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(-) Description

Title :  CRYSTAL STRUCTURE OF CYTOCHROME C6 FROM RED ALGA PORPHYRA YEZOENSIS AT 1.57 A RESOLUTION
 
Authors :  S. Yamada, S. -Y. Park, H. Shimizu, Y. Shiro, T. Oku
Date :  06 Oct 00  (Deposition) - 06 Apr 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.57
Chains :  Asym./Biol. Unit :  A
Keywords :  Cytochrome C6, Crystal Structure, Red Alga, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Yamada, S. Y. Park, H. Shimizu, Y. Koshizuka, K. Kadokura, T. Satoh, K. Suruga, M. Ogawa, Y. Isogai, T. Nishio, Y. Shiro, T. Oku
Structure Of Cytochrome C6 From The Red Alga Porphyra Yezoensis At 1. 57 A Resolution.
Acta Crystallogr. , Sect. D V. 56 1577 2000
PubMed-ID: 11092924  |  Reference-DOI: 10.1107/S090744490001461X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOCHROME C6
    Chains: A
    Organism Scientific: PORPHYRA YEZOENSIS
    Organism Taxid: 2788

 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:13 , CYS A:14 , CYS A:17 , HIS A:18 , ASN A:23 , LYS A:29 , THR A:30 , VAL A:35 , ASN A:39 , MET A:41 , GLN A:50 , ASN A:56 , ALA A:57 , MET A:58 , HOH A:118 , HOH A:134BINDING SITE FOR RESIDUE HEM A 101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CYC6_PYRYE26-106  1A:1-81

(-) Exons   (0, 0)

(no "Exon" information available for 1GDV)

(-) 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:85
 aligned with CYC6_PYRYE | Q8WKJ8 from UniProtKB/Swiss-Prot  Length:110

    Alignment length:85
                                    35        45        55        65        75        85        95       105     
           CYC6_PYRYE    26 ADLDNGEKVFSANCAACHAGGNNAIMPDKTLKKDVLEANSMNTIDAITYQVQNGKNAMPAFGGRLVDEDIEDAANYVLSQSEKGW 110
               SCOP domains d1gdva_ A: Cytochrome c6 (synonym: cytochrome c553)                                   SCOP domains
               CATH domains 1gdvA00 A:1-85 Cytochrome c                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhh...hhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE CYTC  PDB: A:1-81 UniProt: 26-106                                                ---- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 1gdv A   1 ADLDNGEKVFSANCAACHAGGNNAIMPDKTLKKDVLEANSMNTIDAITYQVQNGKNAMPAFGGRLVDEDIEDAANYVLSQSEKGW  85
                                    10        20        30        40        50        60        70        80
   Legend:   → Mismatch (orange background)
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  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  (0, 0)

(no "Pfam Domain" information available for 1GDV)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CYC6_PYRYE | Q8WKJ8)
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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