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(-) Description

Title :  CRYSTAL STRUCTURE OF THE C-TERMINAL PH DOMAIN OF PLECKSTRIN IN COMPLEX WITH D-MYO-INS(1,2,3,4,5)P5
 
Authors :  S. G. Jackson, R. J. Haslam, M. S. Junop
Date :  24 Aug 06  (Deposition) - 07 Aug 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Ph Domain, Protein-Inositol Phosphate Complex, Lipid Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. G. Jackson, Y. Zhang, R. J. Haslam, M. S. Junop
Structural Analysis Of The Carboxy Terminal Ph Domain Of Pleckstrin Bound To D-Myo-Inositol 1, 2, 3, 5, 6-Pentakisphosphate.
Bmc Struct. Biol. V. 7 80 2007
PubMed-ID: 18034889  |  Reference-DOI: 10.1186/1472-6807-7-80
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PLECKSTRIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PDEST17
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN, PH2 DOMAIN
    Gene: PLEK, P47
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PLATELET P47 PROTEIN

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1IP53Ligand/Ion(1R,2S,3R,4S,5S,6R)-6-HYDROXYCYCLOHEXANE-1,2,3,4,5-PENTAYL PENTAKIS[DIHYDROGEN (PHOSPHATE)]
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1IP51Ligand/Ion(1R,2S,3R,4S,5S,6R)-6-HYDROXYCYCLOHEXANE-1,2,3,4,5-PENTAYL PENTAKIS[DIHYDROGEN (PHOSPHATE)]
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1IP51Ligand/Ion(1R,2S,3R,4S,5S,6R)-6-HYDROXYCYCLOHEXANE-1,2,3,4,5-PENTAYL PENTAKIS[DIHYDROGEN (PHOSPHATE)]
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1IP51Ligand/Ion(1R,2S,3R,4S,5S,6R)-6-HYDROXYCYCLOHEXANE-1,2,3,4,5-PENTAYL PENTAKIS[DIHYDROGEN (PHOSPHATE)]

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:253 , GLY A:255 , HIS A:256 , ARG A:257 , ARG A:258 , ARG A:264 , TYR A:277 , HOH A:579 , HOH A:582 , HOH A:583 , HOH A:589 , HOH A:592 , HOH A:607 , HOH A:625 , HOH A:628 , HOH A:631 , ARG C:257BINDING SITE FOR RESIDUE IP5 A 550
2AC2SOFTWARELYS A:333 , LYS B:253 , GLY B:255 , HIS B:256 , ARG B:257 , ARG B:258 , ARG B:264 , TYR B:277 , HOH B:569 , HOH B:571 , HOH B:587 , HOH B:602 , HOH B:603 , HOH B:605 , HOH B:630 , HOH B:645BINDING SITE FOR RESIDUE IP5 B 551
3AC3SOFTWAREARG A:257 , LYS C:253 , GLY C:255 , HIS C:256 , ARG C:257 , ARG C:258 , ARG C:264 , TYR C:277 , LYS C:333 , HOH C:564 , HOH C:578 , HOH C:593 , HOH C:594 , HOH C:595 , HOH C:608 , HOH C:619 , HOH C:623 , HOH C:627 , HOH C:632 , HOH C:642BINDING SITE FOR RESIDUE IP5 C 552

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2I5C)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Asp A:271 -Pro A:272
2Asp B:271 -Pro B:272
3Asp C:271 -Pro C:272

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 3)

Asymmetric Unit (1, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_027799R340KPLEK_HUMANPolymorphism1063479A/B/CK340K
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_027799R340KPLEK_HUMANPolymorphism1063479AK340K
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_027799R340KPLEK_HUMANPolymorphism1063479BK340K
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_027799R340KPLEK_HUMANPolymorphism1063479CK340K
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PH_DOMAINPS50003 PH domain profile.PLEK_HUMAN4-101
244-347
 
 		  3-
A:244-347
B:244-347
C:244-347
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PH_DOMAINPS50003 PH domain profile.PLEK_HUMAN4-101
244-347
 
 		  1-
A:244-347
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PH_DOMAINPS50003 PH domain profile.PLEK_HUMAN4-101
244-347
 
 		  1-
-
B:244-347
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PH_DOMAINPS50003 PH domain profile.PLEK_HUMAN4-101
244-347
 
 		  1-
-
-
C:244-347

(-) Exons   (4, 12)

Asymmetric Unit (4, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002343131aENSE00001911788chr2:68592305-68592525221PLEK_HUMAN1-14140--
1.2ENST000002343132ENSE00000963053chr2:68607460-68607615156PLEK_HUMAN15-66520--
1.3ENST000002343133ENSE00000758794chr2:68607855-68608036182PLEK_HUMAN67-127610--
1.4ENST000002343134ENSE00000758796chr2:68609674-6860976592PLEK_HUMAN127-158320--
1.5ENST000002343135ENSE00000758798chr2:68613634-68613818185PLEK_HUMAN158-219620--
1.6bENST000002343136bENSE00000758800chr2:68615519-68615623105PLEK_HUMAN220-254353A:244-254
B:244-254
C:244-254		11
11
11
1.7ENST000002343137ENSE00000758802chr2:68620294-6862037784PLEK_HUMAN255-282283A:255-282
B:255-282
C:255-282		28
28
28
1.8aENST000002343138aENSE00000758804chr2:68621239-6862130870PLEK_HUMAN283-306243A:283-300
B:283-300
C:283-300		18
18
18
1.9bENST000002343139bENSE00001163794chr2:68622812-686245851774PLEK_HUMAN306-350453A:311-347
B:311-347
C:311-347		37
37
37

(-) 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:94
 aligned with PLEK_HUMAN | P08567 from UniProtKB/Swiss-Prot  Length:350

    Alignment length:104
                                   253       263       273       283       293       303       313       323       333       343    
           PLEK_HUMAN   244 VIIKQGCLLKQGHRRKNWKVRKFILREDPAYLHYYDPAGAEDPLGAIHLRGCVVTSVESNSNGRKSEEENLFEIITADEVHYFLQAATPKERTEWIRAIQMASR 347
               SCOP domains d2i5ca_ A: Pleckstrin                                                                                    SCOP domains
               CATH domains 2i5cA00 A:244-347 Pleckstrin-homology domain (PH domain)/          Phosphotyrosine-binding domain (PTB)  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee......eeeeeeeee....eeeee.........eeee....eeee.----------...eeeee.....eeeee..hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------K------- SAPs(SNPs)
                    PROSITE PH_DOMAIN  PDB: A:244-347 UniProt: 244-347                                                               PROSITE
           Transcript 1 (1) Exon 1.6b  Exon 1.7  PDB: A:255-282    Exon 1.8a  PDB: A:283-30----------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------Exon 1.9b  PDB: A:311-347 UniProt: 306-350 Transcript 1 (2)
                 2i5c A 244 VIIKQGCLLKQGHRRKNWKVRKFILREDPAYLHYYDPAGAEDPLGAIHLRGCVVTSV----------EENLFEIITADEVHYFLQAATPKERTEWIKAIQMASR 347
                                   253       263       273       283       293      |  -       313       323       333       343    
                                                                                  300        311                                    


Chain B from PDB  Type:PROTEIN  Length:94
 aligned with PLEK_HUMAN | P08567 from UniProtKB/Swiss-Prot  Length:350

    Alignment length:104
                                   253       263       273       283       293       303       313       323       333       343    
           PLEK_HUMAN   244 VIIKQGCLLKQGHRRKNWKVRKFILREDPAYLHYYDPAGAEDPLGAIHLRGCVVTSVESNSNGRKSEEENLFEIITADEVHYFLQAATPKERTEWIRAIQMASR 347
               SCOP domains d2i5cb_ B: Pleckstrin                                                                                    SCOP domains
               CATH domains 2i5cB00 B:244-347 Pleckstrin-homology domain (PH domain)/          Phosphotyrosine-binding domain (PTB)  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee......eeeeeeeee....eeeee.........eeee....eeee.----------...eeeee.....eeeee..hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------K------- SAPs(SNPs)
                    PROSITE PH_DOMAIN  PDB: B:244-347 UniProt: 244-347                                                               PROSITE
           Transcript 1 (1) Exon 1.6b  Exon 1.7  PDB: B:255-282    Exon 1.8a  PDB: B:283-30----------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------Exon 1.9b  PDB: B:311-347 UniProt: 306-350 Transcript 1 (2)
                 2i5c B 244 VIIKQGCLLKQGHRRKNWKVRKFILREDPAYLHYYDPAGAEDPLGAIHLRGCVVTSV----------EENLFEIITADEVHYFLQAATPKERTEWIKAIQMASR 347
                                   253       263       273       283       293      |  -       313       323       333       343    
                                                                                  300        311                                    


Chain C from PDB  Type:PROTEIN  Length:94
 aligned with PLEK_HUMAN | P08567 from UniProtKB/Swiss-Prot  Length:350

    Alignment length:104
                                   253       263       273       283       293       303       313       323       333       343    
           PLEK_HUMAN   244 VIIKQGCLLKQGHRRKNWKVRKFILREDPAYLHYYDPAGAEDPLGAIHLRGCVVTSVESNSNGRKSEEENLFEIITADEVHYFLQAATPKERTEWIRAIQMASR 347
               SCOP domains d2i5cc_ C: Pleckstrin                                                                                    SCOP domains
               CATH domains 2i5cC00 C:244-347 Pleckstrin-homology domain (PH domain)/          Phosphotyrosine-binding domain (PTB)  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee......eeeeeeeee....eeeee.........eeee....eeee.----------...eeeee.....eeeee..hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------K------- SAPs(SNPs)
                    PROSITE PH_DOMAIN  PDB: C:244-347 UniProt: 244-347                                                               PROSITE
           Transcript 1 (1) Exon 1.6b  Exon 1.7  PDB: C:255-282    Exon 1.8a  PDB: C:283-30----------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------Exon 1.9b  PDB: C:311-347 UniProt: 306-350 Transcript 1 (2)
                 2i5c C 244 VIIKQGCLLKQGHRRKNWKVRKFILREDPAYLHYYDPAGAEDPLGAIHLRGCVVTSV----------EENLFEIITADEVHYFLQAATPKERTEWIKAIQMASR 347
                                   253       263       273       283       293      |  -       313       323       333       343    
                                                                                  300        311
   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, 3)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 3)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2I5C)

(-) Gene Ontology  (33, 33)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (PLEK_HUMAN | P08567)
molecular function
    GO:0043325    phosphatidylinositol-3,4-bisphosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-3,4-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3' and 4' positions.
    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:0005080    protein kinase C binding    Interacting selectively and non-covalently with protein kinase C.
biological process
    GO:0031532    actin cytoskeleton reorganization    A process that is carried out at the cellular level which results in dynamic structural changes to the arrangement of constituent parts of cytoskeletal structures comprising actin filaments and their associated proteins.
    GO:0030030    cell projection organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0030866    cortical actin cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of actin-based cytoskeletal structures in the cell cortex, i.e. just beneath the plasma membrane.
    GO:0002244    hematopoietic progenitor cell differentiation    The process in which precursor cell type acquires the specialized features of a hematopoietic progenitor cell, a class of cell types including myeloid progenitor cells and lymphoid progenitor cells.
    GO:0007229    integrin-mediated signaling pathway    A series of molecular signals initiated by the binding of extracellular ligand to an integrin on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    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:0045744    negative regulation of G-protein coupled receptor protein signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of G-protein coupled receptor protein signaling pathway activity.
    GO:0050849    negative regulation of calcium-mediated signaling    Any process that stops, prevents, or reduces the frequency, rate or extent of calcium-mediated signaling.
    GO:0010920    negative regulation of inositol phosphate biosynthetic process    Any process that decreases the rate, frequency or extent of inositol phosphate biosynthesis. Inositol phosphate biosynthetic processes are the chemical reactions and pathways resulting in the formation of an inositol phosphate, 1,2,3,4,5,6-cyclohexanehexol, with one or more phosphate groups attached.
    GO:0046488    phosphatidylinositol metabolic process    The chemical reactions and pathways involving phosphatidylinositol, any glycophospholipid in which a sn-glycerol 3-phosphate residue is esterified to the 1-hydroxyl group of 1D-myo-inositol.
    GO:0030845    phospholipase C-inhibiting G-protein coupled receptor signaling pathway    A G-protein coupled receptor signaling pathway which proceeds with inhibition of phospholipase C (PLC) activity and a subsequent decrease in the levels of cellular inositol trisphosphate (IP3) and diacylglycerol (DAG).
    GO:0070527    platelet aggregation    The adhesion of one platelet to one or more other platelets via adhesion molecules.
    GO:0002576    platelet degranulation    The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet.
    GO:0032233    positive regulation of actin filament bundle assembly    Any process that activates or increases the frequency, rate or extent of the assembly of actin filament bundles.
    GO:0030836    positive regulation of actin filament depolymerization    Any process that activates or increases the frequency, rate or extent of actin depolymerization.
    GO:0010925    positive regulation of inositol-polyphosphate 5-phosphatase activity    Any process that increases the rate or frequency of inositol-polyphosphate 5-phosphatase activity, the catalysis of the reactions: D-myo-inositol 1,4,5-trisphosphate + H2O = myo-inositol 1,4-bisphosphate + phosphate, and 1D-myo-inositol 1,3,4,5-tetrakisphosphate + H2O = 1D-myo-inositol 1,3,4-trisphosphate + phosphate.
    GO:0033625    positive regulation of integrin activation    Any process that activates or increases the frequency, rate, or extent of integrin activation.
    GO:0010572    positive regulation of platelet activation    Any process that increases the rate or frequency of platelet activation. Platelet activation is a series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue.
    GO:0070528    protein kinase C signaling    A series of reactions, mediated by the intracellular serine/threonine kinase protein kinase C, which occurs as a result of a single trigger reaction or compound.
    GO:0070560    protein secretion by platelet    The regulated release of proteins by a platelet or group of platelets.
    GO:0060305    regulation of cell diameter    Any process that modulates the diameter of a cell, the length of a line segment that crosses through the center of a circular section through a cell.
    GO:0031529    ruffle organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a ruffle, a projection at the leading edge of a crawling cell.
    GO:0070493    thrombin-activated receptor signaling pathway    The series of molecular signals generated as a consequence of a thrombin-activated receptor binding to one of its physiological ligands.
    GO:0006904    vesicle docking involved in exocytosis    The initial attachment of a vesicle membrane to a target membrane, mediated by proteins protruding from the membrane of the vesicle and the target membrane, that contributes to exocytosis.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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: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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0032587    ruffle membrane    The portion of the plasma membrane surrounding a ruffle.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PLEK_HUMAN | P08567: 1pls 1w4m 1x05 1xx0 1zm0 2cso 2i5f

(-) Related Entries Specified in the PDB File

1zm0 CARBOXY TERMINAL PH DOMAIN OF PLECKSTRIN IN THE UNBOUND FORM.