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(-) Description

Title :  HUMAN PATL1 C-TERMINAL DOMAIN (LOOP VARIANT WITH SULFATES)
 
Authors :  F. Tritschler, O. Weichenrieder
Date :  17 May 10  (Deposition) - 16 Jun 10  (Release) - 18 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.95
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Rna Binding Protein, Mrna Decapping, P-Bodies (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. E. Braun, F. Tritschler, G. Haas, C. Igreja, V. Truffault, O. Weichenrieder, E. Izaurralde
The C-Terminal Alpha-Alpha Superhelix Of Pat Is Required For Mrna Decapping In Metazoa.
Embo J. V. 29 2368 2010
PubMed-ID: 20543818  |  Reference-DOI: 10.1038/EMBOJ.2010.124

(-) Compounds

Molecule 1 - PAT1 HOMOLOG 1
    Cell LineHELA
    ChainsA, B, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidMODIFIED PRSFDUET-1
    Expression System StrainK-12
    Expression System Taxid83333
    FragmentC-TERMINAL DOMAIN, RESIDUES 517-767
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPAT1-LIKE PROTEIN 1, PATL1

 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, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 3 (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:592 , ARG C:542 , ARG C:551 , MET C:555BINDING SITE FOR RESIDUE SO4 C1765
2AC2SOFTWAREARG C:591 , LYS C:592 , ARG C:595BINDING SITE FOR RESIDUE SO4 C1766
3AC3SOFTWAREARG A:591 , ARG A:595 , ARG C:542 , ARG C:551 , HOH C:2017BINDING SITE FOR RESIDUE SO4 C1767
4AC4SOFTWAREARG B:591 , LYS B:592 , ARG B:595BINDING SITE FOR RESIDUE SO4 B1767

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu A:662 -Pro A:663

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2XER)

(-) Exons   (0, 0)

(no "Exon" information available for 2XER)

(-) 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:232
 aligned with PATL1_HUMAN | Q86TB9 from UniProtKB/Swiss-Prot  Length:770

    Alignment length:250
                                   526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766
          PATL1_HUMAN   517 DKRRKTLVIIEKTYSLLLDVEDYERRYLLSLEEERPALMDDRKHKICSMYDNLRGKLPGQERPSDDHFVQIMCIRKGKRMVARILPFLSTEQAADILMTTARNLPFLIKKDAQDEVLPCLLSPFSLLLYHLPSVSITSLLRQLMNLPQSAATPALSNPHLTAVLQNKFGLSLLLILLSRGEDLQSSDPATESTQNNQWTEVMFMATRELLRIPQAALAKPISIPTNLVSLFSRYVDRQKLNLLETKLQLV 766
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhh...-----....hhhhhh...hhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhh...........hhhhhhh.....hhhhhhhhhhh......--------...hhhh..hhhhhhhhhhhhhhhhhhh..-----.hhhhhhhhhhhhhhhhhh...............hhhhh.....hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xer A 517 DKRRKTLVIIEKTYSLLLDVEDYERRYLLSLEEERPALMDDRKHKICSMYDNLRGK-----RPSDDHFVQIMCIRKGKRMVARILPFLSTEQAADILMTTARNLPFLIKKDAQDEVLPCLLSPFSLLLYHLPSVSITSLLRQLMNLPGS--------PHLTAVLQNKFGLSLLLILLSRGEDLQSSD-----TQNNQWTEVMFMATRELLRIPQAALAKPISIPTNLVSLFSRYVDRQKLNLLETKLQLV 766
                                   526       536       546       556       566     |   - |     586       596       606       616       626       636       646       656        |-       676       686       696      |  -  |    716       726       736       746       756       766
                                                                                 572   578                                                                                    665      674                          703   709                                                         

Chain B from PDB  Type:PROTEIN  Length:221
 aligned with PATL1_HUMAN | Q86TB9 from UniProtKB/Swiss-Prot  Length:770

    Alignment length:250
                                   526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766
          PATL1_HUMAN   517 DKRRKTLVIIEKTYSLLLDVEDYERRYLLSLEEERPALMDDRKHKICSMYDNLRGKLPGQERPSDDHFVQIMCIRKGKRMVARILPFLSTEQAADILMTTARNLPFLIKKDAQDEVLPCLLSPFSLLLYHLPSVSITSLLRQLMNLPQSAATPALSNPHLTAVLQNKFGLSLLLILLSRGEDLQSSDPATESTQNNQWTEVMFMATRELLRIPQAALAKPISIPTNLVSLFSRYVDRQKLNLLETKLQLV 766
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhh....-----....hhhhhhhhhhhh..------...hhhhhhh...hhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhh...........hhhhhhhh....hhhhhhhhhhhh.....--------hhhhhhh..hhhhhhhhhhhh......----------.hhhhhhhhhhhhhhhh..........eee..hhhhhhhh..hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xer B 517 DKRRKTLVIIEKTYSLLLDVEDYERRYLLSLE-----LMDDRKHKICSMYDNLRG------RPSDDHFVQIMCIRKGKRMVARILPFLSTEQAADILMTTARNLPFLIKKDAQDEVLPCLLSPFSLLLYHLPSVSITSLLRQLMNLPGS--------PHLTAVLQNKFGLSLLLILLSRGEDLQ----------NNQWTEVMFMATRELLRIPQAALAKPISIPTNLVSLFSRYVDRQKLNLLETKLQLV 766
                                   526       536       546 |     556       566    |    - |     586       596       606       616       626       636       646       656        |-       676       686       696   |     -    |  716       726       736       746       756       766
                                                         548   554              571    578                                                                                    665      674                       700        711                                                       

Chain C from PDB  Type:PROTEIN  Length:229
 aligned with PATL1_HUMAN | Q86TB9 from UniProtKB/Swiss-Prot  Length:770

    Alignment length:273
                                   501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761   
          PATL1_HUMAN   492 NPRKMIDAVVTSRSEDDETKEKQVRDKRRKTLVIIEKTYSLLLDVEDYERRYLLSLEEERPALMDDRKHKICSMYDNLRGKLPGQERPSDDHFVQIMCIRKGKRMVARILPFLSTEQAADILMTTARNLPFLIKKDAQDEVLPCLLSPFSLLLYHLPSVSITSLLRQLMNLPQSAATPALSNPHLTAVLQNKFGLSLLLILLSRGEDLQSSDPATESTQNNQWTEVMFMATRELLRIPQAALAKPISIPTNLVSLFSRYVDRQKLNLLETKLQ 764
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --                       PAT1-2xerC01 C:517-728                                                                                                                                                                                              ------------------------------------ Pfam domains (1)
           Pfam domains (2) --                       PAT1-2xerC02 C:517-728                                                                                                                                                                                              ------------------------------------ Pfam domains (2)
           Pfam domains (3) --                       PAT1-2xerC03 C:517-728                                                                                                                                                                                              ------------------------------------ Pfam domains (3)
         Sec.struct. author .h-----------------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee.hhhhhhhhhhhh....----...hhhhhhh...hhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhh...........hhhhhhhhh...hhhhhhhhhhh......--------...hhhh..hhhhhhhhhhhhhhhh..---------.hhhhhhhhhhhhhhhhh...............hhhh......hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xer C 515 DP-----------------------DKRRKTLVIIEKTYSLLLDVEDYERRYLLSLEEERPALMDDRKHKICSMYDNLRGKL----RPSDDHFVQIMCIRKGKRMVARILPFLSTEQAADILMTTARNLPFLIKKDAQDEVLPCLLSPFSLLLYHLPSVSITSLLRQLMNLPGS--------PHLTAVLQNKFGLSLLLILLSRGEDLQ---------QNNQWTEVMFMATRELLRIPQAALAKPISIPTNLVSLFSRYVDRQKLNLLETKLQ 764
                             |       -         -     | 521       531       541       551       561       571 |    |581       591       601       611       621       631       641       651       661   |     -  |    681       691        |-       711       721       731       741       751       761   
                           516                     517                                                     573  578                                                                                    665      674                       700       710                                                      

   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 2XER)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Family: PAT1 (3)
1aPAT1-2xerC01C:517-728
1bPAT1-2xerC02C:517-728
1cPAT1-2xerC03C:517-728

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (PATL1_HUMAN | Q86TB9)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0034046    poly(G) binding    Interacting selectively and non-covalently with a sequence of guanine residues in an RNA molecule.
    GO:0008266    poly(U) RNA binding    Interacting selectively and non-covalently with a sequence of uracil residues in an RNA molecule.
    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:0033962    cytoplasmic mRNA processing body assembly    The aggregation, arrangement and bonding together of proteins and RNA molecules to form a cytoplasmic mRNA processing body.
    GO:0000290    deadenylation-dependent decapping of nuclear-transcribed mRNA    Cleavage of the 5'-cap of a nuclear mRNA triggered by shortening of the poly(A) tail to below a minimum functional length.
    GO:0043928    exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay    The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear-transcribed mRNA that occurs when the ends are not protected by the 3'-poly(A) tail.
cellular component
    GO:0030014    CCR4-NOT complex    The evolutionarily conserved CCR4-NOT complex is involved in several aspects of mRNA metabolism, including repression and activation of mRNA initiation, control of mRNA elongation, and the deadenylation and subsequent degradation of mRNA. In Saccharomyces the CCR4-NOT complex comprises a core complex of 9 proteins (Ccr4p, Caf1p, Caf40p, Caf130p, Not1p, Not2p, Not3p, Not4p, and Not5p), Caf4p, Caf16p, and several less well characterized proteins.
    GO:0000932    P-body    A focus in the cytoplasm where mRNAs may become inactivated by decapping or some other mechanism. Protein and RNA localized to these foci are involved in mRNA degradation, nonsense-mediated mRNA decay (NMD), translational repression, and RNA-mediated gene silencing.
    GO:0016605    PML body    A class of nuclear body; they react against SP100 auto-antibodies (PML, promyelocytic leukemia); cells typically contain 10-30 PML bodies per nucleus; alterations in the localization of PML bodies occurs after viral infection.
    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: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:0016607    nuclear speck    A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
    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
        PATL1_HUMAN | Q86TB92xeq 2xes

(-) Related Entries Specified in the PDB File

2xeq HUMAN PATL1 C-TERMINAL DOMAIN
2xes HUMAN PATL1 C-TERMINAL DOMAIN (LOOP VARIANT)