:445
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh........hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uld B  18 LHRNSLIVLADVALFLALYHFLPFEHNVVLGISMLAFIAVLWLTEALHVTVTAILVPVMAVFFGIFETQAALNNFANSIIFLFLGGFALAAAMHHQGLDKVIADKVLAMAQGKMSVAVFMLFGVTALLSMWISNTATAAMMLPLVLGVLSKVDADKQRSTYVFVLLGVAYSASIGGIATLVGTGPNAIAAAEVGLSFTDWMKFGLPTAMMMLPMAIAILYFLLKPTLNGMFELDRAPVNWDKGKVVTLGIFGLTVFLWIFSSPINAALGGFKSFDTLVALGAILMLSFARVVHWKEIQKTADWGILLLFGGGLCLSNVLKQTGTSVFLANALSDMVSHMGIFVVILVVATFVVFLTEFTSNVATTTLLIPVFATVAEAFGMSPVLLSVLIAVAASCAFMLPVATPPNAIVFASGHIKQSEMMRVGLYLNIACIGLLTAIAMLFWQ 462
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457     


Chain C from PDB  Type:PROTEIN  Length:445
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh........hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uld C  18 LHRNSLIVLADVALFLALYHFLPFEHNVVLGISMLAFIAVLWLTEALHVTVTAILVPVMAVFFGIFETQAALNNFANSIIFLFLGGFALAAAMHHQGLDKVIADKVLAMAQGKMSVAVFMLFGVTALLSMWISNTATAAMMLPLVLGVLSKVDADKQRSTYVFVLLGVAYSASIGGIATLVGTGPNAIAAAEVGLSFTDWMKFGLPTAMMMLPMAIAILYFLLKPTLNGMFELDRAPVNWDKGKVVTLGIFGLTVFLWIFSSPINAALGGFKSFDTLVALGAILMLSFARVVHWKEIQKTADWGILLLFGGGLCLSNVLKQTGTSVFLANALSDMVSHMGIFVVILVVATFVVFLTEFTSNVATTTLLIPVFATVAEAFGMSPVLLSVLIAVAASCAFMLPVATPPNAIVFASGHIKQSEMMRVGLYLNIACIGLLTAIAMLFWQ 462
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457     


Chain D from PDB  Type:PROTEIN  Length:445
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh........hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uld D  18 LHRNSLIVLADVALFLALYHFLPFEHNVVLGISMLAFIAVLWLTEALHVTVTAILVPVMAVFFGIFETQAALNNFANSIIFLFLGGFALAAAMHHQGLDKVIADKVLAMAQGKMSVAVFMLFGVTALLSMWISNTATAAMMLPLVLGVLSKVDADKQRSTYVFVLLGVAYSASIGGIATLVGTGPNAIAAAEVGLSFTDWMKFGLPTAMMMLPMAIAILYFLLKPTLNGMFELDRAPVNWDKGKVVTLGIFGLTVFLWIFSSPINAALGGFKSFDTLVALGAILMLSFARVVHWKEIQKTADWGILLLFGGGLCLSNVLKQTGTSVFLANALSDMVSHMGIFVVILVVATFVVFLTEFTSNVATTTLLIPVFATVAEAFGMSPVLLSVLIAVAASCAFMLPVATPPNAIVFASGHIKQSEMMRVGLYLNIACIGLLTAIAMLFWQ 462
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457
   Legend:   → Mismatch (orange background)
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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 5ULD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q9KNE0_VIBCH | Q9KNE0: 5ul7 5ul9 5ule
UniProtKB/TrEMBL
        Q9KNE0_VIBCH | Q9KNE0: 4f35

(-) Related Entries Specified in the PDB File

5ul7 5ul9 5ule