Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - model 1, sites
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - model 1, sites
NMR Structure - model 1, sites  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION STRUCTURE OF CU(I) P174L HSCO1
 
Authors :  L. Banci, I. Bertini, S. Ciofi-Baffoni, I. Leontari, M. Martinelli, P. Palumaa, R. Sillard, S. Wang, Structural Proteomics In Europe (Spine)
Date :  20 Jul 06  (Deposition) - 16 Jan 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A
Keywords :  Chaperone, Mitochondrion, 3D-Structure, Metal-Binding, Disease Mutation, Structural Genomics, Structural Proteomics In Europe, Spine, Metal Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Banci, I. Bertini, S. Ciofi-Baffoni, I. Leontari, M. Martinelli, P. Palumaa, R. Sillard, S. Wang
Human Sco1 Functional Studies And Pathological Implications Of The P174L Mutant.
Proc. Natl. Acad. Sci. Usa V. 104 15 2007
PubMed-ID: 17182746  |  Reference-DOI: 10.1073/PNAS.0606189103
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SCO1 PROTEIN HOMOLOG, MITOCHONDRIAL
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETG-30A
    Expression System Strain: BL21DE3 GOLD
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN (RESIDUES 132-301)
    Gene: SCO1, SCOD1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Strain: HUMAN

 Structural Features

(-) Chains, Units

  
NMR Structure : 

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
1CU11Ligand/IonCOPPER (I) ION

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:169 , VAL A:172 , CYS A:173 , HIS A:260BINDING SITE FOR RESIDUE CU1 A 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2HRF)

(-) Cis Peptide Bonds  (3, 3)

NMR Structure
No.Residues
1Ser A:129 -Phe A:130
2Phe A:130 -Thr A:131
3Lys A:300 -Ser A:301

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_012109P174LSCO1_HUMANDisease (MT-C4D)104894630AL174L
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2HRF)

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002553901aENSE00001523689chr17:10600885-10600552334SCO1_HUMAN1-91910--
1.2ENST000002553902ENSE00000907744chr17:10599148-1059905891SCO1_HUMAN92-122310--
1.3bENST000002553903bENSE00000907743chr17:10596278-10596081198SCO1_HUMAN122-188671A:129-18860
1.4ENST000002553904ENSE00000907742chr17:10595281-1059518993SCO1_HUMAN188-219321A:188-21932
1.5ENST000002553905ENSE00000907741chr17:10590159-10590044116SCO1_HUMAN219-257391A:219-25739
1.6bENST000002553906bENSE00001830664chr17:10584570-10583654917SCO1_HUMAN258-301441A:258-30144

(-) Sequences/Alignments

NMR Structure
   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:173
 aligned with SCO1_HUMAN | O75880 from UniProtKB/Swiss-Prot  Length:301

    Alignment length:173
                                   138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298   
           SCO1_HUMAN   129 RHIGKPLLGGPFSLTTHTGERKTDKDYLGQWLLIYFGFTHCPDVCPEELEKMIQVVDEIDSITTLPDLTPLFISIDPERDTKEAIANYVKEFSPKLVGLTGTREEVDQVARAYRVYYSPGPKDEDEDYIVDHTIIMYLIGPDGEFLDYFGQNKRKGEIAASIATHMRPYRKKS 301
               SCOP domains d2hrfa_ A: automated matches                                                                                                                                                  SCOP domains
               CATH domains 2hrfA00 A:129-301 Glutaredoxin                                                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eee....eehhhhhh...eeeeee.....hhhhhhhhhhhhhhhhhhhhh.....eeeeee......hhhhhhhhhhh.....eeee.hhhhhhhhhhhh......................eeee.....eeeee....hhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------L------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3b  PDB: A:129-188 UniProt: 122-188 [INCOMPLETE]     ------------------------------Exon 1.5  PDB: A:219-257               Exon 1.6b  PDB: A:258-301 UniProt: 258-301   Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------Exon 1.4  PDB: A:188-219        ---------------------------------------------------------------------------------- Transcript 1 (2)
                 2hrf A 129 SFTGKPLLGGPFSLTTHTGERKTDKDYLGQWLLIYFGFTHCPDVCLEELEKMIQVVDEIDSITTLPDLTPLFISIDPERDTKEAIANYVKEFSPKLVGLTGTREEVDQVARAYRVYYSPGPKDEDEDYIVDHTIIMYLIGPDGEFLDYFGQNKRKGEIAASIATHMRPYRKKS 301
                                   138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298
   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, 1)

NMR Structure
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2HRF)

(-) Gene Ontology  (11, 11)

NMR Structure(hide GO term definitions)
Chain A   (SCO1_HUMAN | O75880)
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:0006878    cellular copper ion homeostasis    Any process involved in the maintenance of an internal steady state of copper ions at the level of a cell.
    GO:0006825    copper ion transport    The directed movement of copper (Cu) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006091    generation of precursor metabolites and energy    The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances.
    GO:0008535    respiratory chain complex IV assembly    The aggregation, arrangement and bonding together of a set of components to form respiratory chain complex IV (also known as cytochrome c oxidase), the terminal member of the respiratory chain of the mitochondrion and some aerobic bacteria. Cytochrome c oxidases are multi-subunit enzymes containing from 13 subunits in the mammalian mitochondrial form to 3-4 subunits in the bacterial forms.
cellular component
    GO:0072492    host cell mitochondrial intermembrane space    The region between the inner and outer lipid bilayers of the host cell mitochondrial envelope.
    GO:0005743    mitochondrial inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0030016    myofibril    The contractile element of skeletal and cardiac muscle; a long, highly organized bundle of actin, myosin, and other proteins that contracts by a sliding filament mechanism.

 Visualization

(-) Interactive Views

NMR Structure
  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
    CU1  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Lys A:300 - Ser A:301   [ RasMol ]  
    Phe A:130 - Thr A:131   [ RasMol ]  
    Ser A:129 - Phe A:130   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - model 1, sites PNG format | NMR Structure - all models 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
  2hrf
    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
  SCO1_HUMAN | O75880
    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)
  220110
    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
  SCO1_HUMAN | O75880
    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
        SCO1_HUMAN | O75880: 1wp0 2ggt 2gqk 2gql 2gqm 2gt5 2gt6 2gvp 2hrn

(-) Related Entries Specified in the PDB File

2gqk THE FAMILY OF 30 STRUCTURES OF WILD TYPE NI(II) HUMAN SCO1
2gql THE AVERAGE MINIMIZED STRUCTURE OF WILD TYPE HUMAN SCO1 COMPLEXED WITH NI(II) IONS.
2gqm THE FAMILY OF 30 STRUCTURES OF WILD TYPE CU(I) HUMAN SCO1
2gt5 THE FAMILY OF 30 STRUCTURES OF WILD TYPE HUMAN SCO1, APO FORM
2gt6 THE AVERAGE MINIMIZED STRUCTURE OF WILD TYPE HUMAN SCO1 COMPLEXED WITH CU(I)
2gvp THE AVERAGE MINIMIZED STRUCTURE OF WILD TYPE HUMAN SCO1, APO FORM
2hrn