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 :  CRYSTAL STRUCTURE OF THE AG(I) FORM OF E. COLI CUER, A COPPER EFFLUX REGULATOR
 
Authors :  A. Changela, K. Chen, Y. Xue, J. Holschen, C. E. Outten, T. V. O'Halloran, A. Mondragon
Date :  15 Jul 03  (Deposition) - 16 Sep 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.07
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Merr Family Transcriptional Regulator, Copper Efflux Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Changela, K. Chen, Y. Xue, J. Holschen, C. E. Outten, T. V. O'Halloran, A. Mondragon
Molecular Basis Of Metal-Ion Selectivity And Zeptomolar Sensitivity By Cuer
Science V. 301 1383 2003
PubMed-ID: 12958362  |  Reference-DOI: 10.1126/SCIENCE.1085950
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR CUER
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET24A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CUER
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: COPPER EFFLUX REGULATOR, COPPER EXPORT REGULATOR

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1AG2Ligand/IonSILVER ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:77 , CYS B:112 , CYS B:120BINDING SITE FOR RESIDUE AG B 300
2AC2SOFTWARECYS A:112 , CYS A:120 , PRO A:121 , ILE A:122 , SER B:77BINDING SITE FOR RESIDUE AG A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Q06)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Q06)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Q06)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_MERR_2PS50937 MerR-type HTH domain profile.CUER_ECOLI1-69
 		  2A:1-69
B:1-69
2HTH_MERR_1PS00552 MerR-type HTH domain signature.CUER_ECOLI4-26
 		  2A:4-26
B:4-26

(-) Exons   (0, 0)

(no "Exon" information available for 1Q06)

(-) 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:122
 aligned with CUER_ECOLI | P0A9G4 from UniProtKB/Swiss-Prot  Length:135

    Alignment length:127
                                    10        20        30        40        50        60        70        80        90       100       110       120       
           CUER_ECOLI     1 MNISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNLFNDPQRHSADVKRRTLEKVAEIERHIEELQSMRDQLLALANACPGDDSADCPIIENLS 127
               SCOP domains d1q06a_ A: Transcriptional regulator CueR                                                                                       SCOP domains
               CATH domains 1q06A00 A:1-127  [code=1.10.1660.10, no name defined]                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.hhhhhhhhhhh......ee.....ee.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...-----hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) HTH_MERR_2  PDB: A:1-69 UniProt: 1-69                                ---------------------------------------------------------- PROSITE (1)
                PROSITE (2) ---HTH_MERR_1  PDB: A:4-26----------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1q06 A   1 MNISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNLFNDPQRHSADVKRRTLEKVAEIERHIEELQSMRDQLLALANACPG-----CPIIENLS 127
                                    10        20        30        40        50        60        70        80        90       100       110   |   120       
                                                                                                                                           114   120       


Chain B from PDB  Type:PROTEIN  Length:126
 aligned with CUER_ECOLI | P0A9G4 from UniProtKB/Swiss-Prot  Length:135

    Alignment length:127
                                    10        20        30        40        50        60        70        80        90       100       110       120       
           CUER_ECOLI     1 MNISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNLFNDPQRHSADVKRRTLEKVAEIERHIEELQSMRDQLLALANACPGDDSADCPIIENLS 127
               SCOP domains d1q06b_ B: Transcriptional regulator CueR                                                                                       SCOP domains
               CATH domains 1q06B00 B:1-127  [code=1.10.1660.10, no name defined]                                                                           CATH domains
           Pfam domains (1) -MerR-1q06B01 B:2-39                   ----MerR-DNA-bind-1q06B03 B:44-108                                   ------------------- Pfam domains (1)
           Pfam domains (2) -MerR-1q06B02 B:2-39                   ----MerR-DNA-bind-1q06B04 B:44-108                                   ------------------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhh.hhhhhhhhhhh......ee.....ee.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..-hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) HTH_MERR_2  PDB: B:1-69 UniProt: 1-69                                ---------------------------------------------------------- PROSITE (1)
                PROSITE (2) ---HTH_MERR_1  PDB: B:4-26----------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1q06 B   1 MNISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNLFNDPQ-HSADVKRRTLEKVAEIERHIEELQSMRDQLLALANACPGDDSADCPIIENLS 127
                                    10        20        30        40        50        60        70   | |  80        90       100       110       120       
                                                                                                    74 |                                                   
                                                                                                      76
   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, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (CUER_ECOLI | P0A9G4)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000986    bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for a bacterial-type RNA polymerase.
    GO:0001204    bacterial-type RNA polymerase transcription factor activity, metal ion regulated sequence-specific DNA binding    Interacting selectively and non-covalently with a specific bacterial-type transcription regulatory DNA sequence and interacting selectively and non-covalently with any metal ion(s) and responding, e.g. by conformational change, to changes in the cellular level of those metal ions, in such a way that metal ion binding regulates the activity of the transcription factor in order to modulate transcription by a bacterial-type RNA polymerase. Specific mechanisms include increasing or decreasing the ability of the transcription factor to interact selectively and non-covalently with a specific DNA sequence (for example S. cerevisiae Cup2p or the prokaryotic SmtB/ArsR family, changing the conformation of transcription factor bound DNA between the apo- and metal-bound forms of the transcription factor. Additional mechanisms may exist.
    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:0001131    transcription factor activity, bacterial-type RNA polymerase core promoter proximal region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for a bacterial-type RNA polymerase in order to modulate transcription by bacterial-type RNA polymerase. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    GO:0071248    cellular response to metal ion    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a metal ion stimulus.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
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
    AG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1q06)
 

(-) 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
  1q06
    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
  CUER_ECOLI | P0A9G4
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
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
  CUER_ECOLI | P0A9G4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CUER_ECOLI | P0A9G4: 1q05 1q07 4wls 4wlw

(-) Related Entries Specified in the PDB File

1q05 THE CU(I) FORM OF E. COLI CUER
1q07 THE AU(I) FORM OF E. COLI CUER