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(-) Description

Title :  CYTOCHROME F FROM CHLAMYDOMONAS REINHARDTII
 
Authors :  Y. I. Chi, L. S. Huang, Z. Zhang, J. G. Fernandez-Velasco, R. Malkin, E. A. Berry
Date :  18 Sep 98  (Deposition) - 27 Apr 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Cytochrome F, Plastocyanin, Proton Wire, Heme, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. I. Chi, L. S. Huang, Z. Zhang, J. G. Fernandez-Velasco, E. A. Berry
X-Ray Structure Of A Truncated Form Of Cytochrome F From Chlamydomonas Reinhardtii.
Biochemistry V. 39 7689 2000
PubMed-ID: 10869174  |  Reference-DOI: 10.1021/BI000090K
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOCHROME F
    Chains: A, B, C
    Organism Scientific: CHLAMYDOMONAS REINHARDTII
    Organism Taxid: 3055
    Strain: F283ST

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1HEM3Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:1 , PHE A:4 , ALA A:5 , TYR A:9 , CYS A:21 , CYS A:24 , HIS A:25 , GLN A:59 , LEU A:69 , ASN A:70 , VAL A:71 , GLY A:72 , MET A:73 , ASN A:153 , GLY A:155 , ARG A:156 , GLY A:157 , VAL A:159 , TYR A:160 , PRO A:161 , HOH A:1100 , HOH A:1337 , HOH A:1381 , ASN C:16 , HOH C:1514BINDING SITE FOR RESIDUE HEM A 253
2AC2SOFTWARETYR B:1 , PRO B:2 , PHE B:4 , ALA B:5 , TYR B:9 , VAL B:20 , CYS B:21 , CYS B:24 , HIS B:25 , GLN B:59 , LEU B:69 , ASN B:70 , VAL B:71 , GLY B:72 , MET B:73 , ASN B:153 , GLY B:155 , ARG B:156 , GLY B:157 , VAL B:159 , TYR B:160 , PRO B:161 , HOH B:1458 , HOH B:1925BINDING SITE FOR RESIDUE HEM B 254
3AC3SOFTWARETYR C:1 , PRO C:2 , PHE C:4 , ALA C:5 , CYS C:21 , CYS C:24 , HIS C:25 , GLN C:59 , LEU C:69 , ASN C:70 , VAL C:71 , GLY C:72 , MET C:73 , VAL C:74 , ASN C:153 , GLY C:155 , ARG C:156 , GLY C:157 , VAL C:159 , TYR C:160 , PRO C:161 , HOH C:1296 , HOH C:1610 , HOH C:1844BINDING SITE FOR RESIDUE HEM C 255

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly A:116 -Pro A:117
2Gly B:116 -Pro B:117
3Gly C:116 -Pro C:117

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1CFM)

(-) Exons   (0, 0)

(no "Exon" information available for 1CFM)

(-) 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:251
 aligned with CYF_CHLRE | P23577 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:251
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281 
            CYF_CHLRE    32 YPVFAQQNYANPREANGRIVCANCHLAQKAVEIEVPQAVLPDTVFEAVIELPYDKQVKQVLANGKKGDLNVGMVLILPEGFELAPPDRVPAEIKEKVGNLYYQPYSPEQKNILVVGPVPGKKYSEMVVPILSPDPAKNKNVSYLKYPIYFGGNRGRGQVYPDGKKSNNTIYNASAAGKIVAITALSEKKGGFEVSIEKANGEVVVDKIPAGPDLIVKEGQTVQADQPLTNNPNVGGFGQAETEIVLQNPAR 282
               SCOP domains d1cfma1 A:1-168,A:233-251 Cytochrome f, large domain                                                                                                                    d1cfma2 A:169-232 Cytochrome f, small domain                    d1cfma1             SCOP domains
               CATH domains 1cfmA01 A:1-170,A:231-251  [code=2.60.40.830, no name defined]                                                                                                            1cfmA02 A:171-230  [code=2.40.50.100, no name defined]      1cfmA01               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh...........hhhh........eee.........eeeeeee....................eeeeee.........hhh..hhhhhhh..............eeee....hhhh.eeeeeee.............eeeeeeeeee.......................eeeeeee.......eeeeee.....eeeeee...........................eeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cfm A   1 YPVFAQQNYANPREANGRIVCANCHLAQKAVEIEVPQAVLPDTVFEAVIELPYDKQVKQVLANGKKGDLNVGMVLILPEGFELAPPDRVPAEIKEKVGNLYYQPYSPEQKNILVVGPVPGKKYSEMVVPILSPDPAKNKNVSYLKYPIYFGGNRGRGQVYPDGKKSNNTIYNASAAGKIVAITALSEKKGGFEVSIEKANGEVVVDKIPAGPDLIVKEGQTVQADQPLTNNPNVGGFGQAETEIVLQNPAR 251
                                    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:251
 aligned with CYF_CHLRE | P23577 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:251
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281 
            CYF_CHLRE    32 YPVFAQQNYANPREANGRIVCANCHLAQKAVEIEVPQAVLPDTVFEAVIELPYDKQVKQVLANGKKGDLNVGMVLILPEGFELAPPDRVPAEIKEKVGNLYYQPYSPEQKNILVVGPVPGKKYSEMVVPILSPDPAKNKNVSYLKYPIYFGGNRGRGQVYPDGKKSNNTIYNASAAGKIVAITALSEKKGGFEVSIEKANGEVVVDKIPAGPDLIVKEGQTVQADQPLTNNPNVGGFGQAETEIVLQNPAR 282
               SCOP domains d1cfmb1 B:1-168,B:233-251 Cytochrome f, large domain                                                                                                                    d1cfmb2 B:169-232 Cytochrome f, small domain                    d1cfmb1             SCOP domains
               CATH domains 1cfmB01 B:1-170,B:231-251  [code=2.60.40.830, no name defined]                                                                                                            1cfmB02 B:171-230  [code=2.40.50.100, no name defined]      1cfmB01               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh...........hhhh........eee.........eeeeeee....................eeeeee.........hhh..hhhhhhh..............eeee....hhhh.eeeeeee.............eeeeeeeeee.......................eeeeeee.......eeeeee.....eeeeee...........................eeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cfm B   1 YPVFAQQNYANPREANGRIVCANCHLAQKAVEIEVPQAVLPDTVFEAVIELPYDKQVKQVLANGKKGDLNVGMVLILPEGFELAPPDRVPAEIKEKVGNLYYQPYSPEQKNILVVGPVPGKKYSEMVVPILSPDPAKNKNVSYLKYPIYFGGNRGRGQVYPDGKKSNNTIYNASAAGKIVAITALSEKKGGFEVSIEKANGEVVVDKIPAGPDLIVKEGQTVQADQPLTNNPNVGGFGQAETEIVLQNPAR 251
                                    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 C from PDB  Type:PROTEIN  Length:251
 aligned with CYF_CHLRE | P23577 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:251
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281 
            CYF_CHLRE    32 YPVFAQQNYANPREANGRIVCANCHLAQKAVEIEVPQAVLPDTVFEAVIELPYDKQVKQVLANGKKGDLNVGMVLILPEGFELAPPDRVPAEIKEKVGNLYYQPYSPEQKNILVVGPVPGKKYSEMVVPILSPDPAKNKNVSYLKYPIYFGGNRGRGQVYPDGKKSNNTIYNASAAGKIVAITALSEKKGGFEVSIEKANGEVVVDKIPAGPDLIVKEGQTVQADQPLTNNPNVGGFGQAETEIVLQNPAR 282
               SCOP domains d1cfmc1 C:1-168,C:233-251 Cytochrome f, large domain                                                                                                                    d1cfmc2 C:169-232 Cytochrome f, small domain                    d1cfmc1             SCOP domains
               CATH domains 1cfmC01 C:1-170,C:231-251  [code=2.60.40.830, no name defined]                                                                                                            1cfmC02 C:171-230  [code=2.40.50.100, no name defined]      1cfmC01               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh...........hhhh........eee...eee...eeeeeee....................eeeeee.........hhh..hhhhhhh..............eeee....hhhh.eeeeeee.............eeeeeeeeee......................eeeeeeee.......eeeeeee....eeeeee...........................eeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cfm C   1 YPVFAQQNYANPREANGRIVCANCHLAQKAVEIEVPQAVLPDTVFEAVIELPYDKQVKQVLANGKKGDLNVGMVLILPEGFELAPPDRVPAEIKEKVGNLYYQPYSPEQKNILVVGPVPGKKYSEMVVPILSPDPAKNKNVSYLKYPIYFGGNRGRGQVYPDGKKSNNTIYNASAAGKIVAITALSEKKGGFEVSIEKANGEVVVDKIPAGPDLIVKEGQTVQADQPLTNNPNVGGFGQAETEIVLQNPAR 251
                                    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
   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  (2, 6)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (2, 6)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (CYF_CHLRE | P23577)
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CYF_CHLRE | P23577: 1e2v 1e2w 1e2z 1ewh 1q90

(-) Related Entries Specified in the PDB File

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