Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF PHYCOBILISOME 32.1 KDA LINKER POLYPEPTIDE, PHYCOCYANIN-ASSOCIATED, ROD 1 (FRAGMENT 14-158) FROM SYNECHOCYSTIS SP. PCC 6803, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET SGR182A
 
Authors :  A. Kuzin, M. Su, P. Patel, R. Xiao, C. Ciccosanti, D. Lee, J. K. Everett, R T. B. Acton, B. Rost, G. T. Montelione, L. Tong, J. F. Hunt, Northeast S Genomics Consortium (Nesg)
Date :  30 Nov 10  (Deposition) - 15 Dec 10  (Release) - 22 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.68
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  C  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Structural Genomics, Psi-Biology, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Photosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Kuzin, M. Su, P. Patel, R. Xiao, C. Ciccosanti, D. Lee, J. K. Everett, R. Nair, T. B. Acton, B. Rost, G. T. Montelione, L. Tong, J. F. Hunt
Northeast Structural Genomics Consortium Target Sgr182A
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PHYCOBILISOME 32.1 KDA LINKER POLYPEPTIDE, PHYCOCYANIN- ASSOCIATED, ROD 1
    Chains: C, A, B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: SEQUENCE DATABASE RESIDUES 14-158
    Gene: CPCC1, SLL1580
    Organism Scientific: SYNECHOCYSTIS SP.
    Organism Taxid: 1148
    Strain: PCC 6803

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x):   C 
Biological Unit 2 (1x): A   
Biological Unit 3 (1x):  B  
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2MSE8Mod. Amino AcidSELENOMETHIONINE
3NA1Ligand/IonSODIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE2Mod. Amino AcidSELENOMETHIONINE
3NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE2Mod. Amino AcidSELENOMETHIONINE
3NA-1Ligand/IonSODIUM ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE2Mod. Amino AcidSELENOMETHIONINE
3NA-1Ligand/IonSODIUM ION
Biological Unit 4 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE2Mod. Amino AcidSELENOMETHIONINE
3NA-1Ligand/IonSODIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:55 , GLY A:57 , ALA A:58 , LEU C:55 , GLY C:57 , ALA C:58BINDING SITE FOR RESIDUE CL C 1
2AC2SOFTWAREARG A:70 , TYR A:139 , GLY A:144 , ILE A:147BINDING SITE FOR RESIDUE NA A 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3PRU)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Arg A:19 -Pro A:20

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3PRU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3PRU)

(-) Exons   (0, 0)

(no "Exon" information available for 3PRU)

(-) 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:142
 aligned with PYR1_SYNY3 | P73203 from UniProtKB/Swiss-Prot  Length:291

    Alignment length:142
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154  
           PYR1_SYNY3    15 YNESRPVELRPDFSLDDAKMVIRAVYRQVLGNDYIMDSERLKGAESLLTNGSISVREFVRTVAKSELYKKKFLYNNFQTRVIELNYKHLLGRAPFSEDEVIFHLDLYENQGFDADIDSYIDSVEYQENFGENIVPYYRFNNQ 156
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pru A  15 YNESRPVELRPDFSLDDAKmVIRAVYRQVLGNDYImDSERLKGAESLLTNGSISVREFVRTVAKSELYKKKFLYNNFQTRVIELNYKHLLGRAPFSEDEVIFHLDLYENQGFDADIDSYIDSVEYQENFGENIVPYYRFNNQ 156
                                    24        34        44     |  54        64        74        84        94       104       114       124       134       144       154  
                                              34-MSE          50-MSE                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:144
 aligned with PYR1_SYNY3 | P73203 from UniProtKB/Swiss-Prot  Length:291

    Alignment length:170
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188
           PYR1_SYNY3    19 RPVELRPDFSLDDAKMVIRAVYRQVLGNDYIMDSERLKGAESLLTNGSISVREFVRTVAKSELYKKKFLYNNFQTRVIELNYKHLLGRAPFSEDEVIFHLDLYENQGFDADIDSYIDSVEYQENFGENIVPYYRFNNQVGDRTVGFTRMFRLYRGYANSDRSQLERSSSR 188
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........--------------------------hhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pru B  19 RPVELRPDFSLDDAKmVIRAVYRQVLGNDYImDSERLKGAESLLTNGSISVREFVRTVAKSELYKKKFLYNNFQTRVIELNYKHLLGRAPFSEDEVIFHLDLYENQGFDADIDSYIDSVEYQENFGENIVPYYRFN--------------------------GLEHHHHH 165
                                    28     |  38        48 |      58        68        78        88        98       108       118       128       138       148     |   -         -         -  |    165
                                          34-MSE          50-MSE                                                                                                 154                        158       


Chain C from PDB  Type:PROTEIN  Length:137
 aligned with PYR1_SYNY3 | P73203 from UniProtKB/Swiss-Prot  Length:291

    Alignment length:137
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       
           PYR1_SYNY3    19 RPVELRPDFSLDDAKMVIRAVYRQVLGNDYIMDSERLKGAESLLTNGSISVREFVRTVAKSELYKKKFLYNNFQTRVIELNYKHLLGRAPFSEDEVIFHLDLYENQGFDADIDSYIDSVEYQENFGENIVPYYRFNN 155
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pru C  19 RPVELRPDFSLDDAKmVIRAVYRQVLGNDYImDSERLKGAESLLTNGSISVREFVRTVAKSELYKKKFLYNNFQTRVIELNYKHLLGRAPFSEDEVIFHLDLYENQGFDADIDSYIDSVEYQENFGENIVPYYRFNN 155
                                    28     |  38        48 |      58        68        78        88        98       108       118       128       138       148       
                                          34-MSE          50-MSE                                                                                                     


Chain D from PDB  Type:PROTEIN  Length:135
 aligned with PYR1_SYNY3 | P73203 from UniProtKB/Swiss-Prot  Length:291

    Alignment length:135
                                    28        38        48        58        68        78        88        98       108       118       128       138       148     
           PYR1_SYNY3    19 RPVELRPDFSLDDAKMVIRAVYRQVLGNDYIMDSERLKGAESLLTNGSISVREFVRTVAKSELYKKKFLYNNFQTRVIELNYKHLLGRAPFSEDEVIFHLDLYENQGFDADIDSYIDSVEYQENFGENIVPYYRF 153
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----PBS_linker_poly-3pruD01 D:23-153                                                                                                    Pfam domains (1)
           Pfam domains (2) ----PBS_linker_poly-3pruD02 D:23-153                                                                                                    Pfam domains (2)
           Pfam domains (3) ----PBS_linker_poly-3pruD03 D:23-153                                                                                                    Pfam domains (3)
           Pfam domains (4) ----PBS_linker_poly-3pruD04 D:23-153                                                                                                    Pfam domains (4)
         Sec.struct. author .........hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pru D  19 RPVELRPDFSLDDAKmVIRAVYRQVLGNDYImDSERLKGAESLLTNGSISVREFVRTVAKSELYKKKFLYNNFQTRVIELNYKHLLGRAPFSEDEVIFHLDLYENQGFDADIDSYIDSVEYQENFGENIVPYYRF 153
                                    28     |  38        48 |      58        68        78        88        98       108       118       128       138       148     
                                          34-MSE          50-MSE
   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 3PRU)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3PRU)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: PBS_linker_poly] (8)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (PYR1_SYNY3 | P73203)
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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0030089    phycobilisome    Any of the granules, approximately 32 nm x 48 nm and consisting of highly aggregated phycobiliproteins, that are attached in arrays to the external face of a thylakoid membrane in algae of the phyla Cyanophyta and Rhodophyta, where they function as light-harvesting devices in photosynthesis. Excitation energy in the phycobilisome flows in the sequence: phycoerythrin, phycocyanin, allophycocyanin before passing to the antenna chlorophyll of photosystem II.
    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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Arg A:19 - Pro A:20   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format | Biol. Unit 4 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
  3pru
    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
  PYR1_SYNY3 | P73203
    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
  PYR1_SYNY3 | P73203
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3PRU)

(-) Related Entries Specified in the PDB File

2l3w 61% HOMOLOGY RELATED ID: SGR182A RELATED DB: TARGETDB