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Theoretical Model  (Jmol Viewer)

(-) Description

Title :  MODELLED COMPLEX BETWEEN CYTOCHROME F AND CYTOCHROME C6
 
Authors :  M. Fragata, A. Kajava
Date :  06 Sep 01  (Deposition) - 08 Feb 02  (Release) - 08 Feb 02  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A,B,_#
( #:   chains that contain no standard or modified protein/DNA/RNA residue)
 
Keywords :  Theoretical Model Of Cytochrome F With Cytochrome C6 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Fragata, A. Kajava
Structural Model Of The Cytochrome F-Cytochrome C6 Complex. Characterization Of The Docked Surfaces And The Heme-To-Heme Route Of Electron Transfer
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOCHROME F
    Cellular Location: THYLAKOID MEMBRANE, LUMENAL SIDE
    Chains: A
    Fragment: SOLUBLE SUBUNIT
    Organism Common: TURNIP
    Organism Scientific: BRASSICA RAPA
    Synonym: PLASTOQUINOL--PLASTOCYANIN REDUCTASE
 
Molecule 2 - CYTOCHROME C6
    Cellular Location: THYLAKOID LUMEN
    Chains: B
    Organism Common: GREEN ALGA
    Organism Scientific: MONORAPHIDIUM BRAUNII
    Synonym: CYTOCHROME C552

 Structural Features

(-) Chains, Units

  
Theoretical Model : 
( #:   chains that contain no standard or modified protein/DNA/RNA residue)
 

Summary Information (see also Sequences/Alignments below)

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

Theoretical Model (1, 2)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (0, 0)

(no "Site" information available for 1JX8)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1JX8)

(-) Cis Peptide Bonds  (1, 1)

Theoretical Model
No.Residues
1Gly A:116 -Pro A:117

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1JX8)

(-) PROSITE Motifs  (1, 1)

Theoretical Model (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CYC6_CHLBR2-84  1B:2-84

(-) Exons   (0, 0)

(no "Exon" information available for 1JX8)

(-) Sequences/Alignments

Theoretical Model
   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:250
 aligned with CYF_BRARR | P36438 from UniProtKB/Swiss-Prot  Length:320

    Alignment length:250
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285
            CYF_BRARR    36 YPIFAQQNYENPREATGRIVCANCHLASKPVDIEVPQAVLPDTVFEAVVKIPYDMQLKQVLANGKKGALNVGAVLILPEGFELAPPDRISPEMKEKIGNLSFQNYRPNKKNILVIGPVPGQKYSEITFPILAPDPATNKDVHFLKYPIYVGGNRGRGQIYPDGSKSNNTVYNATAGGIISKILRKEKGGYEITIVDASNERQVIDIIPRGLELLVSEGESIKLDQPLTSNPNVGGFGQGDAEIVLQDPLR 285
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh..........hhhhhh......eee...ee....eeeeeee........ee.....ee..eeeeeee.....ee.hhhhhhhhhhhhhh....eeee..eeeeeeeeeeehhhhheeeeeee.............eeeeeeeeee......................eeeeeeee.....eeeeeee....eeeeeee............ee.............eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jx8 A   1 YPIFAQQNYENPREATGRIVCANCHLASKPVDIEVPQAVLPDTVFEAVVKIPYDMQLKQVLANGKKGALNVGAVLILPEGFELAPPDRISPEMKEKIGNLSFQNYRPNKKNILVIGPVPGQKYSEITFPILAPDPATNKDVHFLKYPIYVGGNRGRGQIYPDGSKSNNTVYNATAGGIISKILRKEKGGYEITIVDASNERQVIDIIPRGLELLVSEGESIKLDQPLTSNPNVGGFGQGDAEIVLQDPLR 250
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250


Chain B from PDB  Type:PROTEIN  Length:89
 aligned with CYC6_CHLBR | Q09099 from UniProtKB/Swiss-Prot  Length:89

    Alignment length:89
                                    10        20        30        40        50        60        70        80         
           CYC6_CHLBR     1 EADLALGKAVFDGNCAACHAGGGNNVIPDHTLQKAAIEQFLDGGFNIEAIVYQIENGKGAMPAWDGRLDEDEIAGVAAYVYDQAAGNKW  89
               SCOP domains ----------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.................hhhhhhhhh....hhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -CYTC  PDB: B:2-84 UniProt: 2-84                                                    ----- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 1jx8 B   1 EADLALGKAVFDGNCAACHAGGGNNVIPDHTLQKAAIEQFLDGGFNIEAIVYQIENGKGAMPAWDGRLDEDEIAGVAAYVYDQAAGNKW  89
                                    10        20        30        40        50        60        70        80
   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  (0, 0)

(no "SCOP Domain" information available for 1JX8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1JX8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1JX8)

(-) Gene Ontology  (14, 23)

Theoretical Model(hide GO term definitions)
Chain A   (CYF_BRARR | P36438)
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:0009535    chloroplast thylakoid membrane    The pigmented membrane of a chloroplast thylakoid. An example of this component is found in Arabidopsis thaliana.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0031361    integral component of thylakoid membrane    The component of the thylakoid membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.

Chain B   (CYC6_CHLBR | Q09099)
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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  CYF_BRARR | P36438
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 Related Entries

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

UniProtKB/Swiss-Prot
        CYC6_CHLBR | Q09099: 1a2s 1ced 1ctj
        CYF_BRARR | P36438: 1ctm 1hcz 1tkw 2pcf

(-) Related Entries Specified in the PDB File

1ctj THE STUCTURE OF CYTOCHROME C6 OF MONORAPHIDIUM BRAUNII
1ctm THE STRUCTURE OF CYTOCHROME F OF PLANT TURNIP, BRASSICA RAPA