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(-) Description

Title :  STRUCTURE OF THE CYTOCHROME C6 FROM THE GREEN ALGA CLADOPHORA GLOMERATA
 
Authors :  W. Carpentier
Date :  17 May 02  (Deposition) - 25 Dec 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Omega Loop, Antiparallel Beta-Sheet, Protoporphyrin Ix Containing Fe, Heme, Haem, Cytochrome, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Dikiy, W. Carpentier, I. Vandenberghe, M. Borsari, N. Safarov, E. Dikaya, J. Van Beeumen, S. Ciurli
Structural Basis For The Molecular Properties Of Cytochrome C(6)
Biochemistry V. 41 14689 2002
PubMed-ID: 12475218  |  Reference-DOI: 10.1021/BI026473V
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOCHROME C6
    Chains: A
    Organism Scientific: CLADOPHORA GLOMERATA
    Organism Taxid: 162068

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:16 , CYS A:17 , CYS A:20 , HIS A:21 , ASN A:26 , VAL A:28 , LEU A:29 , LYS A:32 , THR A:33 , LEU A:34 , ALA A:38 , TYR A:42 , GLN A:55 , VAL A:56 , LYS A:60 , MET A:63 , PRO A:64 , TRP A:66 , HOH A:96 , HOH A:113 , HOH A:119BINDING SITE FOR RESIDUE HEM A 92

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1LS9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1LS9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1LS9)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CYC6_CLAGO4-86  1A:4-86

(-) Exons   (0, 0)

(no "Exon" information available for 1LS9)

(-) 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:91
 aligned with CYC6_CLAGO | P83391 from UniProtKB/Swiss-Prot  Length:91

    Alignment length:91
                                    10        20        30        40        50        60        70        80        90 
            CYC6_CLAGO    1 VDAELLADGKKVFAGNCAACHLGGNNSVLADKTLKKDAIEKYLEGGLTLEAIKYQVNNGKGAMPAWADRLDEDDIEAVSNYVYDQAVNSKW 91
               SCOP domains d1ls9a_ A: Cytochrome c6 (synonym: cytochrome c553)                                         SCOP domains
               CATH domains 1ls9A00 A:1-91 Cytochrome c                                                                 CATH domains
               Pfam domains ---Cytochrome_CBB3-1ls9A01 A:4-82                                                 --------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhh....hhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---CYTC  PDB: A:4-86 UniProt: 4-86                                                    ----- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                  1ls9 A  1 VDAELLADGKKVFAGNCAACHLGGNNSVLADKTLKKDAIEKYLEGGLTLEAIKYQVNNGKGAMPAWADRLDEDDIEAVSNYVYDQAVNSKW 91
                                    10        20        30        40        50        60        70        80        90
   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)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Cytochrome-c (108)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CYC6_CLAGO | P83391)
molecular function
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0015979    photosynthesis    The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
cellular component
    GO:0009507    chloroplast    A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
    GO:0009543    chloroplast thylakoid lumen    The cavity enclosed within the chloroplast thylakoid membrane. An example of this component is found in Arabidopsis thaliana.
    GO:0009536    plastid    Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.
    GO:0009579    thylakoid    A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation.

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