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(-) Description

Title :  STRUCTURE OF PIN DOMAIN OF HUMAN SMG6
 
Authors :  F. Glavan, I. Behm-Ansmant, E. Izaurralde, E. Conti
Date :  02 Aug 06  (Deposition) - 14 Nov 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Degradation, Decay, Nmd, Est1A, P Bodies, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. Glavan, I. Behm-Ansmant, E. Izaurralde, E. Conti
Structures Of The Pin Domains Of Smg6 And Smg5 Reveal A Nuclease Within The Mrna Surveillance Complex.
Embo J. V. 25 5117 2006
PubMed-ID: 17053788  |  Reference-DOI: 10.1038/SJ.EMBOJ.7601377
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TELOMERASE-BINDING PROTEIN EST1A
    ChainsA, B, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPGEXCS
    Expression System StrainBL 21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentPIN DOMAIN
    GeneEST1A
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymEVER SHORTER TELOMERES 1A, TELOMERASE SUBUNIT EST1A, EST1-LIKE PROTEIN A, HSMG5/7A

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2HWW)

(-) Sites  (0, 0)

(no "Site" information available for 2HWW)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (4, 12)

Asymmetric Unit (4, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002630731ENSE00001133693chr17:2207069-2206927143EST1A_HUMAN1-30300--
1.2ENST000002630732ENSE00001116084chr17:2203958-22022001759EST1A_HUMAN30-6165870--
1.3ENST000002630733ENSE00001116080chr17:2201349-2201157193EST1A_HUMAN616-680650--
1.4ENST000002630734ENSE00001116081chr17:2200647-2200537111EST1A_HUMAN681-717370--
1.5ENST000002630735ENSE00001116079chr17:2196271-2196165107EST1A_HUMAN718-753360--
1.6ENST000002630736ENSE00001116082chr17:2195924-219584679EST1A_HUMAN753-779270--
1.7ENST000002630737ENSE00001116092chr17:2187029-2186919111EST1A_HUMAN780-816370--
1.8ENST000002630738ENSE00001116083chr17:2186153-2185941213EST1A_HUMAN817-887710--
1.9ENST000002630739ENSE00001116086chr17:2148013-214795262EST1A_HUMAN888-908210--
1.10ENST0000026307310ENSE00001116090chr17:2139931-2139786146EST1A_HUMAN908-957500--
1.11ENST0000026307311ENSE00001048409chr17:2091809-2091693117EST1A_HUMAN957-996400--
1.12ENST0000026307312ENSE00001048425chr17:2090125-2089957169EST1A_HUMAN996-1052570--
1.13ENST0000026307313ENSE00000947188chr17:2076153-2075952202EST1A_HUMAN1052-1119680--
1.15ENST0000026307315ENSE00000875708chr17:1989195-1989019177EST1A_HUMAN1120-1178590--
1.16ENST0000026307316ENSE00000667874chr17:1985250-1985104147EST1A_HUMAN1179-1227490--
1.17ENST0000026307317ENSE00000875710chr17:1972225-1972072154EST1A_HUMAN1228-1279523A:1239-1279
B:1239-1279
C:1241-1279
41
41
39
1.18ENST0000026307318ENSE00000667870chr17:1968973-1968762212EST1A_HUMAN1279-1349713A:1279-1343 (gaps)
B:1279-1343 (gaps)
C:1279-1342 (gaps)
65
65
64
1.19ENST0000026307319ENSE00000875712chr17:1968448-196836782EST1A_HUMAN1350-1377283A:1351-1372
B:1351-1371
C:1353-1369
22
21
17
1.20ENST0000026307320ENSE00001527783chr17:1964916-19631331784EST1A_HUMAN1377-1419433A:1380-1418
B:1379-1418
C:1380-1418
39
40
39

(-) 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:160
 aligned with EST1A_HUMAN | Q86US8 from UniProtKB/Swiss-Prot  Length:1419

    Alignment length:180
                                  1248      1258      1268      1278      1288      1298      1308      1318      1328      1338      1348      1358      1368      1378      1388      1398      1408      1418
         EST1A_HUMAN   1239 MELEIRPLFLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKGQETDHRAGGYARVVQEKARKSIEFLEQRFESRDSCLRALTSRGNELESIAFRSEDITGQLGNNDDLILSCCLHYCKDKAKDFMPASKEEPIRLLREVVLLTDDRNLRVKALTRNVPVRDIPAFLTWAQV 1418
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeeehhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhh------.hhhhhhhhhhhhhhhhhhhhhhhh....eeee.....ee........-------.hhhhhhhhhhhh...hhhhhh-------..eeeeeeee..hhhhhhhhhhh...eehhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.17  PDB: A:1239-1279 [INCOMPLETE] ----------------------------------------------------------------------Exon 1.19  PDB: A:1351-1372 ----------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------Exon 1.18  PDB: A:1279-1343 (gaps) UniProt: 1279-1349 [INCOMPLETE]     ---------------------------Exon 1.20  PDB: A:1380-1418 [INCOMPLETE]   Transcript 1 (2)
                2hww A 1239 MELEIRPLFLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKG------AGGYARVVQEKARKSIEFLEQRFESRDSCLRALTSRGNELESIAFRSE-------NNDDLILSCCLHYCKDKAKDFM-------IRLLREVVLLTDDRNLRVKALTRNVPVRDIPAFLTWAQV 1418
                                  1248      1258      1268      1278      1288|     1298      1308      1318      1328      1338    |    -  |   1358      1368   |     - |    1388      1398      1408      1418
                                                                           1289   1296                                           1343    1351                 1372    1380                                      

Chain B from PDB  Type:PROTEIN  Length:157
 aligned with EST1A_HUMAN | Q86US8 from UniProtKB/Swiss-Prot  Length:1419

    Alignment length:180
                                  1248      1258      1268      1278      1288      1298      1308      1318      1328      1338      1348      1358      1368      1378      1388      1398      1408      1418
         EST1A_HUMAN   1239 MELEIRPLFLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKGQETDHRAGGYARVVQEKARKSIEFLEQRFESRDSCLRALTSRGNELESIAFRSEDITGQLGNNDDLILSCCLHYCKDKAKDFMPASKEEPIRLLREVVLLTDDRNLRVKALTRNVPVRDIPAFLTWAQV 1418
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeeehhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhh---------.hhhhhhhhhhhhhhhhhhhhh....eeee.....ee........-------.hhhhhhhhhhhh...hhhhh-------...eeeeeeee..hhhhhhhhhhh...eehhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.17  PDB: B:1239-1279 [INCOMPLETE] ----------------------------------------------------------------------Exon 1.19  PDB: B:1351-1371 ----------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------Exon 1.18  PDB: B:1279-1343 (gaps) UniProt: 1279-1349 [INCOMPLETE]     ---------------------------Exon 1.20  PDB: B:1379-1418 [INCOMPLETE]   Transcript 1 (2)
                2hww B 1239 MELEIRPLFLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKG---------YARVVQEKARKSIEFLEQRFESRDSCLRALTSRGNELESIAFRSE-------NNDDLILSCCLHYCKDKAKDF-------PIRLLREVVLLTDDRNLRVKALTRNVPVRDIPAFLTWAQV 1418
                                  1248      1258      1268      1278      1288|        -|     1308      1318      1328      1338    |    -  |   1358      1368  |      -|     1388      1398      1408      1418
                                                                           1289      1299                                        1343    1351                1371    1379                                       

Chain C from PDB  Type:PROTEIN  Length:144
 aligned with EST1A_HUMAN | Q86US8 from UniProtKB/Swiss-Prot  Length:1419

    Alignment length:178
                                  1250      1260      1270      1280      1290      1300      1310      1320      1330      1340      1350      1360      1370      1380      1390      1400      1410        
         EST1A_HUMAN   1241 LEIRPLFLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKGQETDHRAGGYARVVQEKARKSIEFLEQRFESRDSCLRALTSRGNELESIAFRSEDITGQLGNNDDLILSCCLHYCKDKAKDFMPASKEEPIRLLREVVLLTDDRNLRVKALTRNVPVRDIPAFLTWAQV 1418
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeehhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhh------------...hhhhhhhhhhhhhhhhhh....eeee.......--.....----------hhhhhhhhhhh...ee.----------..eeeeeeee..hhhhhhhhhhh...eehhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.17  PDB: C:1241-1279            ----------------------------------------------------------------------Exon 1.19  PDB: C:1353-1369 ----------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------Exon 1.18  PDB: C:1279-1342 (gaps) UniProt: 1279-1349 [INCOMPLETE]     ---------------------------Exon 1.20  PDB: C:1380-1418 [INCOMPLETE]   Transcript 1 (2)
                2hww C 1241 LEIRPLFLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLA------------ARVVQEKARKSIEFLEQRFESRDSCLRALTSRGNEL--IAFRS----------DDLILSCCLHYCKDKAK----------IRLLREVVLLTDDRNLRVKALTRNVPVRDIPAFLTWAQV 1418
                                  1250      1260      1270      1280      |  -      1300      1310      1320      1330    | 1340 |       -  |   1360        |-      1380      1390      1400      1410        
                                                                       1287         1300                               1335  |   |       1353            1369       1380                                      
                                                                                                                          1338   |                                                                            
                                                                                                                              1342                                                                            

   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 2HWW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (28, 28)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (EST1A_HUMAN | Q86US8)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0070182    DNA polymerase binding    Interacting selectively and non-covalently with a DNA polymerase.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0004521    endoribonuclease activity    Catalysis of the hydrolysis of ester linkages within ribonucleic acid by creating internal breaks.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    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:0043021    ribonucleoprotein complex binding    Interacting selectively and non-covalently with any complex of RNA and protein.
    GO:0070034    telomerase RNA binding    Interacting selectively and non-covalently with the telomerase RNA template.
    GO:0042162    telomeric DNA binding    Interacting selectively and non-covalently with a telomere, a specific structure at the end of a linear chromosome required for the integrity and maintenance of the end.
biological process
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0006406    mRNA export from nucleus    The directed movement of mRNA from the nucleus to the cytoplasm.
    GO:1904354    negative regulation of telomere capping    Any process that stops, prevents or reduces the frequency, rate or extent of telomere capping.
    GO:0000184    nuclear-transcribed mRNA catabolic process, nonsense-mediated decay    The nonsense-mediated decay pathway for nuclear-transcribed mRNAs degrades mRNAs in which an amino-acid codon has changed to a nonsense codon; this prevents the translation of such mRNAs into truncated, and potentially harmful, proteins.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0035303    regulation of dephosphorylation    Any process that modulates the frequency, rate or extent of removal of phosphate groups from a molecule.
    GO:0032210    regulation of telomere maintenance via telomerase    Any process that modulates the frequency, rate or extent of the addition of telomeric repeats by telomerase.
    GO:0000723    telomere maintenance    Any process that contributes to the maintenance of proper telomeric length and structure by affecting and monitoring the activity of telomeric proteins, the length of telomeric DNA and the replication and repair of the DNA. These processes includes those that shorten, lengthen, replicate and repair the telomeric DNA sequences.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000781    chromosome, telomeric region    The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins.
    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:0035145    exon-exon junction complex    A multi-subunit complex deposited by the spliceosome upstream of messenger RNA exon-exon junctions. The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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.
    GO:0000333    telomerase catalytic core complex    The minimal catalytic core of telomerase is a ribonucleoprotein complex composed of a catalytic reverse transcriptase subunit and an RNA subunit that provides the template for telomeric DNA addition.
    GO:0005697    telomerase holoenzyme complex    Telomerase is a ribonucleoprotein enzyme complex, with a minimal catalytic core composed of a catalytic reverse transcriptase subunit and an RNA subunit that provides the template for telomeric DNA addition. In vivo, the holoenzyme complex often contains additional subunits.

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 Related Entries

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

UniProtKB/Swiss-Prot
        EST1A_HUMAN | Q86US82dok 2hwx 4um2

(-) Related Entries Specified in the PDB File

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