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(-) Description

Title :  ENSEMBLE OF TWENTY STRUCTURES OF THE PROCHLOROTHRIX HOLLANDICA PLASTOCYANIN- CYTOCHROME F COMPLEX
 
Authors :  R. Hulsker, M. Baranova, G. Bullerjahn, M. Ubbink
Date :  22 Nov 07  (Deposition) - 12 Feb 08  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (20x)
Keywords :  Copper, Electron Transport, Metal-Binding, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Hulsker, M. V. Baranova, G. S. Bullerjahn, M. Ubbink
Dynamics In The Transient Complex Of Plastocyanin-Cytochrome F From Prochlorothrix Hollandica.
J. Am. Chem. Soc. V. 130 1985 2008
PubMed-ID: 18201089  |  Reference-DOI: 10.1021/JA077453P
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PLASTOCYANIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PVAPC10
    Gene: PETE
    Organism Scientific: PROCHLOROTHRIX HOLLANDICA
    Organism Taxid: 1223
 
Molecule 2 - CYTOCHROME F
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PBAR
    Gene: PETA
    Organism Scientific: PROCHLOROTHRIX HOLLANDICA
    Organism Taxid: 1223

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (2, 2)
No.NameCountTypeFull Name
1CU1Ligand/IonCOPPER (II) ION
2HEC1Ligand/IonHEME C

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:39 , CYS A:82 , HIS A:85 , MET A:90BINDING SITE FOR RESIDUE CU A 98
2AC2SOFTWARETHR A:83 , TYR B:1 , CYS B:21 , CYS B:24 , HIS B:25 , GLN B:59 , LEU B:69 , ASN B:70 , VAL B:71 , GLY B:72 , PRO B:119 , GLY B:157 , ARG B:158 , GLY B:159 , VAL B:161 , PRO B:163BINDING SITE FOR RESIDUE HEC B 250

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 60)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Glu A:17 -Pro A:18
21, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Gly A:37 -Pro A:38
31, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Gly B:118 -Pro B:119

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2JXM)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1COPPER_BLUEPS00196 Type-1 copper (blue) proteins signature.PLAS_PROHO110-124  1A:76-90

(-) Exons   (0, 0)

(no "Exon" information available for 2JXM)

(-) 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:97
 aligned with PLAS_PROHO | P50057 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:97
                                    44        54        64        74        84        94       104       114       124       
           PLAS_PROHO    35 ATVQIKMGTDKYAPLYEPKALSISAGDTVEFVMNKVGPHNVIFDKVPAGESAPALSNTKLAIAPGSFYSVTLGTPGTYSFYCTPHRGAGMVGTITVE 131
               SCOP domains d2jxma_ A: Plastocyanin                                                                           SCOP domains
               CATH domains 2jxmA00 A:1-97 Cupredoxins -  blue copper proteins                                                CATH domains
               Pfam domains --Copper-bind-2jxmA01 A:3-97                                                                      Pfam domains
         Sec.struct. author ..eeeeeee...eeeee..eeee....eeeeee........eeee.....hhhhhh...........eeee.....eeeee.........eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------COPPER_BLUE    ------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 2jxm A   1 ASVQIKMGTDKYAPLYEPKALSISAGDTVEFVMNKVGPHNVIFDKVPAGESAPALSNTKLAIAPGSFYSVTLGTPGTYSFYCTPHRGAGMVGTITVE  97
                                    10        20        30        40        50        60        70        80        90       


Chain B from PDB  Type:PROTEIN  Length:249
 aligned with Q8RN59_PROHO | Q8RN59 from UniProtKB/TrEMBL  Length:562

    Alignment length:249
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286         
         Q8RN59_PROHO    47 YPFYAQYNYDSPREATGKIVCANCHLAKKTVEIEVPQAVLPDTVFKAVVKVPYDLDIQQVQADGSPSGLNVGAVLMLPEGFKLAPPERVDEELMEEVGDFYYLVTPYSETDENILLAGPLPGEDYQEMIFPILSPNPATDAGVYFGKYSIHLGGNRGRGQVYPTGELSNNNAFSASIAGTIAAIEDNGFGFDVTIQPEDGDAVVTSILPGPELIVAVGDTVEAGQLLTTNPNVGGFGQMDSEIVLQSSS 295
               SCOP domains d2jxmb1 B:1-246 Cytochrome f-plastocyanin complex                                                                                                                                                                                                     --- SCOP domains
               CATH domains 2jxmB01 B:1-172,B:230-248  [code=2.60.40.830, no name defined]                                                                                                              2jxmB02 B:173-229  [code=2.40.50.100, no name defined]   2jxmB01            - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------Apocytochr_F_C-2jxmB01 B:169-249                                                  Pfam domains
         Sec.struct. author hhhhhhhhh..........hhhhhh......eee...ee....eeeeeee........ee.....ee..eeeeeee.....ee.hhhhhhhhhhh...hhhhhhee.......eeeeeeee......eeeeee............eeeeeeeeeee......................eeeeee.....eeeeeee......eeeee............ee.............eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jxm B   1 YPFYAQYNYDSPREATGKIVCANCHLAKKTVEIEVPQAVLPDTVFKAVVKVPYDLDIQQVQADGSPSGLNVGAVLMLPEGFKLAPPERVDEELMEEVGDFYYLVTPYSETDENILLAGPLPGEDYQEMIFPILSPNPATDAGVYFGKYSIHLGGNRGRGQVYPTGELSNNNAFSASIAGTIAAIEDNGFGFDVTIQPEDGDAVVTSILPGPELIVAVGDTVEAGQLLTTNPNVGGFGQMDSEIVLQSSS 249
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
   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, 2)

NMR Structure
(-)
Class: All beta proteins (24004)
(-)
Class: Low resolution protein structures (283)

(-) CATH Domains  (3, 3)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 2)

NMR Structure
(-)
Clan: CU_oxidase (192)
(-)
Clan: Hybrid (58)

(-) Gene Ontology  (12, 15)

NMR Structure(hide GO term definitions)
Chain A   (PLAS_PROHO | P50057)
molecular function
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) ions.
    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: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.
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.
    GO:0042651    thylakoid membrane    The pigmented membrane of any thylakoid.

Chain B   (Q8RN59_PROHO | Q8RN59)
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: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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PLAS_PROHO | P50057: 1b3i 2b3i

(-) Related Entries Specified in the PDB File

1b3i PLASTOCYANIN
1ci3 CYTOCHROME F FROM PHORMIDIUM