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(-) Description

Title :  AN ICOSAHEDRAL ASSEMBLY OF LIGHT-HARVESTING CHLOROPHYLL A/B PROTEIN COMPLEX FROM PEA THYLAKOID MEMBRANES
 
Authors :  T. Hino, E. Kanamori, J. -R. Shen, T. Kouyama
Date :  10 Mar 04  (Deposition) - 30 Mar 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  9.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (60x)
Keywords :  Lhc-Ii, Icosahedron, Chlorophyll, Antenna, Photosystem, Photosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Hino, E. Kanamori, J. R. Shen, T. Kouyama
An Icosahedral Assembly Of The Light-Harvesting Chlorophyll A/B Protein Complex From Pea Chloroplast Thylakoid Membranes.
Acta Crystallogr. , Sect. D V. 60 803 2004
PubMed-ID: 15103124  |  Reference-DOI: 10.1107/S0907444904003233
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CHLOROPHYLL A-B BINDING PROTEIN AB80
    ChainsA
    Organism CommonPEA
    Organism ScientificPISUM SATIVUM
    Organism Taxid3888
    SynonymLIGHT-HARVESTING CHLOROPHYLL A/B PROTEIN, LHCII TYPE I CAB-AB80, LHCP
    TissueTHYLAKOID MEMBRANE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (60x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1CHL5Ligand/IonCHLOROPHYLL B
2CLA7Ligand/IonCHLOROPHYLL A
Biological Unit 1 (2, 720)
No.NameCountTypeFull Name
1CHL300Ligand/IonCHLOROPHYLL B
2CLA420Ligand/IonCHLOROPHYLL A

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:70 , LEU A:176BINDING SITE FOR RESIDUE CLA A 251
2AC2SOFTWAREASN A:208BINDING SITE FOR RESIDUE CLA A 253
3AC3SOFTWAREGLU A:65 , ARG A:185BINDING SITE FOR RESIDUE CLA A 254
4AC4SOFTWAREVAL A:138 , TYR A:141BINDING SITE FOR RESIDUE CHL A 261
5AC5SOFTWARELYS A:182BINDING SITE FOR RESIDUE CHL A 262
6AC6SOFTWAREHIS A:212BINDING SITE FOR RESIDUE CHL A 263
7AC7SOFTWARELEU A:64 , GLU A:139BINDING SITE FOR RESIDUE CHL A 265

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1VCR)

(-) Sequences/Alignments

Asymmetric 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:101
 aligned with CB22_PEA | P07371 from UniProtKB/Swiss-Prot  Length:269

    Alignment length:160
                                   101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251
             CB22_PEA    92 PETFSKNRELEVIHSRWAMLGALGCVFPELLSRNGVKFGEAVWFKAGSQIFSEGGLDYLGNPSLVHAQSILAIWATQVILMGAVEGYRIAGGPLGEVVDPLYPGGSFDPLGLADDPEAFAELKVKELKNGRLAMFSMFGFFVQAIVTGKGPLENLADHLA 251
               SCOP domains d1vcra_ A: Chlorophyll a-b binding                                  protein                                                                                      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Chloroa_b-bind-1vcrA01 A:55-199                                                                                                                  --------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..---------------------------------hhhhhhhhhhhhh..hhhhh.--------------------------..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vcr A  55 PETFSKNRELEVIHSRWAMLGALGCVFPELLSRNG---------------------------------SILAIWATQVILMGAVEGYRI--------------------------PEAFAELKVKELKNGRLAMFSMFGFFVQAIVTGKGPLENLADHLA 214
                                    64        74        84    |    -         -         -       124       134        |-         -         -     | 174       184       194       204       214
                                                             89                               123                 143                        170                                            

   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 Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A   (CB22_PEA | P07371)
molecular function
    GO:0016168    chlorophyll binding    Interacting selectively and non-covalently with chlorophyll; any compound of magnesium complexed in a porphyrin (tetrapyrrole) ring and which functions as a photosynthetic pigment.
    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.
    GO:0009765    photosynthesis, light harvesting    Absorption and transfer of the energy absorbed from light photons between photosystem reaction centers.
    GO:0018298    protein-chromophore linkage    The covalent or noncovalent attachment of a chromophore to a protein.
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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0009522    photosystem I    A photosystem that contains an iron-sulfur reaction center associated with accessory pigments and electron carriers. In cyanobacteria and chloroplasts, photosystem I functions as a light-dependent plastocyanin-ferredoxin oxidoreductase, transferring electrons from plastocyanin to ferredoxin; in photosynthetic bacteria that have only a single type I photosystem, such as the green sulfur bacteria, electrons can go either to ferredoxin (Fd) -> NAD+ or to menaquinone (MK) -> Cytb/FeS -> Cytc555 -> photosystem I (cyclic photophosphorylation).
    GO:0009523    photosystem II    A photosystem that contains a pheophytin-quinone reaction center with associated accessory pigments and electron carriers. In cyanobacteria and chloroplasts, in the presence of light, PSII functions as a water-plastoquinone oxidoreductase, transferring electrons from water to plastoquinone, whereas other photosynthetic bacteria carry out anoxygenic photosynthesis and oxidize other compounds to re-reduce the photoreaction center.
    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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        CB22_PEA | P073712bhw

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