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 :  X-RAY STRUCTURE OF PHYCOBILISOME LCM CORE-MEMBRANE LINKER POLYPEPTIDE (FRAGMENT 254-400) FROM SYNECHOCYSTIS SP. PCC 6803, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET SGR209C
 
Authors :  A. Kuzin, M. Su, S. Lew, J. Seetharaman, S. Sahdev, R. Xiao, C. Ciccosant J. K. Everett, R. Nair, T. B. Acton, B. Rost, G. T. Montelione, L. Tong, J Northeast Structural Genomics Consortium (Nesg)
Date :  09 Sep 10  (Deposition) - 06 Oct 10  (Release) - 22 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Structural Genomics, Psi-Biology, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Kuzin, M. Su, S. Lew, J. Seetharaman, S. Sahdev, 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 Sgr209C
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PHYCOBILISOME LCM CORE-MEMBRANE LINKER POLYPEPTIDE
    Chains: A, B, C, D
    Fragment: SEQUENCE DATABASE RESIDUES 254-400
    Organism Scientific: SYNECHOCYSTIS SP. PCC 6803
    Organism Taxid: 1148

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 16)

Asymmetric Unit (3, 16)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2NA7Ligand/IonSODIUM ION
3NO31Ligand/IonNITRATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
2NA-1Ligand/IonSODIUM ION
3NO3-1Ligand/IonNITRATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
2NA-1Ligand/IonSODIUM ION
3NO3-1Ligand/IonNITRATE ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
2NA-1Ligand/IonSODIUM ION
3NO3-1Ligand/IonNITRATE ION
Biological Unit 4 (2, 3)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
2NA-1Ligand/IonSODIUM ION
3NO31Ligand/IonNITRATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:322BINDING SITE FOR RESIDUE NA A 2
2AC2SOFTWAREPRO A:327BINDING SITE FOR RESIDUE NA A 4
3AC3SOFTWARELYS A:325BINDING SITE FOR RESIDUE NA A 7
4AC4SOFTWARESER B:299BINDING SITE FOR RESIDUE NA B 6
5AC5SOFTWARETYR C:329 , PHE C:333 , ALA C:342 , ALA C:346BINDING SITE FOR RESIDUE NA C 3
6AC6SOFTWAREPRO C:327 , LEU C:328BINDING SITE FOR RESIDUE NA C 5
7AC7SOFTWAREHOH C:226 , LEU C:305 , ARG C:322 , HOH C:436 , LYS D:325BINDING SITE FOR RESIDUE NA D 1
8AC8SOFTWAREILE D:294 , THR D:295 , TYR D:298BINDING SITE FOR RESIDUE NO3 D 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Pro B:271 -Gly B:272

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3OSJ)

(-) 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:135
 aligned with APCE_SYNY3 | Q55544 from UniProtKB/Swiss-Prot  Length:896

    Alignment length:135
                                   274       284       294       304       314       324       334       344       354       364       374       384       394     
           APCE_SYNY3   265 QKYAMKPGLSALEKNAVIKAAYRQIFERDITKAYSQSISYLESQVRNGDISMKEFVRRLAKSPLYRKQFFEPFINSRALELAFRHILGRGPSSREEVQKYFSIVSSGGLPALVDALVDSQEYADYFGEETVPYLR 399
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3osj A 265 QKYAmKPGLSALEKNAVIKAAYRQIFERDITKAYSQSISYLESQVRNGDISmKEFVRRLAKSPLYRKQFFEPFINSRALELAFRHILGRGPSSREEVQKYFSIVSSGGLPALVDALVDSQEYADYFGEETVPYLR 399
                                |  274       284       294       304       314 |     324       334       344       354       364       374       384       394     
                                |                                            316-MSE                                                                               
                              269-MSE                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:136
 aligned with APCE_SYNY3 | Q55544 from UniProtKB/Swiss-Prot  Length:896

    Alignment length:136
                                   273       283       293       303       313       323       333       343       353       363       373       383       393      
           APCE_SYNY3   264 RQKYAMKPGLSALEKNAVIKAAYRQIFERDITKAYSQSISYLESQVRNGDISMKEFVRRLAKSPLYRKQFFEPFINSRALELAFRHILGRGPSSREEVQKYFSIVSSGGLPALVDALVDSQEYADYFGEETVPYLR 399
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3osj B 264 RQKYAmKPGLSALEKNAVIKAAYRQIFERDITKAYSQSISYLESQVRNGDISmKEFVRRLAKSPLYRKQFFEPFINSRALELAFRHILGRGPSSREEVQKYFSIVSSGGLPALVDALVDSQEYADYFGEETVPYLR 399
                                 | 273       283       293       303       313  |    323       333       343       353       363       373       383       393      
                               269-MSE                                        316-MSE                                                                               


Chain C from PDB  Type:PROTEIN  Length:132
 aligned with APCE_SYNY3 | Q55544 from UniProtKB/Swiss-Prot  Length:896

    Alignment length:135
                                   274       284       294       304       314       324       334       344       354       364       374       384       394     
           APCE_SYNY3   265 QKYAMKPGLSALEKNAVIKAAYRQIFERDITKAYSQSISYLESQVRNGDISMKEFVRRLAKSPLYRKQFFEPFINSRALELAFRHILGRGPSSREEVQKYFSIVSSGGLPALVDALVDSQEYADYFGEETVPYLR 399
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhh...---.hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3osj C 265 QKYAmKPGLSALEKNAVIKAAYRQIFERDI---YSQSISYLESQVRNGDISmKEFVRRLAKSPLYRKQFFEPFINSRALELAFRHILGRGPSSREEVQKYFSIVSSGGLPALVDALVDSQEYADYFGEETVPYLR 399
                                |  274       284       294   |   304       314 |     324       334       344       354       364       374       384       394     
                              269-MSE                  294 298               316-MSE                                                                               


Chain D from PDB  Type:PROTEIN  Length:135
 aligned with APCE_SYNY3 | Q55544 from UniProtKB/Swiss-Prot  Length:896

    Alignment length:135
                                   274       284       294       304       314       324       334       344       354       364       374       384       394     
           APCE_SYNY3   265 QKYAMKPGLSALEKNAVIKAAYRQIFERDITKAYSQSISYLESQVRNGDISMKEFVRRLAKSPLYRKQFFEPFINSRALELAFRHILGRGPSSREEVQKYFSIVSSGGLPALVDALVDSQEYADYFGEETVPYLR 399
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----PBS_linker_poly-3osjD01 D:269-399                                                                                                   Pfam domains (1)
           Pfam domains (2) ----PBS_linker_poly-3osjD02 D:269-399                                                                                                   Pfam domains (2)
           Pfam domains (3) ----PBS_linker_poly-3osjD03 D:269-399                                                                                                   Pfam domains (3)
           Pfam domains (4) ----PBS_linker_poly-3osjD04 D:269-399                                                                                                   Pfam domains (4)
         Sec.struct. author .........hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3osj D 265 QKYAmKPGLSALEKNAVIKAAYRQIFERDITKAYSQSISYLESQVRNGDISmKEFVRRLAKSPLYRKQFFEPFINSRALELAFRHILGRGPSSREEVQKYFSIVSSGGLPALVDALVDSQEYADYFGEETVPYLR 399
                                |  274       284       294       304       314 |     324       334       344       354       364       374       384       394     
                              269-MSE                                        316-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 3OSJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (APCE_SYNY3 | Q55544)
molecular function
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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.
    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:0018298    protein-chromophore linkage    The covalent or noncovalent attachment of a chromophore to a protein.
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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NO3  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Pro B:271 - Gly B:272   [ 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
  3osj
    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
  APCE_SYNY3 | Q55544
    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
  APCE_SYNY3 | Q55544
    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
        APCE_SYNY3 | Q55544: 2l06 3ohw

(-) Related Entries Specified in the PDB File

2l06 100% IDENTITY RELATED ID: SGR209C RELATED DB: TARGETDB