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

(-) Description

Title :  CRYSTAL STRUCTURE OF THE TPR DOMAIN OF KINESIN LIGHT CHAIN 1
 
Authors :  Y. Tong, W. Tempel, L. Shen, Y. Shen, L. Nedyalkova, C. H. Arrowsmith, A. M. Edwards, C. Bountra, J. Weigelt, A. Bochkarev, H. Park, Structur Genomics Consortium (Sgc)
Date :  09 Jun 10  (Deposition) - 25 May 11  (Release) - 25 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Kinesin, Tpr, Structural Genomics Consortium (Sgc), Motor Protein, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Tong, W. Tempel, L. Shen, Y. Shen, L. Nedyalkova, C. H. Arrowsmith, A. M. Edwards, C. Bountra, J. Weigelt, A. Bochkarev, H. Park
Crystal Structure Of The Tpr Domain Of Kinesin Light Chain
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - KINESIN LIGHT CHAIN 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28-MHL
    Expression System StrainBL21-V2R-PRARE2
    Expression System Taxid562
    FragmentUNP RESIDUES 203 TO 497
    GeneKLC1, KLC, KNS2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymKLC 1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3NF1)

(-) Sites  (0, 0)

(no "Site" information available for 3NF1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NF1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3NF1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NF1)

(-) PROSITE Motifs  (3, 11)

Asymmetric/Biological Unit (3, 11)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TPRPS50005 TPR repeat profile.KLC1_HUMAN213-246
255-288
297-330
339-372
381-414
464-497
  6A:213-246
A:255-288
A:297-330
A:339-372
A:381-414
A:464-495
2TPR_REGIONPS50293 TPR repeat region circular profile.KLC1_HUMAN213-414
464-497
  2A:213-414
A:464-495
3KINESIN_LIGHTPS01160 Kinesin light chain repeat.KLC1_HUMAN238-279
280-321
322-363
364-405
  4A:238-279
A:280-321
A:322-363
A:364-405

(-) Exons   (0, 0)

(no "Exon" information available for 3NF1)

(-) Sequences/Alignments

Asymmetric/Biological 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:283
 aligned with KLC1_HUMAN | Q07866 from UniProtKB/Swiss-Prot  Length:573

    Alignment length:329
                                   176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486         
           KLC1_HUMAN   167 KDTDSTKEPLDDLFPNDEDDPGQGIQQQHSSAAAAAQQGGYEIPARLRTLHNLVIQYASQGRYEVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKDAANLLNDALAIREKTLGKDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYYYQRALEIYQTKLGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILTRAHEREFGSVDDENKPIWMHAEEREECKGKQKDGTSFGEYGGWYKACKVDSPTVTTTLKNLGALYRRQGKFEAAETLEEAAMRSRK 495
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------Rab5-bind-3nf1A01 A:205-254                       TPR_2-3nf1A06 A:255-287          ---------------------------------------------------------------------------------------------TPR_1-3nf1A02 A:381-413          -------------------------------------------------TPR_10-3nf1A05 A:463-495          Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPR_1-3nf1A03 A:381-413          ---------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPR_1-3nf1A04 A:381-413          ---------------------------------------------------------------------------------- Pfam domains (3)
         Sec.struct. author ...hhhhh---hhh---------------------........hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh------.hhhhhhhhhhhh-------.......---------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------------------------------TPR_REGION  PDB: A:213-414 UniProt: 213-414                                                                                                                                                               -------------------------------------------------TPR_REGION  PDB: A:464-495       PROSITE (1)
                PROSITE (2) ----------------------------------------------TPR  PDB: A:213-246               --------TPR  PDB: A:255-288               --------TPR  PDB: A:297-330               --------TPR  PDB: A:339-372               --------TPR  PDB: A:381-414               -------------------------------------------------TPR  PDB: A:464-495              PROSITE (2)
                PROSITE (3) -----------------------------------------------------------------------KINESIN_LIGHT  PDB: A:238-279             KINESIN_LIGHT  PDB: A:280-321             KINESIN_LIGHT  PDB: A:322-363             KINESIN_LIGHT  PDB: A:364-405             ------------------------------------------------------------------------------------------ PROSITE (3)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nf1 A 191 HHHSSGRE---NLY---------------------FQGGGYEIPARLRTLHNLVIQYASQGRYEVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKDAANLLNDALAIREKTLGKDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYYYQRALEIYQTKLGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILTRAHEREFG------KPIWMHAEEREEC-------TSFGEYG---------SPTVTTTLKNLGALYRRQGKFEAAETLEEAAMRSRK 495
                                   | - | |     -         -     | 206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416|      426       436       446   |     -   |   466       476       486         
                                 198 199 |                   202                                                                                                                                                                                                                    417    424         436     444   450       460                                   
                                       201                                                                                                                                                                                                                                                                                                                           

   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 3NF1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NF1)

(-) Pfam Domains  (4, 6)

Asymmetric/Biological Unit
(-)
Clan: TPR (230)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (KLC1_HUMAN | Q07866)
molecular function
    GO:0003777    microtubule motor activity    Catalysis of movement along a microtubule, coupled to the hydrolysis of a nucleoside triphosphate (usually ATP).
    GO:0003774    motor activity    Catalysis of the generation of force resulting either in movement along a microfilament or microtubule, or in torque resulting in membrane scission, coupled to the hydrolysis of a nucleoside triphosphate.
    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:0019886    antigen processing and presentation of exogenous peptide antigen via MHC class II    The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class II protein complex. The peptide antigen is typically, but not always, processed from a whole protein.
    GO:0007018    microtubule-based movement    A microtubule-based process that results in the movement of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules.
    GO:0006890    retrograde vesicle-mediated transport, Golgi to ER    The directed movement of substances from the Golgi back to the endoplasmic reticulum, mediated by vesicles bearing specific protein coats such as COPI or COG.
    GO:0035617    stress granule disassembly    The disaggregation of a stress granule into its constituent protein and RNA parts.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
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:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0030426    growth cone    The migrating motile tip of a growing nerve cell axon or dendrite.
    GO:0005871    kinesin complex    Any complex that includes a dimer of molecules from the kinesin superfamily, a group of related proteins that contain an extended region of predicted alpha-helical coiled coil in the main chain that likely produces dimerization. The native complexes of several kinesin family members have also been shown to contain additional peptides, often designated light chains as all of the noncatalytic subunits that are currently known are smaller than the chain that contains the motor unit. Kinesin complexes generally possess a force-generating enzymatic activity, or motor, which converts the free energy of the gamma phosphate bond of ATP into mechanical work.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005874    microtubule    Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
(no "Ligands, Modified Residues, Ions" information available for 3nf1)
 
  Sites
(no "Sites" information available for 3nf1)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3nf1)
 

(-) 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
  3nf1
    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
  KLC1_HUMAN | Q07866
    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
  KLC1_HUMAN | Q07866
    Protein Disorder PredictionDisEMBL | 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 3NF1)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3NF1)