Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Theoretical Model
collapse expand < >
Image Theoretical Model
Theoretical Model  (Jmol Viewer)

(-) Description

Title :  MODEL OF THE B820 FORM OF THE LIGHT-HARVESTING COMPLEX I FROM RHODOSPIRILLUM RUBRUM
 
Authors :  V. Arluison, J. Seguin, C. Mayer, B. Robert
Date :  05 Feb 03  (Deposition) - 20 Jan 04  (Release) - 23 Mar 04  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A,B,_#
( #:   chains that contain no standard or modified protein/DNA/RNA residue)
 
Keywords :  Light Harvesting Complex I, B820, Rsp Rubrum (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Arluison, J. Seguin, J. P. Le Caer, J. N. Sturgis, B. Robert
Hydrophobic Pockets At The Membrane Interface: An Original Mechanism For Membrane Protein Interactions.
Biochemistry V. 43 1276 2004
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LIGHT-HARVESTING PROTEIN B-870, ALPHA CHAIN
    Chains: A
    Organism Common: BACTERIA
    Organism Scientific: RHODOSPIRILLUM RUBRUM
    Synonym: ANTENNA PIGMENT PROTEIN, ALPHA CHAIN
 
Molecule 2 - LIGHT-HARVESTING PROTEIN B-870, BETA CHAIN
    Chains: B
    Organism Common: BACTERIA
    Organism Scientific: RHODOSPIRILLUM RUBRUM
    Synonym: ANTENNA PIGMENT PROTEIN, BETA CHAIN

 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
1BCL2Ligand/IonBACTERIOCHLOROPHYLL A

(-) Sites  (0, 0)

(no "Site" information available for 1NW0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1NW0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1NW0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1NW0)

(-) PROSITE Motifs  (2, 2)

Theoretical Model (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ANTENNA_COMP_BETAPS00969 Antenna complexes beta subunits signature.LHB_RHORU14-45  1B:14-45
LHB_RHORT16-47  1B:14-45
2ANTENNA_COMP_ALPHAPS00968 Antenna complexes alpha subunits signature.LHA_RHORU23-41  1A:23-41

(-) Exons   (0, 0)

(no "Exon" information available for 1NW0)

(-) 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:51
 aligned with LHA_RHORU | P02947 from UniProtKB/Swiss-Prot  Length:62

    Alignment length:51
                                    10        20        30        40        50 
             LHA_RHORU    1 MWRIWQLFDPRQALVGLATFLFVLALLIHFILLSTERFNWLEGASTKPVQT 51
               SCOP domains --------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh...hhhhhhhhhhhhhhhhhhhhhhhh................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------------------------------------------- PROSITE (2)
                PROSITE (3) ----------------------ANTENNA_COMP_ALPHA ---------- PROSITE (3)
                 Transcript --------------------------------------------------- Transcript
                  1nw0 A  1 MWRIWQLFDPRQALVGLATFLFVLALLIHFILLSTERFNWLEGASTKPVQT 51
                                    10        20        30        40        50 


Chain B from PDB  Type:PROTEIN  Length:43
 aligned with LHB_RHORT | Q2RQ23 from UniProtKB/Swiss-Prot  Length:69

    Alignment length:43
                                    16        26        36        46   
             LHB_RHORT    7 ESLSGITEGEAKEFHKIFTSSILVFFGVAAFAHLLVWIWRPWV 49
               SCOP domains ------------------------------------------- SCOP domains
               CATH domains ------------------------------------------- CATH domains
               Pfam domains ------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhh........hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------ANTENNA_COMP_BETA  PDB: B:14-45 -- PROSITE (2)
                 Transcript ------------------------------------------- Transcript
                  1nw0 B  5 ESLSGITEGEAKEFHKIFTSSILVFFGVAAFAHLLVWIWRPWV 47
                                    14        24        34        44   


Chain B from PDB  Type:PROTEIN  Length:43
 aligned with LHB_RHORU | P0C190 from UniProtKB/Swiss-Prot  Length:54

    Alignment length:43
                                    14        24        34        44   
             LHB_RHORU    5 ESLSGITEGEAKEFHKIFTSSILVFFGVAAFAHLLVWIWRPWV 47
               SCOP domains ------------------------------------------- SCOP domains
               CATH domains ------------------------------------------- CATH domains
               Pfam domains ------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhh........hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------- SAPs(SNPs)
                    PROSITE ---------ANTENNA_COMP_BETA  PDB: B:14-45 -- PROSITE
                 Transcript ------------------------------------------- Transcript
                  1nw0 B  5 ESLSGITEGEAKEFHKIFTSSILVFFGVAAFAHLLVWIWRPWV 47
                                    14        24        34        44
   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 1NW0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1NW0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1NW0)

(-) Gene Ontology  (12, 34)

Theoretical Model(hide GO term definitions)
Chain A   (LHA_RHORU | P02947)
molecular function
    GO:0042314    bacteriochlorophyll binding    Interacting selectively and non-covalently with bacteriochlorophyll, a form of chlorophyll found in photosynthetic bacteria, such as the purple and green bacteria. There are several types, designated a to g. Bacteriochlorophyll a and bacteriochlorophyll b are structurally similar to the chlorophyll a and chlorophyll b found in plants.
    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:0045156    electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity    Enables the directed movement of electrons within the cyclic electron transport pathway of photosynthesis.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0019684    photosynthesis, light reaction    The light reactions of photosynthesis, which take place in photosystems II and I. Light energy is harvested and used to power the transfer of electrons among a series of electron donors and acceptors. The final electron acceptor is NADP+, which is reduced to NADPH. NADPH generated from light reactions is used in sugar synthesis in dark reactions. Light reactions also generate a proton motive force across the thylakoid membrane, and the proton gradient is used to synthesize ATP. There are two chemical reactions involved in the light reactions: water oxidation in photosystem II, and NADP reduction in photosystem I.
    GO:0018298    protein-chromophore linkage    The covalent or noncovalent attachment of a chromophore to a protein.
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:0030076    light-harvesting complex    A protein-pigment complex that may be closely or peripherally associated to photosynthetic reaction centers that participate in harvesting and transferring radiant energy to the reaction center.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0019866    organelle inner membrane    The inner, i.e. lumen-facing, lipid bilayer of an organelle envelope; usually highly selective to most ions and metabolites.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0030077    plasma membrane light-harvesting complex    A plasma membrane protein-pigment complex that may be closely or peripherally associated to photosynthetic reaction centers that participate in harvesting and transferring radiant energy to the reaction center. Examples of this complex are found in bacterial species.

Chain B   (LHB_RHORT | Q2RQ23)
molecular function
    GO:0042314    bacteriochlorophyll binding    Interacting selectively and non-covalently with bacteriochlorophyll, a form of chlorophyll found in photosynthetic bacteria, such as the purple and green bacteria. There are several types, designated a to g. Bacteriochlorophyll a and bacteriochlorophyll b are structurally similar to the chlorophyll a and chlorophyll b found in plants.
    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:0045156    electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity    Enables the directed movement of electrons within the cyclic electron transport pathway of photosynthesis.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0019684    photosynthesis, light reaction    The light reactions of photosynthesis, which take place in photosystems II and I. Light energy is harvested and used to power the transfer of electrons among a series of electron donors and acceptors. The final electron acceptor is NADP+, which is reduced to NADPH. NADPH generated from light reactions is used in sugar synthesis in dark reactions. Light reactions also generate a proton motive force across the thylakoid membrane, and the proton gradient is used to synthesize ATP. There are two chemical reactions involved in the light reactions: water oxidation in photosystem II, and NADP reduction in photosystem I.
    GO:0018298    protein-chromophore linkage    The covalent or noncovalent attachment of a chromophore to a protein.
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:0030076    light-harvesting complex    A protein-pigment complex that may be closely or peripherally associated to photosynthetic reaction centers that participate in harvesting and transferring radiant energy to the reaction center.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0030077    plasma membrane light-harvesting complex    A plasma membrane protein-pigment complex that may be closely or peripherally associated to photosynthetic reaction centers that participate in harvesting and transferring radiant energy to the reaction center. Examples of this complex are found in bacterial species.

Chain B   (LHB_RHORU | P0C190)
molecular function
    GO:0042314    bacteriochlorophyll binding    Interacting selectively and non-covalently with bacteriochlorophyll, a form of chlorophyll found in photosynthetic bacteria, such as the purple and green bacteria. There are several types, designated a to g. Bacteriochlorophyll a and bacteriochlorophyll b are structurally similar to the chlorophyll a and chlorophyll b found in plants.
    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:0045156    electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity    Enables the directed movement of electrons within the cyclic electron transport pathway of photosynthesis.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0019684    photosynthesis, light reaction    The light reactions of photosynthesis, which take place in photosystems II and I. Light energy is harvested and used to power the transfer of electrons among a series of electron donors and acceptors. The final electron acceptor is NADP+, which is reduced to NADPH. NADPH generated from light reactions is used in sugar synthesis in dark reactions. Light reactions also generate a proton motive force across the thylakoid membrane, and the proton gradient is used to synthesize ATP. There are two chemical reactions involved in the light reactions: water oxidation in photosystem II, and NADP reduction in photosystem I.
    GO:0018298    protein-chromophore linkage    The covalent or noncovalent attachment of a chromophore to a protein.
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:0030076    light-harvesting complex    A protein-pigment complex that may be closely or peripherally associated to photosynthetic reaction centers that participate in harvesting and transferring radiant energy to the reaction center.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0030077    plasma membrane light-harvesting complex    A plasma membrane protein-pigment complex that may be closely or peripherally associated to photosynthetic reaction centers that participate in harvesting and transferring radiant energy to the reaction center. Examples of this complex are found in bacterial species.

 Visualization

(-) Interactive Views

Theoretical Model
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    BCL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 1nw0)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1nw0)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Theoretical Model PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1nw0
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  LHA_RHORU | P02947
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  LHB_RHORT | Q2RQ23
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  LHB_RHORU | P0C190
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  LHA_RHORU | P02947
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  LHB_RHORT | Q2RQ23
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  LHB_RHORU | P0C190
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        LHA_RHORU | P02947: 1xrd
        LHB_RHORT | Q2RQ23: 1wrg
        LHB_RHORU | P0C190: 1wrg

(-) Related Entries Specified in the PDB File

1lgh CRYSTAL STRUCTURE OF THE LIGHT-HARVESTING COMPLEX II (B800- 850) FROM RHODOSPIRILLUM MOLISCHIANUM