Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CROSSTALK BETWEEN CU(I) AND ZN(II) HOMEOSTASIS
 
Authors :  A. Badarau, A. Basle, S. J. Firbank, C. Denninson
Date :  07 Oct 11  (Deposition) - 12 Dec 12  (Release) - 05 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Transport Protein, Copper Homeostasis, Zinc Homeostasis, Metal-Transporting Atpases (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Badarau, A. Basle, S. J. Firbank, C. Dennison
Crosstalk Between Cu(I) And Zn(Ii) Homeostasis Via Atx1 And Cognate Domains.
Chem. Commun. (Camb. ) V. 49 8000 2013
PubMed-ID: 23926594  |  Reference-DOI: 10.1039/C3CC42709A

(-) Compounds

Molecule 1 - SSR2857 PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET29A
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 2-64
    Organism Scientific: SYNECHOCYSTIS SP. PCC 6803
    Organism Taxid: 1148
    Synonym: ATX1

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2NA2Ligand/IonSODIUM ION
3ZN2Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:12 , CYS A:15 , CYS B:12 , CYS B:15BINDING SITE FOR RESIDUE ZN A 65
2AC2SOFTWAREHOH A:2016 , HOH C:2040BINDING SITE FOR RESIDUE NA A1065
3AC3SOFTWARECYS C:12 , CYS C:15 , CYS D:12 , CYS D:15BINDING SITE FOR RESIDUE ZN C 65
4AC4SOFTWAREGLN A:51 , GLN C:29BINDING SITE FOR RESIDUE CL C1065
5AC5SOFTWAREHOH A:2025 , HOH C:2027 , HOH C:2038 , HOH C:2039BINDING SITE FOR RESIDUE NA C1066
6AC6SOFTWARELEU B:36 , LEU D:36BINDING SITE FOR RESIDUE CL D1065

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4A46)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4A46)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4A46)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4A46)

(-) Exons   (0, 0)

(no "Exon" information available for 4A46)

(-) 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:63
 aligned with P73213_SYNY3 | P73213 from UniProtKB/TrEMBL  Length:64

    Alignment length:63
                                    11        21        31        41        51        61   
          P73213_SYNY3    2 TIQLTVPTIACEACAEAVTKAVQNEDAQATVQVDLTSKKVTITSALGEEQLRTAIASAGHEVE 64
               SCOP domains d4a46a_ A: Copper chaperone                                     SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....hhhhhhhhhhhhhhhh...eeee.....eeeee...hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                  4a46 A  2 TIQLTVPTIACEACAEAVTKAVQNEDAQATVQVDLTSKKVTITSALGEEQLRTAIASAGHEVE 64
                                    11        21        31        41        51        61   


Chain B from PDB  Type:PROTEIN  Length:63
 aligned with P73213_SYNY3 | P73213 from UniProtKB/TrEMBL  Length:64

    Alignment length:63
                                    11        21        31        41        51        61   
          P73213_SYNY3    2 TIQLTVPTIACEACAEAVTKAVQNEDAQATVQVDLTSKKVTITSALGEEQLRTAIASAGHEVE 64
               SCOP domains d4a46b_ B: Copper chaperone                                     SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....hhhhhhhhhhhhhhhh...eeeee....eeeee...hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                  4a46 B  2 TIQLTVPTIACEACAEAVTKAVQNEDAQATVQVDLTSKKVTITSALGEEQLRTAIASAGHEVE 64
                                    11        21        31        41        51        61   


Chain C from PDB  Type:PROTEIN  Length:63
 aligned with P73213_SYNY3 | P73213 from UniProtKB/TrEMBL  Length:64

    Alignment length:63
                                    11        21        31        41        51        61   
          P73213_SYNY3    2 TIQLTVPTIACEACAEAVTKAVQNEDAQATVQVDLTSKKVTITSALGEEQLRTAIASAGHEVE 64
               SCOP domains d4a46c_ C: Copper chaperone                                     SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....hhhhhhhhhhhhhhhh...eeee.....eeeee...hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                  4a46 C  2 TIQLTVPTIACEACAEAVTKAVQNEDAQATVQVDLTSKKVTITSALGEEQLRTAIASAGHEVE 64
                                    11        21        31        41        51        61   


Chain D from PDB  Type:PROTEIN  Length:63
 aligned with P73213_SYNY3 | P73213 from UniProtKB/TrEMBL  Length:64

    Alignment length:63
                                    11        21        31        41        51        61   
          P73213_SYNY3    2 TIQLTVPTIACEACAEAVTKAVQNEDAQATVQVDLTSKKVTITSALGEEQLRTAIASAGHEVE 64
               SCOP domains d4a46d_ D: Copper chaperone                                     SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....hhhhhhhhhhhhhhhh...eeeee....eeeee...hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                  4a46 D  2 TIQLTVPTIACEACAEAVTKAVQNEDAQATVQVDLTSKKVTITSALGEEQLRTAIASAGHEVE 64
                                    11        21        31        41        51        61
   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  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4A46)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4A46)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (P73213_SYNY3 | P73213)
molecular function
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0046916    cellular transition metal ion homeostasis    Any process involved in the maintenance of an internal steady state of transition metal ions at the level of a cell. A transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver.
    GO:0030001    metal ion transport    The directed movement of metal ions, any metal ion with an electric charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4a46)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4a46
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  P73213_SYNY3 | P73213
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  P73213_SYNY3 | P73213
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        P73213_SYNY3 | P73213: 1sb6 2xmj 2xmk 2xmm 2xmt 2xmu 2xmv 4a47

(-) Related Entries Specified in the PDB File

1sb6 SOLUTION STRUCTURE OF A CYANOBACTERIAL COPPERMETALLOCHAPERONE, SCATX1
2xmj VISUALISING THE METAL-BINDING VERSATILITY OF COPPER TRAFFICKING SITES: ATX1 SIDE-TO-SIDE (AEROBIC)
2xmk VISUALISING THE METAL-BINDING VERSATILITY OF COPPER TRAFFICKING SITES: ATX1 SIDE-TO-SIDE (ANAEROBIC)
2xmm VISUALISING THE METAL-BINDING VERSATILITY OF COPPER TRAFFICKING SITES: H61Y ATX1 SIDE-TO-SIDE
2xmt COPPER CHAPERONE ATX1 FROM SYNECHOCYSTIS PCC6803 (CU1 FORM)
2xmu COPPER CHAPERONE ATX1 FROM SYNECHOCYSTIS PCC6803 (CU2 FORM)
2xmv COPPER CHAPERONE ATX1 FROM SYNECHOCYSTIS PCC6803 (CU1, TRIMERIC FORM, HIS61TYR MUTANT)
4a47 CROSSTALK BETWEEN CU(I) AND ZN(II) HOMEOSTASIS
4a48 CROSSTALK BETWEEN CU(I) AND ZN(II) HOMEOSTASIS