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(-) Description

Title :  HUMAN PATL1 C-TERMINAL DOMAIN
 
Authors :  F. Tritschler, O. Weichenrieder
Date :  17 May 10  (Deposition) - 16 Jun 10  (Release) - 18 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Mrna Decapping, P-Bodies, Rna Binding Protein (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 Line: HELA
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MODIFIED PRSFDUET-1
    Expression System Strain: K-12
    Expression System Taxid: 83333
    Fragment: C-TERMINAL DOMAIN, RESIDUES 517-767
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PAT1-LIKE PROTEIN 1, PATL1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 32)

Asymmetric Unit (1, 32)
No.NameCountTypeFull Name
1MSE32Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 4 (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2XEQ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2XEQ)

(-) 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:239
 aligned with PATL1_HUMAN | Q86TB9 from UniProtKB/Swiss-Prot  Length:770

    Alignment length:274
                                   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 NPRKMIDAVVTSRSEDDETKEKQVRDKRRKTLVIIEKTYSLLLDVEDYERRYLLSLEEERPALMDDRKHKICSMYDNLRGKLPGQERPSDDHFVQIMCIRKGKRMVARILPFLSTEQAADILMTTARNLPFLIKKDAQDEVLPCLLSPFSLLLYHLPSVSITSLLRQLMNLPQSAATPALSNPHLTAVLQNKFGLSLLLILLSRGEDLQSSDPATESTQNNQWTEVMFMATRELLRIPQAALAKPISIPTNLVSLFSRYVDRQKLNLLETKLQL 765
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .h-----------------------hhhhhhhhhhhhhhhhhhhh..hhhh.......hhhhhhhhhhhhhhhhhhhhh..----......hhhhh...hhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhh.........hhhhhhh.....hhhhhhhhhhh..............hhhhhhh..hhhhhhhhhhhhhhhhhhh..--------..hhhhhhhhhhhh.................hhhhh.....hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xeq A 515 DP-----------------------DKRRKTLVIIEKTYSLLLDVEDYERRYLLSLEEERPALmDDRKHKICSmYDNLRGK----ERPSDDHFVQImCIRKGKRmVARILPFLSTEQAADILmTTARNLPFLIKKDAQDEVLPCLLSPFSLLLYHLPSVSITSLLRQLmNLPQSAATPALSNPHLTAVLQNKFGLSLLLILLSRGEDLQSSD--------NQWTEVmFmATRELLRIPQAALAKPISIPTNLVSLFSRYVDRQKLNLLETKLQL 765
                             |       -         -     | 521       531       541       551   |   561   |   571|    | 581      |591    |  601       611  |    621       631       641       651       661       671       681       691       701 |       -|     |721       731       741       751       761    
                             |                     517                                   555-MSE   565-MSE572  577        588-MSE 596-MSE           614-MSE                                       660-MSE                                    703      712     | |                                             
                           516                                                                                                                                                                                                                              718-MSE                                           
                                                                                                                                                                                                                                                              720-MSE                                         


Chain B from PDB  Type:PROTEIN  Length:238
 aligned with PATL1_HUMAN | Q86TB9 from UniProtKB/Swiss-Prot  Length:770

    Alignment length:274
                                   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 NPRKMIDAVVTSRSEDDETKEKQVRDKRRKTLVIIEKTYSLLLDVEDYERRYLLSLEEERPALMDDRKHKICSMYDNLRGKLPGQERPSDDHFVQIMCIRKGKRMVARILPFLSTEQAADILMTTARNLPFLIKKDAQDEVLPCLLSPFSLLLYHLPSVSITSLLRQLMNLPQSAATPALSNPHLTAVLQNKFGLSLLLILLSRGEDLQSSDPATESTQNNQWTEVMFMATRELLRIPQAALAKPISIPTNLVSLFSRYVDRQKLNLLETKLQL 765
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..-----------------------.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...-----...hhhhhhh...hhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhh..........hhhhhhh.....hhhhhhhhhhh..............hhhhhhh..hhhhhhhhhhhhhhhhhhh.--------.hhhhhhhhhhhhhhhh...............hhhhhhhh..hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xeq B 515 DP-----------------------DKRRKTLVIIEKTYSLLLDVEDYERRYLLSLEEERPALmDDRKHKICSmYDNLRGK-----RPSDDHFVQImCIRKGKRmVARILPFLSTEQAADILmTTARNLPFLIKKDAQDEVLPCLLSPFSLLLYHLPSVSITSLLRQLmNLPQSAATPALSNPHLTAVLQNKFGLSLLLILLSRGEDLQSS--------NNQWTEVmFmATRELLRIPQAALAKPISIPTNLVSLFSRYVDRQKLNLLETKLQL 765
                             |       -         -     | 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    
                           516                     517                                   555-MSE   565-MSE572   578       588-MSE 596-MSE           614-MSE                                       660-MSE                                   702      711      | |                                             
                                                                                                                                                                                                                                                            718-MSE                                           
                                                                                                                                                                                                                                                              720-MSE                                         


Chain C from PDB  Type:PROTEIN  Length:241
 aligned with PATL1_HUMAN | Q86TB9 from UniProtKB/Swiss-Prot  Length:770

    Alignment length:274
                                   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 NPRKMIDAVVTSRSEDDETKEKQVRDKRRKTLVIIEKTYSLLLDVEDYERRYLLSLEEERPALMDDRKHKICSMYDNLRGKLPGQERPSDDHFVQIMCIRKGKRMVARILPFLSTEQAADILMTTARNLPFLIKKDAQDEVLPCLLSPFSLLLYHLPSVSITSLLRQLMNLPQSAATPALSNPHLTAVLQNKFGLSLLLILLSRGEDLQSSDPATESTQNNQWTEVMFMATRELLRIPQAALAKPISIPTNLVSLFSRYVDRQKLNLLETKLQL 765
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .h-----------------------hhhhhhhhhhhhhhhhhhhh..hhhhhhh.....hhhhhhhhhhhhhhhhhhhh...----....hhhhhh...hhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhh...........hhhhhhh.....hhhhhhhhhhh..............hhhhhhhh.hhhhhhhhhhhhhhhhhhh...------.hhhhhhhhhhhhhhhh...............hhhhhh....hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xeq C 515 DP-----------------------DKRRKTLVIIEKTYSLLLDVEDYERRYLLSLEEERPALmDDRKHKICSmYDNLRGKL----RPSDDHFVQImCIRKGKRmVARILPFLSTEQAADILmTTARNLPFLIKKDAQDEVLPCLLSPFSLLLYHLPSVSITSLLRQLmNLPQSAATPALSNPHLTAVLQNKFGLSLLLILLSRGEDLQSSDP------NNQWTEVmFmATRELLRIPQAALAKPISIPTNLVSLFSRYVDRQKLNLLETKLQL 765
                             |       -         -     | 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    
                           516                     517                                   555-MSE   565-MSE 573  578       588-MSE 596-MSE           614-MSE                                       660-MSE                                     704    711      | |                                             
                                                                                                                                                                                                                                                            718-MSE                                           
                                                                                                                                                                                                                                                              720-MSE                                         


Chain D from PDB  Type:PROTEIN  Length:235
 aligned with PATL1_HUMAN | Q86TB9 from UniProtKB/Swiss-Prot  Length:770

    Alignment length:250
                                   525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765
          PATL1_HUMAN   516 RDKRRKTLVIIEKTYSLLLDVEDYERRYLLSLEEERPALMDDRKHKICSMYDNLRGKLPGQERPSDDHFVQIMCIRKGKRMVARILPFLSTEQAADILMTTARNLPFLIKKDAQDEVLPCLLSPFSLLLYHLPSVSITSLLRQLMNLPQSAATPALSNPHLTAVLQNKFGLSLLLILLSRGEDLQSSDPATESTQNNQWTEVMFMATRELLRIPQAALAKPISIPTNLVSLFSRYVDRQKLNLLETKLQL 765
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -PAT1-2xeqD01 D:517-728                                                                                                                                                                                              ------------------------------------- Pfam domains (1)
           Pfam domains (2) -PAT1-2xeqD02 D:517-728                                                                                                                                                                                              ------------------------------------- Pfam domains (2)
           Pfam domains (3) -PAT1-2xeqD03 D:517-728                                                                                                                                                                                              ------------------------------------- Pfam domains (3)
           Pfam domains (4) -PAT1-2xeqD04 D:517-728                                                                                                                                                                                              ------------------------------------- Pfam domains (4)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh..hhhhh.......hhhhhhhhhhhhhhhhhhh............hhhhhh...hhhhhhhh.......hhhhhhhhhhhhh.hhhhhh...........hhhhhhh.....hhhhhhhhhhhh..--------...hhhhhhh..hhhhhhhhhhhhhhhhhhhh.-------...hhhhhhhhhhhhhh................hhhh.....hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xeq D 516 PDKRRKTLVIIEKTYSLLLDVEDYERRYLLSLEEERPALmDDRKHKICSmYDNLRGKLPGQERPSDDHFVQImCIRKGKRmVARILPFLSTEQAADILmTTARNLPFLIKKDAQDEVLPCLLSPFSLLLYHLPSVSITSLLRQLmNL--------LSNPHLTAVLQNKFGLSLLLILLSRGEDLQSSD-------NNQWTEVmFmATRELLRIPQAALAKPISIPTNLVSLFSRYVDRQKLNLLETKLQL 765
                                   525       535       545       555       565       575       585  |    595|      605       615       625       635       645       655    | |  -     | 675       685       695       | -     | 715  | |  725       735       745       755       765
                                                                 555-MSE   565-MSE                588-MSE 596-MSE           614-MSE                                       660-MSE    671                             703     711      | |                                             
                                                                                                                                                                            662                                                     718-MSE                                           
                                                                                                                                                                                                                                      720-MSE
   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 2XEQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: PAT1] (3)
(-)
Family: PAT1 (3)
(-)
Homo sapiens (Human) (3)
1aPAT1-2xeqD01D:517-728
1bPAT1-2xeqD02D:517-728
1cPAT1-2xeqD03D:517-728
1dPAT1-2xeqD04D:517-728

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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 | Q86TB9: 2xer 2xes

(-) Related Entries Specified in the PDB File

2xer HUMAN PATL1 C-TERMINAL DOMAIN (LOOP VARIANT WITH SULFATES)
2xes HUMAN PATL1 C-TERMINAL DOMAIN (LOOP VARIANT)