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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN P100 TUDOR DOMAIN: LARGE FRAGMENT
 
Authors :  N. Shah, M. Zhao, C. Cheng, H. Xu, J. Yang, O. Silvennoinen, Z. J. Liu, B. C. Wang, Southeast Collaboratory For Structural Genomics (Secsg)
Date :  18 Jul 06  (Deposition) - 03 Jul 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  P100 Tudor Domain, Large Fragment, Human, Structural Genomics, Psi, Protein Structure Initiative, Southeast Collaboratory For Structural Genomics, Secsg, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Shah, M. Zhao, C. Cheng, H. Xu, J. Yang, O. Silvennoinen, B. C. Wang, Z. J. Liu
Crystal Structure Of A Large Fragment Of The Human P100 Tudor Domain
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - P100 CO-ACTIVATOR TUDOR DOMAIN
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System StrainBL21
    Expression System Taxid511693
    FragmentLARGE FRAGMENT, RESIDUES 665-910
    GeneSND1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymP100 CO- ACTIVATOR, 100 KDA COACTIVATOR, EBNA2 COACTIVATOR P100

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

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

(-) Sites  (0, 0)

(no "Site" information available for 2HQE)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:700 -Gly A:701

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TUDORPS50304 Tudor domain profile.SND1_HUMAN729-787
 
  2A:704-762
B:704-762

(-) Exons   (7, 10)

Asymmetric/Biological Unit (7, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003547251bENSE00001903029chr7:127292234-127292505272SND1_HUMAN1-26260--
1.4aENST000003547254aENSE00000882264chr7:127326667-127326816150SND1_HUMAN27-76500--
1.7bENST000003547257bENSE00000720774chr7:127334882-127335002121SND1_HUMAN77-117410--
1.8bENST000003547258bENSE00000720777chr7:127338929-12733900779SND1_HUMAN117-143270--
1.9bENST000003547259bENSE00000720780chr7:127341217-127341377161SND1_HUMAN143-197550--
1.10ENST0000035472510ENSE00000720784chr7:127342489-12734258092SND1_HUMAN197-227310--
1.11cENST0000035472511cENSE00000720787chr7:127343219-127343377159SND1_HUMAN228-280530--
1.12ENST0000035472512ENSE00000720791chr7:127344893-127344999107SND1_HUMAN281-316360--
1.13ENST0000035472513ENSE00000720793chr7:127347611-12734770191SND1_HUMAN316-346310--
1.15ENST0000035472515ENSE00000720795chr7:127361341-127361454114SND1_HUMAN347-384380--
1.16ENST0000035472516ENSE00000977906chr7:127447538-12744762790SND1_HUMAN385-414300--
1.17ENST0000035472517ENSE00000977907chr7:127484377-127484477101SND1_HUMAN415-448340--
1.18bENST0000035472518bENSE00000977908chr7:127527955-127528065111SND1_HUMAN448-485380--
1.20bENST0000035472520bENSE00001089728chr7:127544800-12754487273SND1_HUMAN485-509250--
1.22bENST0000035472522bENSE00000977910chr7:127569241-127569382142SND1_HUMAN510-557480--
1.24cENST0000035472524cENSE00000977911chr7:127631000-127631109110SND1_HUMAN557-593370--
1.28bENST0000035472528bENSE00000977912chr7:127714554-127714742189SND1_HUMAN594-656630--
1.29bENST0000035472529bENSE00001208784chr7:127721412-127721553142SND1_HUMAN657-704481A:654-679
-
26
-
1.30bENST0000035472530bENSE00000977914chr7:127724776-127724899124SND1_HUMAN704-745422A:679-720
B:680-720 (gaps)
42
41
1.31ENST0000035472531ENSE00000977915chr7:127725763-12772583270SND1_HUMAN745-768242A:720-743
B:720-743
24
24
1.32bENST0000035472532bENSE00000977916chr7:127726990-127727103114SND1_HUMAN769-806382A:744-781
B:744-770
38
27
1.33aENST0000035472533aENSE00000977917chr7:127729541-127729744204SND1_HUMAN807-874681A:782-849
-
68
-
1.34ENST0000035472534ENSE00000977918chr7:127731889-12773193345SND1_HUMAN875-889151A:850-864
-
15
-
1.35cENST0000035472535cENSE00001925952chr7:127732045-127732659615SND1_HUMAN890-910211A:865-870
-
6
-

(-) 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:217
 aligned with SND1_HUMAN | Q7KZF4 from UniProtKB/Swiss-Prot  Length:910

    Alignment length:217
                                   688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838       848       858       868       878       888       
           SND1_HUMAN   679 SASYKPVFVTEITDDLHFYVQDVETGTQLEKLMENMRNDIASHPPVEGSYAPRRGEFCIAKFVDGEWYRARVEKVESPAKIHVFYIDYGNREVLPSTRLGTLSPAFSTRVLPAQATEYAFAFIQVPQDDDARTDAVDSVVRDIQNTQCLLNVEHLSAGCPHVTLQFADSKGDVGLGLVKEGLVMVEVRKEKQFQKVITEYLNAQESAKSARLNLWRY 895
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2hqeA01               2hqeA02 A:676-768  [code=2.30.30.140, no name defined]                                       2hqeA01 A:654-675,A:769-870  [code=2.40.50.90, no name defined]                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee....eeeeee..hhhhhhhhhhhhhhhhhhh.............eeeee.....eeeeeeeeeee..eeeeee.....eeeehhh.ee..hhhhh........eeeee..ee...hhhhhhhhhhhhhhhhh.eeeeeeeee......eeeee......hhhhhhhhh...ee....hhhhhhhhhhhhhhhhhhhhh.hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------TUDOR  PDB: A:704-762 UniProt: 729-787                     ------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.29b  PDB: A:654-679----------------------------------------Exon 1.31  PDB: A:720-74Exon 1.32b  PDB: A:744-781            Exon 1.33a  PDB: A:782-849 UniProt: 807-874                         Exon 1.34      1.35c  Transcript 1 (1)
           Transcript 1 (2) -------------------------Exon 1.30b  PDB: A:679-720                ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 2hqe A 654 SASYKPVFVTEITDDLHFYVQDVETGTQFQKLMENMRNDIASHPPVEGSYAPRRGEFCIAKFVDGEWYRARVEKVESPAKIHVFYIDYGNREVLPSTRLGTLSPAFSTRVLPAQATEYAFAFIQVPQDDDARTDAVDSVVRDIQNTQCLLNVEHLSAGCPHVTLQFADSKGDVGLGLVKEGLVMVEVRKEKQFQKVITEYLNAQESAKSARLNLWRY 870
                                   663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       

Chain B from PDB  Type:PROTEIN  Length:87
 aligned with SND1_HUMAN | Q7KZF4 from UniProtKB/Swiss-Prot  Length:910

    Alignment length:91
                                   714       724       734       744       754       764       774       784       794 
           SND1_HUMAN   705 TQLEKLMENMRNDIASHPPVEGSYAPRRGEFCIAKFVDGEWYRARVEKVESPAKIHVFYIDYGNREVLPSTRLGTLSPAFSTRVLPAQATE 795
               SCOP domains d2hqeb_ B: P100 co-    activator, SND1                                                      SCOP domains
               CATH domains 2hqeB01 B:680-760      [code=2.30.30.140, no name defined]                       ---------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh..----.......eeeee.....eeeeeeeeeee..eeeeee.....eeeehhh.ee..hhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------TUDOR  PDB: B:704-762 UniProt: 729-787                     -------- PROSITE
           Transcript 1 (1) ----------------------------------------Exon 1.31  PDB: B:720-74Exon 1.32b  PDB: B:744-770  Transcript 1 (1)
           Transcript 1 (2) Exon 1.30b  PDB: B:680-720 (gaps)        -------------------------------------------------- Transcript 1 (2)
                 2hqe B 680 TQFQKLMENMRNDIASHPP----YAPRRGEFCIAKFVDGEWYRARVEKVESPAKIHVFYIDYGNREVLPSTRLGTLSPAFSTRVLPAQATE 770
                                   689        |-   |   709       719       729       739       749       759       769 
                                            698  703                                                                   

   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

(-) CATH Domains  (2, 3)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SND1_HUMAN | Q7KZF4)
molecular function
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    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:0003712    transcription cofactor activity    Interacting selectively and non-covalently with a regulatory transcription factor and also with the basal transcription machinery in order to modulate transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between regulatory transcription factors and the basal transcription machinery.
biological process
    GO:0031047    gene silencing by RNA    Any process in which RNA molecules inactivate expression of target genes.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0001649    osteoblast differentiation    The process whereby a relatively unspecialized cell acquires the specialized features of an osteoblast, a mesodermal or neural crest cell that gives rise to bone.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0016442    RISC complex    A ribonucleoprotein complex that contains members of the Argonaute family of proteins, small interfering RNAs (siRNAs) or microRNAs (miRNAs), and miRNA or siRNA-complementary mRNAs, in addition to a number of accessory factors. The RISC complex is involved in posttranscriptional repression of gene expression through downregulation of translation or induction of mRNA degradation.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0097433    dense body    An electron dense body which may contain granules.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0042470    melanosome    A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    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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    Glu A:700 - Gly A:701   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        SND1_HUMAN | Q7KZF42e6n 2hqx 2o4x 3bdl 3omc 3omg 4qmg 5m9o

(-) Related Entries Specified in the PDB File

2hqx P100 TUDOR DOMAIN CONSERVED REGION RELATED ID: P100-TLD RELATED DB: TARGETDB