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(-) Description

Title :  1.15 ANGSTROM CRYSTAL STRUCTURE OF THE MA3 DOMAIN OF PDCD4
 
Authors :  N. Laronde-Leblanc, A. Wlodawer
Date :  06 Nov 06  (Deposition) - 21 Nov 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.15
Chains :  Asym./Biol. Unit :  A
Keywords :  Pdcd4, Tumor Suppressor, Translation, Antitumor Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Laronde-Leblanc, A. N. Santhanam, A. R. Baker, A. Wlodawer, N. H. Colburn
Structural Basis For Inhibition Of Translation By The Tumor Suppressor Pdcd4.
Mol. Cell. Biol. V. 27 147 2007
PubMed-ID: 17060447  |  Reference-DOI: 10.1128/MCB.00867-06

(-) Compounds

Molecule 1 - PROGRAMMED CELL DEATH PROTEIN 4
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDEST14
    Expression System Strain: ROSETTA(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL MA3 DOMAIN, RESIDUES 322-450
    Gene: PDCD4, MA3, TIS
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: TOPOISOMERASE-INHIBITOR SUPPRESSED PROTEIN, PROTEIN MA-3

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO42Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:421 , TYR A:423 , SER A:424BINDING SITE FOR RESIDUE SO4 A 201
2AC2SOFTWAREHOH A:63 , HOH A:133 , HOH A:142 , HOH A:163 , HIS A:358 , GLN A:400 , ARG A:403BINDING SITE FOR RESIDUE SO4 A 202
3AC3SOFTWAREHOH A:68 , HOH A:120 , VAL A:328 , GLU A:337 , SER A:341 , ASP A:343 , GLU A:346 , PHE A:359 , HIS A:361 , GLU A:362 , ARG A:407BINDING SITE FOR RESIDUE GOL A 203

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MIPS51366 MI domain profile.PDCD4_MOUSE163-284
326-449		  1-
A:326-449

(-) Exons   (0, 0)

(no "Exon" information available for 2NSZ)

(-) Sequences/Alignments

Asymmetric/Biological 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:129
 aligned with PDCD4_MOUSE | Q61823 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:129
                                   331       341       351       361       371       381       391       401       411       421       431       441         
          PDCD4_MOUSE   322 QPVNHLVKEIDMLLKEYLLSGDISEAEHCLKELEVPHFHHELVYEAIVMVLESTGESAFKMILDLLKSLWKSSTITIDQMKRGYERIYNEIPDINLDVPHSYSVLERFVEECFQAGIISKQLRDLCPSR 450
               SCOP domains d2nsza1 A:322-450 Programmed cell death 4, PDCD4                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----MI  PDB: A:326-449 UniProt: 326-449                                                                                         - PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nsz A 322 QPVNHLVKEIDMLLKEYLLSGDISEAEHCLKELEVPHFHHELVYEAIVMVLESTGESAFKMILDLLKSLWKSSTITIDQMKRGYERIYNEIPDINLDVPHSYSVLERFVEECFQAGIISKQLRDLCPSR 450
                                   331       341       351       361       371       381       391       401       411       421       431       441
   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)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PDCD4_MOUSE | Q61823)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0007569    cell aging    An aging process that has as participant a cell after a cell has stopped dividing. Cell aging may occur when a cell has temporarily stopped dividing through cell cycle arrest (GO:0007050) or when a cell has permanently stopped dividing, in which case it is undergoing cellular senescence (GO:0090398). May precede cell death (GO:0008219) and succeed cell maturation (GO:0048469).
    GO:0043508    negative regulation of JUN kinase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of JUN kinase activity.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:1904761    negative regulation of myofibroblast differentiation    Any process that stops, prevents or reduces the frequency, rate or extent of myofibroblast differentiation.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0034393    positive regulation of smooth muscle cell apoptotic process    Any process that activates or increases the frequency, rate, or extent of smooth muscle cell apoptotic process.
    GO:0051246    regulation of protein metabolic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a protein.
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:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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
        PDCD4_MOUSE | Q61823: 2hm8 2iol 2ion 2ios 2kzt 3eiq

(-) Related Entries Specified in the PDB File

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