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(-) Description

Title :  INTEGRAL MEMBRANE PERIPHERAL LIGHT HARVESTING COMPLEX FROM RHODOPSEUDOMONAS ACIDOPHILA STRAIN 10050
 
Authors :  R. J. Cogdell, A. A. Freer, N. W. Isaacs, A. M. Hawthornthwaite-Lawless G. Mcdermott, M. Z. Papiz, S. M. Prince
Date :  31 Aug 96  (Deposition) - 01 Apr 97  (Release) - 30 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,D,E,G,H
Biol. Unit 1:  A,B,D,E,G,H  (3x)
Keywords :  Antenna Complex, Light-Harvesting Protein, Lh2 Complex, Bacteriochlorophyll, Purple Bacteria (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. M. Prince, M. Z. Papiz, A. A. Freer, G. Mcdermott, A. M. Hawthornthwaite-Lawless, R. J. Cogdell, N. W. Isaacs
Apoprotein Structure In The Lh2 Complex From Rhodopseudomonas Acidophila Strain 10050: Modular Assembly And Protein Pigment Interactions.
J. Mol. Biol. V. 268 412 1997
PubMed-ID: 9159480  |  Reference-DOI: 10.1006/JMBI.1997.0966
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LIGHT HARVESTING PROTEIN B-800/850
    Chains: A, D, G
    Organism Scientific: RHODOBLASTUS ACIDOPHILUS
    Organism Taxid: 1074
    Strain: 10050
    Synonym: LH2
 
Molecule 2 - LIGHT HARVESTING PROTEIN B-800/850
    Chains: B, E, H
    Organism Scientific: RHODOBLASTUS ACIDOPHILUS
    Organism Taxid: 1074
    Strain: 10050
    Synonym: LH2

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABDEGH
Biological Unit 1 (3x): ABDEGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 18)

Asymmetric Unit (3, 18)
No.NameCountTypeFull Name
1BCL9Ligand/IonBACTERIOCHLOROPHYLL A
2FME3Mod. Amino AcidN-FORMYLMETHIONINE
3RG16Ligand/IonRHODOPIN B-D-GLUCOSIDE
Biological Unit 1 (3, 54)
No.NameCountTypeFull Name
1BCL27Ligand/IonBACTERIOCHLOROPHYLL A
2FME9Mod. Amino AcidN-FORMYLMETHIONINE
3RG118Ligand/IonRHODOPIN B-D-GLUCOSIDE

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:23 , ILE A:26 , BCL A:56 , LEU B:3 , GLN B:7 , LEU B:11 , TYR B:14 , GLY B:18 , THR B:19 , BCL B:43 , TRP D:45 , BCL D:55 , GLN G:3 , THR G:8 , BCL G:56 , BCL H:43BINDING SITE FOR RESIDUE RG1 B 42
02AC2SOFTWARETYR A:44 , BCL A:55 , ALA B:29 , LEU B:32 , ALA B:36 , BCL H:43BINDING SITE FOR RESIDUE RG1 A 54
03AC3SOFTWAREGLN A:3 , THR A:8 , BCL A:56 , BCL B:43 , VAL D:23 , ILE D:26 , BCL D:56 , LEU E:3 , GLN E:7 , LEU E:11 , TYR E:14 , GLY E:18 , THR E:19 , BCL E:43 , TRP G:45 , BCL G:55BINDING SITE FOR RESIDUE RG1 E 42
04AC4SOFTWAREBCL B:43 , TYR D:44 , BCL D:55 , ALA E:29 , LEU E:32 , ALA E:36BINDING SITE FOR RESIDUE RG1 D 54
05AC5SOFTWARETRP A:45 , BCL A:55 , GLN D:3 , THR D:8 , BCL D:56 , BCL E:43 , VAL G:23 , ILE G:26 , BCL G:56 , LEU H:3 , GLN H:7 , LEU H:11 , TYR H:14 , GLY H:18 , THR H:19 , BCL H:43BINDING SITE FOR RESIDUE RG1 H 42
06AC6SOFTWAREBCL E:43 , TYR G:44 , BCL G:55 , ALA H:29 , LEU H:32 , ALA H:36BINDING SITE FOR RESIDUE RG1 G 54
07AC7SOFTWARETHR A:24 , ALA A:27 , HIS A:31 , TRP A:45 , RG1 A:54 , PHE B:22 , LEU B:25 , ALA B:26 , ALA B:29 , HIS B:30 , BCL B:43 , VAL G:10 , BCL G:56 , RG1 H:42 , BCL H:43BINDING SITE FOR RESIDUE BCL A 55
08AC8SOFTWAREVAL A:23 , ALA A:27 , VAL A:30 , HIS A:31 , ILE A:34 , BCL A:55 , BCL A:56 , THR B:19 , PHE B:22 , ALA B:26 , HIS B:30 , TRP B:39 , RG1 B:42 , TYR D:44 , TRP D:45 , RG1 D:54 , BCL D:55 , PHE E:22 , RG1 E:42BINDING SITE FOR RESIDUE BCL B 43
09AC9SOFTWAREFME A:1 , ASN A:2 , HOH A:57 , ILE B:16 , THR B:19 , ARG B:20 , HIS B:30 , TRP B:39 , RG1 B:42 , BCL B:43 , BCL D:55 , GLY E:18 , RG1 E:42BINDING SITE FOR RESIDUE BCL A 56
10BBUNKNOWNFME A:1 , ARG B:20B800 BACTERIOCHLOROPHYLL COORDINATING RESIDUES.
11BBAUNKNOWNHIS A:31 , TRP A:45B850 BACTERIOCHLOROPHYLL COORDINATING RESIDUES.
12BBBUNKNOWNHIS B:30 , TYR A:44B850 BACTERIOCHLOROPHYLL COORDINATING RESIDUES.
13BC1SOFTWAREVAL A:10 , BCL A:56 , RG1 B:42 , BCL B:43 , THR D:24 , ALA D:27 , HIS D:31 , TRP D:45 , RG1 D:54 , PHE E:22 , LEU E:25 , ALA E:26 , ALA E:29 , HIS E:30 , BCL E:43BINDING SITE FOR RESIDUE BCL D 55
14BC2SOFTWAREVAL D:23 , ALA D:27 , VAL D:30 , HIS D:31 , ILE D:34 , BCL D:55 , BCL D:56 , THR E:19 , PHE E:22 , ALA E:26 , HIS E:30 , TRP E:39 , RG1 E:42 , TYR G:44 , TRP G:45 , RG1 G:54 , BCL G:55 , PHE H:22 , RG1 H:42BINDING SITE FOR RESIDUE BCL E 43
15BC3SOFTWAREFME D:1 , ASN D:2 , HOH D:57 , ILE E:16 , THR E:19 , ARG E:20 , HIS E:30 , TRP E:39 , RG1 E:42 , BCL E:43 , BCL G:55 , GLY H:18 , RG1 H:42BINDING SITE FOR RESIDUE BCL D 56
16BC4SOFTWAREVAL D:10 , BCL D:56 , RG1 E:42 , BCL E:43 , THR G:24 , ALA G:27 , HIS G:31 , TRP G:45 , RG1 G:54 , PHE H:22 , LEU H:25 , ALA H:26 , ALA H:29 , HIS H:30 , BCL H:43BINDING SITE FOR RESIDUE BCL G 55
17BC5SOFTWARETYR A:44 , TRP A:45 , RG1 A:54 , BCL A:55 , PHE B:22 , RG1 B:42 , VAL G:23 , ALA G:27 , VAL G:30 , HIS G:31 , ILE G:34 , BCL G:55 , BCL G:56 , THR H:19 , PHE H:22 , ALA H:26 , HIS H:30 , TRP H:39 , RG1 H:42BINDING SITE FOR RESIDUE BCL H 43
18BC6SOFTWAREBCL A:55 , GLY B:18 , RG1 B:42 , FME G:1 , ASN G:2 , HOH G:57 , ILE H:16 , THR H:19 , ARG H:20 , HIS H:30 , TRP H:39 , RG1 H:42 , BCL H:43BINDING SITE FOR RESIDUE BCL G 56
19EEUNKNOWNFME D:1 , ARG E:20B800 BACTERIOCHLOROPHYLL COORDINATING RESIDUES.
20EEAUNKNOWNHIS D:31 , TRP D:45B850 BACTERIOCHLOROPHYLL COORDINATING RESIDUES.
21EEBUNKNOWNHIS E:30 , TYR D:44B850 BACTERIOCHLOROPHYLL COORDINATING RESIDUES.
22HHUNKNOWNFME G:1 , ARG H:20B800 BACTERIOCHLOROPHYLL COORDINATING RESIDUES.
23HHAUNKNOWNHIS G:31 , TRP G:45B850 BACTERIOCHLOROPHYLL COORDINATING RESIDUES.
24HHBUNKNOWNHIS H:30 , TYR G:44B850 BACTERIOCHLOROPHYLL COORDINATING RESIDUES.

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 6)

Asymmetric Unit (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ANTENNA_COMP_BETAPS00969 Antenna complexes beta subunits signature.LHB5_RHOAC7-38
 
 		  3B:7-38
E:7-38
H:7-38
2ANTENNA_COMP_ALPHAPS00968 Antenna complexes alpha subunits signature.LHA4_RHOAC25-41
 
 		  3A:25-41
D:25-41
G:25-41
Biological Unit 1 (2, 18)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ANTENNA_COMP_BETAPS00969 Antenna complexes beta subunits signature.LHB5_RHOAC7-38
 
 		  9B:7-38
E:7-38
H:7-38
2ANTENNA_COMP_ALPHAPS00968 Antenna complexes alpha subunits signature.LHA4_RHOAC25-41
 
 		  9A:25-41
D:25-41
G:25-41

(-) Exons   (0, 0)

(no "Exon" information available for 1KZU)

(-) 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:49
 aligned with LHA4_RHOAC | P26789 from UniProtKB/Swiss-Prot  Length:53

    Alignment length:49
                                    10        20        30        40         
            LHA4_RHOAC    1 MNQGKIWTVVNPAIGIPALLGSVTVIAILVHLAILSHTTWFPAYWQGGV 49
               SCOP domains d1kzua_ A: Light-harvesting complex subunits      SCOP domains
               CATH domains -1kzuA00 A:2-49                                   CATH domains
               Pfam domains ------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------ANTENNA_COMP_ALPH-------- PROSITE (2)
                 Transcript ------------------------------------------------- Transcript
                  1kzu A  1 mNQGKIWTVVNPAIGIPALLGSVTVIAILVHLAILSHTTWFPAYWQGGV 49
                            |       10        20        30        40         
                            |                                                
                            1-FME                                            


Chain B from PDB  Type:PROTEIN  Length:41
 aligned with LHB5_RHOAC | P26790 from UniProtKB/Swiss-Prot  Length:41

    Alignment length:41
                                    10        20        30        40 
            LHB5_RHOAC    1 ATLTAEQSEELHKYVIDGTRVFLGLALVAHFLAFSATPWLH 41
               SCOP domains d1kzub_ B:                                SCOP domains
               CATH domains 1kzuB00 B:1-41                            CATH domains
               Pfam domains ----------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------- SAPs(SNPs)
                    PROSITE ------ANTENNA_COMP_BETA  PDB: B:7-38  --- PROSITE
                 Transcript ----------------------------------------- Transcript
                  1kzu B  1 ATLTAEQSEELHKYVIDGTRVFLGLALVAHFLAFSATPWLH 41
                                    10        20        30        40 


Chain D from PDB  Type:PROTEIN  Length:49
 aligned with LHA4_RHOAC | P26789 from UniProtKB/Swiss-Prot  Length:53

    Alignment length:49
                                    10        20        30        40         
            LHA4_RHOAC    1 MNQGKIWTVVNPAIGIPALLGSVTVIAILVHLAILSHTTWFPAYWQGGV 49
               SCOP domains d1kzud_ D: Light-harvesting complex subunits      SCOP domains
               CATH domains -1kzuD00 D:2-49                                   CATH domains
               Pfam domains ------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------ANTENNA_COMP_ALPH-------- PROSITE (2)
                 Transcript ------------------------------------------------- Transcript
                  1kzu D  1 mNQGKIWTVVNPAIGIPALLGSVTVIAILVHLAILSHTTWFPAYWQGGV 49
                            |       10        20        30        40         
                            1-FME                                            


Chain E from PDB  Type:PROTEIN  Length:41
 aligned with LHB5_RHOAC | P26790 from UniProtKB/Swiss-Prot  Length:41

    Alignment length:41
                                    10        20        30        40 
            LHB5_RHOAC    1 ATLTAEQSEELHKYVIDGTRVFLGLALVAHFLAFSATPWLH 41
               SCOP domains d1kzue_ E:                                SCOP domains
               CATH domains 1kzuE00 E:1-41                            CATH domains
               Pfam domains ----------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------- SAPs(SNPs)
                    PROSITE ------ANTENNA_COMP_BETA  PDB: E:7-38  --- PROSITE
                 Transcript ----------------------------------------- Transcript
                  1kzu E  1 ATLTAEQSEELHKYVIDGTRVFLGLALVAHFLAFSATPWLH 41
                                    10        20        30        40 


Chain G from PDB  Type:PROTEIN  Length:49
 aligned with LHA4_RHOAC | P26789 from UniProtKB/Swiss-Prot  Length:53

    Alignment length:49
                                    10        20        30        40         
            LHA4_RHOAC    1 MNQGKIWTVVNPAIGIPALLGSVTVIAILVHLAILSHTTWFPAYWQGGV 49
               SCOP domains d1kzug_ G: Light-harvesting complex subunits      SCOP domains
               CATH domains -1kzuG00 G:2-49                                   CATH domains
           Pfam domains (1) --LHC-1kzuG01 G:3-42                      ------- Pfam domains (1)
           Pfam domains (2) --LHC-1kzuG02 G:3-42                      ------- Pfam domains (2)
           Pfam domains (3) --LHC-1kzuG03 G:3-42                      ------- Pfam domains (3)
         Sec.struct. author ...hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------ANTENNA_COMP_ALPH-------- PROSITE (2)
                 Transcript ------------------------------------------------- Transcript
                  1kzu G  1 mNQGKIWTVVNPAIGIPALLGSVTVIAILVHLAILSHTTWFPAYWQGGV 49
                            |       10        20        30        40         
                            1-FME                                            


Chain H from PDB  Type:PROTEIN  Length:41
 aligned with LHB5_RHOAC | P26790 from UniProtKB/Swiss-Prot  Length:41

    Alignment length:41
                                    10        20        30        40 
            LHB5_RHOAC    1 ATLTAEQSEELHKYVIDGTRVFLGLALVAHFLAFSATPWLH 41
               SCOP domains d1kzuh_ H:                                SCOP domains
               CATH domains 1kzuH00 H:1-41                            CATH domains
           Pfam domains (1) ----LHC-1kzuH01 H:5-41                    Pfam domains (1)
           Pfam domains (2) ----LHC-1kzuH02 H:5-41                    Pfam domains (2)
           Pfam domains (3) ----LHC-1kzuH03 H:5-41                    Pfam domains (3)
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------- SAPs(SNPs)
                    PROSITE ------ANTENNA_COMP_BETA  PDB: H:7-38  --- PROSITE
                 Transcript ----------------------------------------- Transcript
                  1kzu H  1 ATLTAEQSEELHKYVIDGTRVFLGLALVAHFLAFSATPWLH 41
                                    10        20        30        40
   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, 6)

Asymmetric Unit
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (2, 6)

Asymmetric Unit
(-)
Class: Few Secondary Structures (1120)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 6)

Asymmetric Unit
(-)
Clan: no clan defined [family: LHC] (5)

(-) Gene Ontology  (12, 23)

Asymmetric Unit(hide GO term definitions)
Chain A,D,G   (LHA4_RHOAC | P26789)
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,E,H   (LHB5_RHOAC | P26790)
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.

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  1kzu
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  LHB5_RHOAC | P26790
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 Related Entries

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

UniProtKB/Swiss-Prot
        LHA4_RHOAC | P26789: 1nkz 2fkw
        LHB5_RHOAC | P26790: 1nkz 2fkw

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1KZU)