Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - model 1, sites
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - model 1, sites
NMR Structure - model 1, sites  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION STRUCTURE OF CA2+-BOUND YCAM
 
Authors :  K. Ogura, K. Takahashi, Y. Kobashigawa, R. Yoshida, H. Itoh, M. Yazawa,
Date :  10 Aug 11  (Deposition) - 29 Aug 12  (Release) - 29 Aug 12  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Yeast Calmodulin, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Ogura, H. Kumeta, K. Takahasi, Y. Kobashigawa, R. Yoshida, H. Itoh, M. Yazawa, F. Inagaki
Solution Structures Of Yeast Saccharomyces Cerevisiae Calmodulin In Calcium- And Target Peptide-Bound States Reveal Similarities And Differences To Vertebrate Calmodulin.
Genes Cells V. 17 159 2012
PubMed-ID: 22280008  |  Reference-DOI: 10.1111/J.1365-2443.2012.01580.X

(-) Compounds

Molecule 1 - CALMODULIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPET22B
    Expression System Vector TypeVECTOR
    FragmentUNP RESIDUES 2-121
    GeneCMD1, YBR109C, YBR0904
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid559292
    StrainATCC 204508 / S288C
    SynonymCAM

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x)A
NMR Structure * (1x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

NMR Structure (1, 3)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
NMR Structure * (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (3, 3)

NMR Structure (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:20 , ASP A:22 , ASN A:24 , SER A:26 , GLU A:31BINDING SITE FOR RESIDUE CA A 201
2AC2SOFTWAREASP A:56 , VAL A:57 , ASP A:58 , ASN A:60 , GLN A:62 , GLU A:67BINDING SITE FOR RESIDUE CA A 202
3AC3SOFTWAREASP A:93 , ASN A:95 , ASP A:97 , LEU A:99 , GLU A:104BINDING SITE FOR RESIDUE CA A 203

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2LHH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 6)

NMR Structure (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.CALM_YEAST8-43
44-79
81-116
  3A:7-42
A:43-78
A:80-115
2EF_HAND_1PS00018 EF-hand calcium-binding domain.CALM_YEAST21-33
57-69
94-106
  3A:20-32
A:56-68
A:93-105
NMR Structure * (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.CALM_YEAST8-43
44-79
81-116
  3A:7-42
A:43-78
A:80-115
2EF_HAND_1PS00018 EF-hand calcium-binding domain.CALM_YEAST21-33
57-69
94-106
  3A:20-32
A:56-68
A:93-105

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YBR109C1YBR109C.1II:458356-457913444CALM_YEAST1-1471471A:1-128128

(-) Sequences/Alignments

NMR Structure
   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:128
 aligned with CALM_YEAST | P06787 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:128
                                    11        21        31        41        51        61        71        81        91       101       111       121        
           CALM_YEAST     2 SSNLTEEQIAEFKEAFALFDKDNNGSISSSELATVMRSLGLSPSEAEVNDLMNEIDVDGNHQIEFSEFLALMSRQLKSNDSEQELLEAFKVFDKNGDGLISAAELKHVLTSIGEKLTDAEVDDMLREV 129
               SCOP domains d2lhha_ A: automated matches                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh...hhhhhhhhhhhhh.......hhhhhhhhhhh.........hhhhhhhhhh.......hhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------EF_HAND_2  PDB: A:7-42 UniProt: 8-43EF_HAND_2  PDB: A:43-78             -EF_HAND_2  PDB: A:80-115            ------------- PROSITE (1)
                PROSITE (2) -------------------EF_HAND_1    -----------------------EF_HAND_1    ------------------------EF_HAND_1    ----------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: A:1-128 UniProt: 1-147 [INCOMPLETE]                                                                               Transcript 1
                 2lhh A   1 SSNLTEEQIAEFKEAFALFDKDNNGSISSSELATVMRSLGLSPSEAEVNDLMNEIDVDGNHQIEFSEFLALMSRQLKSNDSEQELLEAFKVFDKNGDGLISAAELKHVLTSIGEKLTDAELEHHHHHH 128
                                    10        20        30        40        50        60        70        80        90       100       110       120        

   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, 1)

NMR Structure

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (22, 22)

NMR Structure(hide GO term definitions)
Chain A   (CALM_YEAST | P06787)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0048306    calcium-dependent 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), in the presence of calcium.
    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).
biological process
    GO:0006607    NLS-bearing protein import into nucleus    The directed movement of a protein bearing a nuclear localization signal (NLS) from the cytoplasm into the nucleus, across the nuclear membrane.
    GO:0007114    cell budding    A form of asexual reproduction, occurring in certain bacteria and fungi (e.g. yeasts) and some primitive animals in which an individual arises from a daughter cell formed by pinching off a part of the parent cell. The budlike outgrowths so formed may sometimes remain attached to the parent cell.
    GO:0007010    cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures.
    GO:0000742    karyogamy involved in conjugation with cellular fusion    During sexual reproduction, the creation of a single nucleus from multiple nuclei as a result of fusing the lipid bilayers that surround each nuclei. This occurs after cytogamy.
    GO:0016237    lysosomal microautophagy    The transfer of cytosolic components into the lysosomal compartment by direct invagination of the lysosomal membrane without prior sequestration into an autophagosome. The engulfing membranes fuse, resulting in the lysosomal delivery of the cargo wrapped in a single membrane derived from the invaginated lysosomal membrane. In S. cerevisiae, the vacuole is the lysosomal compartment.
    GO:0006661    phosphatidylinositol biosynthetic process    The chemical reactions and pathways resulting in the formation of phosphatidylinositol, any glycophospholipid in which the sn-glycerol 3-phosphate residue is esterified to the 1-hydroxyl group of 1D-myo-inositol.
    GO:0006898    receptor-mediated endocytosis    An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles.
    GO:0051300    spindle pole body organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the spindle pole body (SPB). The SPB is the microtubule organizing center in fungi, and is functionally homologous to the animal cell centrosome.
    GO:0042991    transcription factor import into nucleus    The directed movement of a transcription factor from the cytoplasm to the nucleus.
    GO:0042144    vacuole fusion, non-autophagic    The fusion of two vacuole membranes to form a single vacuole.
cellular component
    GO:0005935    cellular bud neck    The constriction between the mother cell and daughter cell (bud) in an organism that reproduces by budding.
    GO:0005934    cellular bud tip    The end of a cellular bud distal to the site of attachment to the mother cell.
    GO:0005823    central plaque of spindle pole body    One of three laminate structures that form the spindle pole body; the central plaque is embedded in the nuclear envelope.
    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:0000131    incipient cellular bud site    The portion of the budding yeast plasma membrane where a daughter cell will emerge. The yeast marks this spot with bud-site selection proteins before bud emergence occurs. Actin is polarized to this spot just prior to and during bud emergence.
    GO:0043332    mating projection tip    The apex of the mating projection in unicellular fungi exposed to mating pheromone; site of polarized growth.
    GO:0005816    spindle pole body    The microtubule organizing center in fungi; functionally homologous to the animal cell centrosome.

 Visualization

(-) Interactive Views

NMR Structure
  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 ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2lhh)
 

(-) 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
  2lhh
    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
  CALM_YEAST | P06787
    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
  CALM_YEAST | P06787
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CALM_YEAST | P067871f54 1f55 1lkj 2lhi

(-) Related Entries Specified in the PDB File

1lkj 2lhi