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
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)

(-) Description

Title :  INTRAFLAGELLAR TRANSPORT COMPLEX 25-27 FROM CHLAMYDOMONAS
 
Authors :  S. Bhogaraju, M. Taschner, E. Lorentzen
Date :  11 Mar 11  (Deposition) - 23 Mar 11  (Release) - 01 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.59
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Transport Protein, Cilium, Ift Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Bhogaraju, M. Taschner, M. Morawetz, C. Basquin, E. Lorentzen
Crystal Structure Of The Intraflagellar Transport Complex 25/27.
Embo J. V. 30 1907 2011
PubMed-ID: 21505417  |  Reference-DOI: 10.1038/EMBOJ.2011.110

(-) Compounds

Molecule 1 - INTRAFLAGELLAR TRANSPORT PROTEIN 25
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentRESIDUES 1-135
    Organism CommonGREEN ALGAE
    Organism ScientificCHLAMYDOMONAS REINHARDTII
    Organism Taxid3055
    SynonymIFT25
 
Molecule 2 - SMALL RAB-RELATED GTPASE
    ChainsC, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Organism CommonGREEN ALGAE
    Organism ScientificCHLAMYDOMONAS REINHARDTII
    Organism Taxid3055
    SynonymIFT27

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A  D
Biological Unit 2 (1x) BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:27 , ASP A:30 , LYS A:32 , THR A:35 , ASN A:127BINDING SITE FOR RESIDUE CA A 201
2AC2SOFTWAREASN B:27 , ASP B:30 , LYS B:32 , THR B:35 , ASN B:127BINDING SITE FOR RESIDUE CA B 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YC2)

(-) Cis Peptide Bonds  (9, 9)

Asymmetric Unit
No.Residues
1Phe A:43 -Pro A:44
2Phe B:43 -Pro B:44
3Pro C:63 -Asp C:64
4Gly C:78 -Ser C:79
5Arg C:202 -Asn C:203
6Pro D:8 -Ile D:9
7Pro D:63 -Asp D:64
8Gly D:78 -Ser D:79
9Ser D:167 -Ala D:168

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YC2)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RABPS51419 small GTPase Rab1 family profile.IFT27_CHLRE12-204
 
  2C:12-203
D:12-202
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RABPS51419 small GTPase Rab1 family profile.IFT27_CHLRE12-204
 
  1-
D:12-202
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RABPS51419 small GTPase Rab1 family profile.IFT27_CHLRE12-204
 
  1C:12-203
-

(-) Exons   (0, 0)

(no "Exon" information available for 2YC2)

(-) 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:132
 aligned with IFT25_CHLRE | B8LIX8 from UniProtKB/Swiss-Prot  Length:189

    Alignment length:134
                                    10        20        30        40        50        60        70        80        90       100       110       120       130    
          IFT25_CHLRE     1 MKDYAREENGGLVVMASCSDERFPPENMLDGKDNTFWVTTGMFPQEFVLRLESCIRVSKITTLSLNVRKLAVEKCDQDKPDQFEKVFEVELANRGDRLQTEVHQVNIRAKYLKFILLQGHGEFATVNRVSVVGG 134
               SCOP domains d2yc2a_ A: automated matches                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee........ee..........hhhhhhh......ee......eeeeeeeeeeeeeeeeeeeee.eeeeeeeee........eeeeeee....--..eeeeeeeeeeeeeeeeeeeee.....eeeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yc2 A   1 MKDYAREENGGLVVMASCSDERFPPENMLDGKDNTFWVTTGMFPQEFVLRLESCIRVSKITTLSLNVRKLAVEKCDQDKPDQFEKVFEVELANR--RLQTEVHQVNIRAKYLKFILLQGHGEFATVNRVSVVGG 134
                                    10        20        30        40        50        60        70        80        90   |  |100       110       120       130    
                                                                                                                        94 97                                     

Chain B from PDB  Type:PROTEIN  Length:132
 aligned with IFT25_CHLRE | B8LIX8 from UniProtKB/Swiss-Prot  Length:189

    Alignment length:134
                                    10        20        30        40        50        60        70        80        90       100       110       120       130    
          IFT25_CHLRE     1 MKDYAREENGGLVVMASCSDERFPPENMLDGKDNTFWVTTGMFPQEFVLRLESCIRVSKITTLSLNVRKLAVEKCDQDKPDQFEKVFEVELANRGDRLQTEVHQVNIRAKYLKFILLQGHGEFATVNRVSVVGG 134
               SCOP domains d2yc2b_ B: automated matches                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee........ee..........hhhhhhh......ee......eeeeeeeeeeeeeeeeeeeee.eeeeeeeee........eeeeeee....--..eeeeeeeeeeeeeeeeeeeee.....eeeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yc2 B   1 MKDYAREENGGLVVMASCSDERFPPENMLDGKDNTFWVTTGMFPQEFVLRLESCIRVSKITTLSLNVRKLAVEKCDQDKPDQFEKVFEVELANR--RLQTEVHQVNIRAKYLKFILLQGHGEFATVNRVSVVGG 134
                                    10        20        30        40        50        60        70        80        90   |  |100       110       120       130    
                                                                                                                        94 97                                     

Chain C from PDB  Type:PROTEIN  Length:149
 aligned with IFT27_CHLRE | A8HN58 from UniProtKB/Swiss-Prot  Length:204

    Alignment length:197
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       
          IFT27_CHLRE     7 KPIDITATLRCKVAVVGEATVGKSALISMFTSKGSKFLKDYAMTSGVEVVVAPVTIPDTTVSVELFLLDTAGSDLYKEQISQYWNGVYYAILVFDVSSMESFESCKAWFELLKSARPDRERPLRAVLVANKTDLPPQRHQVRLDMAQDWATTNTLDFFDVSANPPGKDADAPFLSIATTFYRNYEDKVAAFQDACRN 203
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.eeeeeeeee.----------------------------------.eeee.....eeeeeeeee...hhhhhhhhh.......eeeeeee..hhhhhhhhhhhhhhhhhhh.......eeeeeee..-------..hhhhhhhhhhhh..eeee..-------.hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----RAB  PDB: C:12-203 UniProt: 12-204                                                                                                                                                               PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yc2 C   7 KPIDITATLRCKVAVV----------------------------------VAPVTIPDTTVSVELFLLDTAGSDLYKEQISQYWNGVYYAILVFDVSSMESFESCKAWFELLKSARPDRERPLRAVLVANKT-------QVRLDMAQDWATTNTLDFFDVS-------ADAPFLSIATTFYRNYEDKVAAFQDACRN 203
                                    16     |   -         -         -         -|       66        76        86        96       106       116       126       136 |     146       156       166|      176       186       196       
                                          22                                 57                                                                              138     146                  167     175                            

Chain D from PDB  Type:PROTEIN  Length:148
 aligned with IFT27_CHLRE | A8HN58 from UniProtKB/Swiss-Prot  Length:204

    Alignment length:195
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197     
          IFT27_CHLRE     8 PIDITATLRCKVAVVGEATVGKSALISMFTSKGSKFLKDYAMTSGVEVVVAPVTIPDTTVSVELFLLDTAGSDLYKEQISQYWNGVYYAILVFDVSSMESFESCKAWFELLKSARPDRERPLRAVLVANKTDLPPQRHQVRLDMAQDWATTNTLDFFDVSANPPGKDADAPFLSIATTFYRNYEDKVAAFQDACR 202
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeee.----------------------------------.eeee.....eeeeeeeee...hhhhhhhhh.......eeeeeee..hhhhhhhhhhhhhhhhhhh.......eeeeeee..-------..hhhhhhhhhhhhh.eeee...------.hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----RAB  PDB: D:12-202 UniProt: 12-204                                                                                                                                                              PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yc2 D   8 PIDITATLRCKVAVV----------------------------------VAPVTIPDTTVSVELFLLDTAGSDLYKEQISQYWNGVYYAILVFDVSSMESFESCKAWFELLKSARPDRERPLRAVLVANKT-------QVRLDMAQDWATTNTLDFFDVSA------ADAPFLSIATTFYRNYEDKVAAFQDACR 202
                                    17    |    -         -         -        57        67        77        87        97       107       117       127       137|      147       157       167|      177       187       197     
                                         22                                 57                                                                              138     146                   168    175                           

   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, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YC2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2YC2)

(-) Gene Ontology  (11, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (IFT25_CHLRE | B8LIX8)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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).
cellular component
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005929    cilium    A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0030992    intraciliary transport particle B    The larger subcomplex of the intraciliary transport particle; characterized complexes have molecular weights around 550 kDa.
    GO:0031514    motile cilium    A cilium which may have a variable arrangement of axonemal microtubules and also contains molecular motors. It may beat with a whip-like pattern that promotes cell motility or transport of fluids and other cells across a cell surface, such as on epithelial cells that line the lumenal ducts of various tissues; or they may display a distinct twirling motion that directs fluid flow asymmetrically across the cellular surface to affect asymmetric body plan organization. Motile cilia can be found in single as well as multiple copies per cell.

Chain C,D   (IFT27_CHLRE | A8HN58)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0007264    small GTPase mediated signal transduction    Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
cellular component
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0030992    intraciliary transport particle B    The larger subcomplex of the intraciliary transport particle; characterized complexes have molecular weights around 550 kDa.
    GO:0031514    motile cilium    A cilium which may have a variable arrangement of axonemal microtubules and also contains molecular motors. It may beat with a whip-like pattern that promotes cell motility or transport of fluids and other cells across a cell surface, such as on epithelial cells that line the lumenal ducts of various tissues; or they may display a distinct twirling motion that directs fluid flow asymmetrically across the cellular surface to affect asymmetric body plan organization. Motile cilia can be found in single as well as multiple copies per cell.

 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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Arg C:202 - Asn C:203   [ RasMol ]  
    Gly C:78 - Ser C:79   [ RasMol ]  
    Gly D:78 - Ser D:79   [ RasMol ]  
    Phe A:43 - Pro A:44   [ RasMol ]  
    Phe B:43 - Pro B:44   [ RasMol ]  
    Pro C:63 - Asp C:64   [ RasMol ]  
    Pro D:63 - Asp D:64   [ RasMol ]  
    Pro D:8 - Ile D:9   [ RasMol ]  
    Ser D:167 - Ala D:168   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2yc2
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  IFT25_CHLRE | B8LIX8
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  IFT27_CHLRE | A8HN58
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  IFT25_CHLRE | B8LIX8
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  IFT27_CHLRE | A8HN58
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        IFT25_CHLRE | B8LIX82yc4
        IFT27_CHLRE | A8HN582yc4

(-) Related Entries Specified in the PDB File

2yc4 INTRAFLAGELLAR TRANSPORT COMPLEX 25-27 FROM CHLAMYDOMONAS