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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN SIGMA ISOFORM OF 14-3-3 IN COMPLEX WITH A MODE-1 PHOSPHOPEPTIDE
 
Authors :  E. W. Wilker, R. A. Grant, S. C. Artim, M. B. Yaffe
Date :  18 Feb 05  (Deposition) - 01 Mar 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  A,B,C,D  (2x)
Keywords :  Protein-Phosphopeptide Complex, 14-3-3, Signaling Protein/De Novo Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. W. Wilker, R. A. Grant, S. C. Artim, M. B. Yaffe
A Structural Basis For 14-3-3Sigma Functional Specificity.
J. Biol. Chem. V. 280 18891 2005
PubMed-ID: 15731107  |  Reference-DOI: 10.1074/JBC.M500982200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 14-3-3 PROTEIN SIGMA
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainDH5ALPHA
    Expression System Taxid562
    Expression System VectorPKK233-2
    Expression System Vector TypePLASMID
    GeneSFN, HME1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSTRATIFIN, EPITHELIAL CELL MARKER PROTEIN 1
 
Molecule 2 - SYTHETIC OPTIMAL PHOSPHOPEPTIDE (MODE-1)
    ChainsC, D
    EngineeredYES
    Other DetailsSOLID PHASE SYNTHESIS OF OPTIMAL PHOSPHOPEPTIDE SEQUENCE AS DETERMINED FROM LIBRARY SCREEN
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)ABCD
Biological Unit 2 (2x)ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2SEP2Mod. Amino AcidPHOSPHOSERINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2SEP2Mod. Amino AcidPHOSPHOSERINE
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2SEP4Mod. Amino AcidPHOSPHOSERINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU B:31 , HIS B:106 , HOH B:279BINDING SITE FOR RESIDUE CA B 249

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Tyr C:7 -Pro C:8
2Tyr D:7 -Pro D:8

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_048095M155I1433S_HUMANPolymorphism11542705A/BM155I

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_048095M155I1433S_HUMANPolymorphism11542705A/BM155I

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_048095M155I1433S_HUMANPolymorphism11542705A/BM155I

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
11433_1PS00796 14-3-3 proteins signature 1.1433S_HUMAN41-51
 
  2A:41-51
B:41-51
21433_2PS00797 14-3-3 proteins signature 2.1433S_HUMAN213-232
 
  2A:213-231
B:213-231
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
11433_1PS00796 14-3-3 proteins signature 1.1433S_HUMAN41-51
 
  2A:41-51
B:41-51
21433_2PS00797 14-3-3 proteins signature 2.1433S_HUMAN213-232
 
  2A:213-231
B:213-231
Biological Unit 2 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
11433_1PS00796 14-3-3 proteins signature 1.1433S_HUMAN41-51
 
  4A:41-51
B:41-51
21433_2PS00797 14-3-3 proteins signature 2.1433S_HUMAN213-232
 
  4A:213-231
B:213-231

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003392761ENSE00001406083chr1:27189653-2719094712951433S_HUMAN1-2652652A:1-231 (gaps)
B:1-231 (gaps)
231
231

(-) 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:223
 aligned with 1433S_HUMAN | P31947 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:231
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230 
          1433S_HUMAN     1 MERASLIQKAKLAEQAERYEDMAAFMKGAVEKGEELSCEERNLLSVAYKNVVGGQRAAWRVLSSIEQKSNEEGSEEKGPEVREYREKVETELQGVCDTVLGLLDSHLIKEAGDAESRVFYLKMKGDYYRYLAEVATGDDKKRIIDSARSAYQEAMDISKKEMPPTNPIRLGLALNFSVFHYEIANSPEEAISLAKTTFDEAMADLHTLSEDSYKDSTLIMQLLRDNLTLWT 231
               SCOP domains d1ywta_ A: automated matches                                                                                                                                                                                                            SCOP domains
               CATH domains 1ywtA00 A:1-231  [code=1.20.190.20, no name defined]                                                                                                                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh--------hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------I---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------1433_1     -----------------------------------------------------------------------------------------------------------------------------------------------------------------1433_2              PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-231 (gaps) UniProt: 1-265 [INCOMPLETE]                                                                                                                                                                               Transcript 1
                 1ywt A   1 MERASLIQKAKLAEQAERYEDMAAFMKGAVEKGEELSCEERNLLSVAYKNVVGGQRAAWRVLSSIEQKSN--------PEVREYREKVETELQGVCDTVLGLLDSHLIKEAGDAESRVFYLKMKGDYYRYLAEVATGDDKKRIIDSARSAYQEAMDISKKEMPPTNPIRLGLALNFSVFHYEIANSPEEAISLAKTTFDEAMADLHTLSEDSYKDSTLIMQLLRDNLTLWT 231
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230 
                                                                                                70       79                                                                                                                                                        

Chain B from PDB  Type:PROTEIN  Length:222
 aligned with 1433S_HUMAN | P31947 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:231
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230 
          1433S_HUMAN     1 MERASLIQKAKLAEQAERYEDMAAFMKGAVEKGEELSCEERNLLSVAYKNVVGGQRAAWRVLSSIEQKSNEEGSEEKGPEVREYREKVETELQGVCDTVLGLLDSHLIKEAGDAESRVFYLKMKGDYYRYLAEVATGDDKKRIIDSARSAYQEAMDISKKEMPPTNPIRLGLALNFSVFHYEIANSPEEAISLAKTTFDEAMADLHTLSEDSYKDSTLIMQLLRDNLTLWT 231
               SCOP domains d1ywtb_ B: automated matches                                                                                                                                                                                                            SCOP domains
               CATH domains 1ywtB00 B:1-231  [code=1.20.190.20, no name defined]                                                                                                                                                                                    CATH domains
           Pfam domains (1) --14-3-3-1ywtB01 B:3-231                                                                                                                                                                                                                Pfam domains (1)
           Pfam domains (2) --14-3-3-1ywtB02 B:3-231                                                                                                                                                                                                                Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.---------hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------I---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------1433_1     -----------------------------------------------------------------------------------------------------------------------------------------------------------------1433_2              PROSITE
               Transcript 1 Exon 1.1  PDB: B:1-231 (gaps) UniProt: 1-265 [INCOMPLETE]                                                                                                                                                                               Transcript 1
                 1ywt B   1 MERASLIQKAKLAEQAERYEDMAAFMKGAVEKGEELSCEERNLLSVAYKNVVGGQRAAWRVLSSIEQKS---------PEVREYREKVETELQGVCDTVLGLLDSHLIKEAGDAESRVFYLKMKGDYYRYLAEVATGDDKKRIIDSARSAYQEAMDISKKEMPPTNPIRLGLALNFSVFHYEIANSPEEAISLAKTTFDEAMADLHTLSEDSYKDSTLIMQLLRDNLTLWT 231
                                    10        20        30        40        50        60        |-        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230 
                                                                                               69        79                                                                                                                                                        

Chain C from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 1ywt C   4 SHsYPA   9
                              |   
                              6-SEP

Chain D from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 1ywt D   1 MARSHsYPA   9
                                 |   
                                 6-SEP

   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  (1, 2)

Asymmetric Unit

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (34, 34)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (1433S_HUMAN | P31947)
molecular function
    GO:0051219    phosphoprotein binding    Interacting selectively and non-covalently with a phosphorylated protein.
    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:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
    GO:0008426    protein kinase C inhibitor activity    Stops, prevents or reduces the activity of protein kinase C, an enzyme which phosphorylates a protein.
    GO:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
biological process
    GO:0006977    DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest    A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage and resulting in the stopping or reduction in rate of the cell cycle.
    GO:0061436    establishment of skin barrier    Establishment of the epithelial barrier, the functional barrier in the skin that limits its permeability.
    GO:0008630    intrinsic apoptotic signaling pathway in response to DNA damage    A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced by the detection of DNA damage, and ends when the execution phase of apoptosis is triggered.
    GO:0031424    keratinization    The process in which the cytoplasm of the outermost cells of the vertebrate epidermis is replaced by keratin. Keratinization occurs in the stratum corneum, feathers, hair, claws, nails, hooves, and horns.
    GO:0003334    keratinocyte development    The process whose specific outcome is the progression of a keratinocyte over time, from its formation to the mature structure.
    GO:0030216    keratinocyte differentiation    The process in which a relatively unspecialized cell acquires specialized features of a keratinocyte.
    GO:0061024    membrane organization    A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins.
    GO:0043154    negative regulation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of a cysteine-type endopeptidase activity involved in the apoptotic process.
    GO:0010839    negative regulation of keratinocyte proliferation    Any process that decreases the rate, frequency or extent of keratinocyte proliferation. Keratinocyte proliferation is the multiplication or reproduction of keratinocytes, resulting in the expansion of a cell population.
    GO:0006469    negative regulation of protein kinase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity.
    GO:0071901    negative regulation of protein serine/threonine kinase activity    Any process that decreases the rate, frequency, or extent of protein serine/threonine kinase activity.
    GO:0030307    positive regulation of cell growth    Any process that activates or increases the frequency, rate, extent or direction of cell growth.
    GO:0045606    positive regulation of epidermal cell differentiation    Any process that activates or increases the frequency, rate or extent of epidermal cell differentiation.
    GO:0046827    positive regulation of protein export from nucleus    Any process that activates or increases the frequency, rate or extent of directed movement of proteins from the nucleus into the cytoplasm.
    GO:1900740    positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway    Any process that activates or increases the frequency, rate or extent of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway.
    GO:0051726    regulation of cell cycle    Any process that modulates the rate or extent of progression through the cell cycle.
    GO:0000079    regulation of cyclin-dependent protein serine/threonine kinase activity    Any process that modulates the frequency, rate or extent of cyclin-dependent protein serine/threonine kinase activity.
    GO:0010482    regulation of epidermal cell division    Any process that modulates the frequency, rate or extent of the physical partitioning and separation of an epidermal cell into daughter cells. An epidermal cell is any of the cells that make up the epidermis.
    GO:0001836    release of cytochrome c from mitochondria    The process that results in the movement of cytochrome c from the mitochondrial intermembrane space into the cytosol, which is part of the apoptotic signaling pathway and leads to caspase activation.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0043588    skin development    The process whose specific outcome is the progression of the skin over time, from its formation to the mature structure. The skin is the external membranous integument of an animal. In vertebrates the skin generally consists of two layers, an outer nonsensitive and nonvascular epidermis (cuticle or skarfskin) composed of cells which are constantly growing and multiplying in the deeper, and being thrown off in the superficial layers, as well as an inner vascular dermis (cutis, corium or true skin) composed mostly of connective tissue.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0030659    cytoplasmic vesicle membrane    The lipid bilayer surrounding a cytoplasmic vesicle.
    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:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        1433S_HUMAN | P319471yz5 3iqj 3iqu 3iqv 3lw1 3mhr 3o8i 3p1n 3p1o 3p1p 3p1q 3p1r 3p1s 3smk 3sml 3smm 3smn 3smo 3sp5 3spr 3t0l 3t0m 3u9x 3ux0 4dat 4dau 4dhm 4dhn 4dho 4dhp 4dhq 4dhr 4dhs 4dht 4dhu 4fl5 4fr3 4hqw 4hru 4iea 4jc3 4jdd 4qli 4y32 4y3b 4y5i 5btv 5hf3 5ltw 5lu1 5lu2 5my9 5myc

(-) Related Entries Specified in the PDB File

1qja 14-3-3 ZETA/PHOSPHOPEPTIDE COMPLEX (MODE 2)
1qjb 14-3-3 ZETA/PHOSPHOPEPTIDE COMPLEX (MODE 1)