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(-) Description

Title :  SOLUTION STRUCTURE OF CALCIUM LOADED S100B COMPLEXED TO A PEPTIDE FROM N-TERMINAL REGULATORY DOMAIN OF NDR KINASE.
 
Authors :  S. Bhattacharya, E. Large, C. W. Heizmann, B. Hemmings, W. J. Chazin
Date :  21 Jun 03  (Deposition) - 16 Dec 03  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B,C,D  (20x)
Keywords :  Helix-Loop-Helix, Protein-Peptide Complex, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Bhattacharya, E. Large, C. W. Heizmann, B. Hemmings, W. J. Chazin
Structure Of The Ca(2+)/S100B/Ndr Kinase Peptide Complex: Insights Into S100 Target Specificity And Activation Of The Kinase.
Biochemistry V. 42 14416 2003
PubMed-ID: 14661952  |  Reference-DOI: 10.1021/BI035089A
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - S-100 PROTEIN, BETA CHAIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PH6 TEV
    Expression System Strain: BL21 CODON PLUS (DE3) RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: S100B
    Organism Common: CATTLE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
 
Molecule 2 - NDR SER/THR KINASE-LIKE PROTEIN
    Chains: C, D
    Engineered: YES
    Fragment: N-TERMINAL REGULATORY DOMAIN FRAGMENT, SEQUENCE DATABASE RESIDUE 60-85
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN HOMO SAPIENS.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1PSB)

(-) Sites  (0, 0)

(no "Site" information available for 1PSB)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1PSB)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1PSB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PSB)

(-) PROSITE Motifs  (3, 6)

NMR Structure (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.S100B_BOVIN49-84
 		  2A:48-83
B:48-83
2S100_CABPPS00303 S-100/ICaBP type calcium binding protein signature.S100B_BOVIN57-78
 		  2A:56-77
B:56-77
3EF_HAND_1PS00018 EF-hand calcium-binding domain.S100B_BOVIN62-74
 		  2A:61-73
B:61-73

(-) Exons   (3, 6)

NMR Structure (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSBTAT000000062751ENSBTAE00000256656chr1:149249251-14924919953S100B_BOVIN-00--
1.2ENSBTAT000000062752ENSBTAE00000256655chr1:149246090-149245953138S100B_BOVIN1-46462A:1-45
B:1-45		45
45
1.3ENSBTAT000000062753ENSBTAE00000050031chr1:149243137-1492418491289S100B_BOVIN47-92462A:46-91
B:46-91		46
46
2.1bENST000002298121bENSE00001233802chr6:36515247-36514967281STK38_HUMAN-00--
2.2aENST000002298122aENSE00001233821chr6:36507984-36507849136STK38_HUMAN1-44440--
2.3ENST000002298123ENSE00000748970chr6:36493419-3649336852STK38_HUMAN44-61180--
2.4ENST000002298124ENSE00000748967chr6:36492240-36492118123STK38_HUMAN62-102412C:62-87
D:62-87		26
26
2.5ENST000002298125ENSE00001723066chr6:36489594-3648951184STK38_HUMAN103-130280--
2.6ENST000002298126ENSE00000748962chr6:36485617-36485494124STK38_HUMAN131-172420--
2.7ENST000002298127ENSE00001639224chr6:36483269-36483115155STK38_HUMAN172-223520--
2.8ENST000002298128ENSE00000748958chr6:36475379-36475277103STK38_HUMAN224-258350--
2.9ENST000002298129ENSE00000748955chr6:36474421-3647436062STK38_HUMAN258-278210--
2.10ENST0000022981210ENSE00000748952chr6:36467767-36467650118STK38_HUMAN279-318400--
2.11ENST0000022981211ENSE00001707872chr6:36466263-36466140124STK38_HUMAN318-359420--
2.12ENST0000022981212ENSE00000748945chr6:36465652-3646555796STK38_HUMAN359-391330--
2.13ENST0000022981213ENSE00000748942chr6:36464582-3646448895STK38_HUMAN391-423330--
2.14bENST0000022981214bENSE00001880647chr6:36463691-364616692023STK38_HUMAN423-465430--

(-) 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:91
 aligned with S100B_BOVIN | P02638 from UniProtKB/Swiss-Prot  Length:92

    Alignment length:91
                                    11        21        31        41        51        61        71        81        91 
           S100B_BOVIN    2 SELEKAVVALIDVFHQYSGREGDKHKLKKSELKELINNELSHFLEEIKEQEVVDKVMETLDSDGDGECDFQEFMAFVAMITTACHEFFEHE 92
               SCOP domains d1psba_ A: Calcyclin (S100)                                                                 SCOP domains
               CATH domains 1psbA00 A:1-91 EF-hand                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhh........hhhhhhhhhhhhh.....eeehhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------------------------EF_HAND_2  PDB: A:48-83             -------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------S100_CABP  PDB: A:56-7-------------- PROSITE (2)
                PROSITE (3) ------------------------------------------------------------EF_HAND_1    ------------------ PROSITE (3)
               Transcript 1 Exon 1.2  PDB: A:1-45 UniProt: 1-46          Exon 1.3  PDB: A:46-91 UniProt: 47-92          Transcript 1
                  1psb A  1 SELEKAVVALIDVFHQYSGREGDKHKLKKSELKELINNELSHFLEEIKEQEVVDKVMETLDSDGDGECDFQEFMAFVAMITTACHEFFEHE 91
                                    10        20        30        40        50        60        70        80        90 


Chain B from PDB  Type:PROTEIN  Length:91
 aligned with S100B_BOVIN | P02638 from UniProtKB/Swiss-Prot  Length:92

    Alignment length:91
                                    11        21        31        41        51        61        71        81        91 
           S100B_BOVIN    2 SELEKAVVALIDVFHQYSGREGDKHKLKKSELKELINNELSHFLEEIKEQEVVDKVMETLDSDGDGECDFQEFMAFVAMITTACHEFFEHE 92
               SCOP domains d1psbb_ B: Calcyclin (S100)                                                                 SCOP domains
               CATH domains 1psbB00 B:1-91 EF-hand                                                                      CATH domains
           Pfam domains (1) --S_100-1psbB01 B:3-46                        -----efhand-1psbB03 B:52-80       ----------- Pfam domains (1)
           Pfam domains (2) --S_100-1psbB02 B:3-46                        -----efhand-1psbB04 B:52-80       ----------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhh......eeehhhhhhhhhhhh........hhhhhhhhhhhhh.....eeehhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------------------------EF_HAND_2  PDB: B:48-83             -------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------S100_CABP  PDB: B:56-7-------------- PROSITE (2)
                PROSITE (3) ------------------------------------------------------------EF_HAND_1    ------------------ PROSITE (3)
               Transcript 1 Exon 1.2  PDB: B:1-45 UniProt: 1-46          Exon 1.3  PDB: B:46-91 UniProt: 47-92          Transcript 1
                  1psb B  1 SELEKAVVALIDVFHQYSGREGDKHKLKKSELKELINNELSHFLEEIKEQEVVDKVMETLDSDGDGECDFQEFMAFVAMITTACHEFFEHE 91
                                    10        20        30        40        50        60        70        80        90 


Chain C from PDB  Type:PROTEIN  Length:26
 aligned with STK38_HUMAN | Q15208 from UniProtKB/Swiss-Prot  Length:465

    Alignment length:26
                                    71        81      
           STK38_HUMAN   62 KRLRRSAHARKETEFLRLKRTRLGLE 87
               SCOP domains -------------------------- SCOP domains
               CATH domains -------------------------- CATH domains
               Pfam domains -------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------- SAPs(SNPs)
                    PROSITE -------------------------- PROSITE
               Transcript 2 Exon 2.4  PDB: C:62-87     Transcript 2
                  1psb C 62 KRLRRSAHARKETEFLRLKRTRLGLE 87
                                    71        81      


Chain D from PDB  Type:PROTEIN  Length:26
 aligned with STK38_HUMAN | Q15208 from UniProtKB/Swiss-Prot  Length:465

    Alignment length:26
                                    71        81      
           STK38_HUMAN   62 KRLRRSAHARKETEFLRLKRTRLGLE 87
               SCOP domains -------------------------- SCOP domains
               CATH domains -------------------------- CATH domains
               Pfam domains -------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------- SAPs(SNPs)
                    PROSITE -------------------------- PROSITE
               Transcript 2 Exon 2.4  PDB: D:62-87     Transcript 2
                  1psb D 62 KRLRRSAHARKETEFLRLKRTRLGLE 87
                                    71        81
   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)

NMR Structure
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

NMR Structure
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 4)

NMR Structure
(-)
Clan: EF_hand (270)

(-) Gene Ontology  (42, 47)

NMR Structure(hide GO term definitions)
Chain A,B   (S100B_BOVIN | P02638)
molecular function
    GO:0050786    RAGE receptor binding    Interacting selectively and non-covalently with the RAGE receptor, the receptor for advanced glycation end-products.
    GO:0044548    S100 protein binding    Interacting selectively and non-covalently with a S100 protein. S100 is a small calcium and zinc binding protein produced in astrocytes that is implicated in Alzheimer's disease, Down Syndrome and ALS.
    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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0019210    kinase inhibitor activity    Stops, prevents or reduces the activity of a kinase, an enzyme which catalyzes of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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).
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0048156    tau protein binding    Interacting selectively and non-covalently with tau protein. tau is a microtubule-associated protein, implicated in Alzheimer's disease, Down Syndrome and ALS.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0048143    astrocyte activation    A change in morphology and behavior of an astrocyte resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor.
    GO:0007409    axonogenesis    De novo generation of a long process of a neuron, that carries efferent (outgoing) action potentials from the cell body towards target cells. Refers to the morphogenesis or creation of shape or form of the developing axon.
    GO:0007611    learning or memory    The acquisition and processing of information and/or the storage and retrieval of this information over time.
    GO:0007613    memory    The activities involved in the mental information processing system that receives (registers), modifies, stores, and retrieves informational stimuli. The main stages involved in the formation and retrieval of memory are encoding (processing of received information by acquisition), storage (building a permanent record of received information as a result of consolidation) and retrieval (calling back the stored information and use it in a suitable way to execute a given task).
    GO:0071638    negative regulation of monocyte chemotactic protein-1 production    Any process that stops, prevents, or reduces the frequency, rate, or extent of production of monocyte chemotactic protein-1.
    GO:0042326    negative regulation of phosphorylation    Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0043123    positive regulation of I-kappaB kinase/NF-kappaB signaling    Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling.
    GO:0045917    positive regulation of complement activation    Any process that activates or increases the frequency, rate or extent of complement activation.
    GO:0048168    regulation of neuronal synaptic plasticity    A process that modulates neuronal synaptic plasticity, the ability of neuronal synapses to change as circumstances require. They may alter function, such as increasing or decreasing their sensitivity, or they may increase or decrease in actual numbers.
    GO:0006417    regulation of translation    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    GO:0001726    ruffle    Projection at the leading edge of a crawling cell; the protrusions are supported by a microfilament meshwork.

Chain C,D   (STK38_HUMAN | Q15208)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0031435    mitogen-activated protein kinase kinase kinase binding    Interacting selectively and non-covalently with a mitogen-activated protein kinase kinase kinase, any protein that can phosphorylate a MAP kinase kinase.
    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).
    GO:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006464    cellular protein modification process    The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
    GO:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    GO:0043407    negative regulation of MAP kinase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of MAP kinase activity.
    GO:0018105    peptidyl-serine phosphorylation    The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
cellular component
    GO:0070688    MLL5-L complex    A protein complex that can methylate lysine-4 of histone H3 and plays an essential role in retinoic-acid-induced granulopoiesis. MLL5 is the catalytic methyltransferase subunit, and the complex also contains serine/threonine kinase 38 (STK38), protein phosphatase 1 catalytic subunits, the host cell factor-1 N-terminal subunit, beta-actin, and O-GlcNAc transferase; the human genes encoding the subunits are MLL5, STK38, PPP1CA, PPP1CB, PPP1CC, HCFC1, ACTB and OGT, respectively.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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  1psb
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 Related Entries

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

UniProtKB/Swiss-Prot
        S100B_BOVIN | P02638: 1cfp 1mho 3cr2 3cr4 3cr5 3gk1 3gk2 3gk4 3iqo 3iqq 3lk0 3lk1 3lle 3rlz 3rm1 4fqo 4pdz 4pe0 4pe1 4pe4 4pe7 5dkn 5dkq 5dkr 5er4 5er5

(-) Related Entries Specified in the PDB File

1dt7 S100B-P53 COMPLEX
1mho CA2+ LOADED BOVINE S100B STRUCTURE
1mq1 S100B-TRTK-12 COMPLEX
1mwn S100B-TRTK-12 COMPLEX
1qlk CA2+ LOADED RAT S100B STRUCTURE
1uwo CA2+ LOADED HUMAN S100B STRUCTURE