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(-) Description

Title :  SOLUTION STRUCTURE OF CA2+/CNA1 PEPTIDE-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, Cna1, 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, SERINE/THREONINE-PROTEIN PHOSPHATASE 2B CATALYTIC SUBUNIT A1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPGEX6P
    Expression System Vector TypeVECTOR
    GeneCMD1, YBR109C, YBR0904, CMP1, CNA1, L9753.6, YLR433C
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE, SYNTHETIC, SACCHAROMYCES CEREVISIAE
    Organism Taxid559292, 32630, 559292
    Other DetailsTHE FUSION PROTEIN OF CALMODULIN (RESIDUE 1-146), LINKER (GSSTG) AND CALCINEURIN A1 (RESIDUES 453-476)
    StrainATCC 204508 / S288C
    SynonymYCAM-GS-CNA1, CAM-CALCINEURIN A1, CAM-CALMODULIN-BINDING PROTEIN

 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 , ASP A:58 , ASN A:60 , GLN A:62 , GLU A:64 , 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 2LHI)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 7)

NMR Structure (3, 7)
 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
3SER_THR_PHOSPHATASEPS00125 Serine/threonine specific protein phosphatases signature.PP2B1_YEAST176-181  1A:99-104
NMR Structure * (3, 7)
 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
3SER_THR_PHOSPHATASEPS00125 Serine/threonine specific protein phosphatases signature.PP2B1_YEAST176-181  1A:99-104

(-) Exons   (0, 0)

(no "Exon" information available for 2LHI)

(-) 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:176
 aligned with CALM_YEAST | P06787 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:176
                                                                                                                                                                            147                             
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      |  -         -         -      
           CALM_YEAST     1 MSSNLTEEQIAEFKEAFALFDKDNNGSISSSELATVMRSLGLSPSEAEVNDLMNEIDVDGNHQIEFSEFLALMSRQLKSNDSEQELLEAFKVFDKNGDGLISAAELKHVLTSIGEKLTDAEVDDMLREVSDGSGEINIQQFAALLSK-----------------------------   -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhh.........hhhhhhhhhhhhh...hhhhhhhhhh............hhhhhhhh.....hhhhhhhhhhhhhhh.......hhhhhhhhhhh.....hhhhhhhhhhhhhh.......hhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh. 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 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2lhi A   0 GSSNLTEEQIAEFKEAFALFDKDNNGSISSSELATVMRSLGLSPSEAEVNDLMNEIDVDGNHQIEFSEFLALMSRQLKSNDSEQELLEAFKVFDKNGDGLISAAELKHVLTSIGEKLTDAEVDDMLREVSDGSGEINIQQFAALLSKGSSTGTRRKALRNKILAIAKVSRMFSVLR 476
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149 ||    460       470      
                                                                                                                                                                                 151|                       
                                                                                                                                                                                  453                       

Chain A from PDB  Type:PROTEIN  Length:176
 aligned with PP2B1_YEAST | P23287 from UniProtKB/Swiss-Prot  Length:553

    Alignment length:476
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470      
          PP2B1_YEAST     1 MSKDLNSSRIKIIKPNDSYIKVDRKKDLTKYELENGKVISTKDRPIASVPAITGKIPSDEEVFDSKTGLPNHSFLREHFFHEGRLSKEQAIKILNMSTVALSKEPNLLKLKAPITICGDIHGQYYDLLKLFEVGGDPAEIDYLFLGDYVDRGAFSFECLIYLYSLKLNNLGRFWMLRGNHECKHLTSYFTFKNEMLHKYDMEVYDACCRSFNVLPLAALMNGQYFCVHGGISPELKSVEDVNKINRFREIPSRGLMCDLLWADPVENYDDARDGSEFDQSEDEFVPNSLRGCSFAFTFKASCKFLKANGLLSIIRAHEAQDAGYRMYKNNKVTGFPSLITMFSAPNYLDTYHNKAAVLKYEENVMNIRQFHMSPHPYWLPDFMDVFTWSLPFVGEKVTSMLVSILNICSEQELDPESEPKAAEETVKARANATKETGTPSDEKASSAILEDETRRKALRNKILAIAKVSRMFSVLR 476
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhh-----------hhhhh.........hhhh--hhhhhhhhh...hhhhhhhhhh----------------------............h---hhhhhhh.....hhhhhhhhhhhhhhh....--------------------------------------...hhhhhhhhhhh....---------------------------------------------.hhhhhhhhhhhhh---------------------h..---------------------------------------------------------------------------------------.....hhhhhhhh------------------------------------------------------------......-----------.hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SER_TH------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2lhi A   0 GSSNLTEEQIAEFK-----------EAFALFDKDNNGSISSSE--LATVMRSLGLSPSEAEVNDLMN----------------------EIDVDGNHQIEFS---EFLALMSRQLKSNDSEQELLEAFKVFDKNGD--------------------------------------GLISAAELKHVLTSIGEK---------------------------------------------LTDAEVDDMLREVS---------------------DGS---------------------------------------------------------------------------------------GEINIQQFAALLS------------------------------------------------------------KGSSTG-----------TRRKALRNKILAIAKVSRMFSVLR 476
                                     9   |     -     |  18        28  |  |  36        46      |  -         -        54        64 |   |  71        81        91     |   -         -         -         -    |  103       113 |       -         -         -         -       118       128|        -         -  | |    -         -         -         -         -         -         -         -         -  |    140    |    -         -         -         -         -         -     | 150|        -  |    460       470      
                                        13          14               31 32                   53                     54          66  67                            97                                     98              115                                           116          129                   130 |                                                                                     133         145                                                          146  151         453                       
                                                                                                                                                                                                                                                                                                            132                                                                                                                                                                                                         

   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 2LHI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (31, 34)

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.

Chain A   (PP2B1_YEAST | P23287)
molecular function
    GO:0004723    calcium-dependent protein serine/threonine phosphatase activity    Catalysis of the reactions: protein serine phosphate + H2O = protein serine + phosphate; and protein threonine phosphate + H2O = protein threonine + phosphate. These reactions require the presence of calcium ions.
    GO:0005516    calmodulin binding    Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004721    phosphoprotein phosphatase activity    Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity.
    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:0000754    adaptation of signaling pathway by response to pheromone involved in conjugation with cellular fusion    In organisms that undergo conjugation with cellular fusion, the process resulting in desensitization following exposure to pheromone stimulus that act to down-regulate further stimulation or block initial conjugation responses. An example of this is the adaptation to pheromone during conjugation with cellular fusion in Saccharomyces cerevisiae.
    GO:0006873    cellular ion homeostasis    Any process involved in the maintenance of an internal steady state of ions at the level of a cell.
    GO:0031505    fungal-type cell wall organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the fungal-type cell wall.
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
cellular component
    GO:0005955    calcineurin complex    A heterodimeric calcium ion and calmodulin dependent protein phosphatase composed of catalytic and regulatory subunits; the regulatory subunit is very similar in sequence to calmodulin.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

2lhh