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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN P100 TUDOR DOMAIN CONSERVED REGION
 
Authors :  M. Zhao, Z. J. Liu, H. Xu, J. Yang, O. Silvennoinen, B. C. Wang, Southeast Collaboratory For Structural Genomics (Secsg)
Date :  19 Jul 06  (Deposition) - 10 Oct 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.42
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Human P100 Tudor Domain, Proteolytic Fragment, Psi, Structural Genomics, Southeast Collaboratory For Structural Genomics, Protein Structure Initiative, Secsg, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Zhao, Z. J. Liu, H. Xu, J. Yang, O. Silvennoinen, B. C. Wang
Crystal Structure Of Human P100 Tudor Domain Conserved Region
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
    Expression System Taxid562
    FragmentCONSERVED REGION
    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 2HQX)

(-) Sites  (0, 0)

(no "Site" information available for 2HQX)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TUDORPS50304 Tudor domain profile.SND1_HUMAN729-787
 
  2A:32-90
B:32-90

(-) Exons   (3, 6)

Asymmetric/Biological Unit (3, 6)
 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_HUMAN657-704480--
1.30bENST0000035472530bENSE00000977914chr7:127724776-127724899124SND1_HUMAN704-745422A:8-48
B:8-48
41
41
1.31ENST0000035472531ENSE00000977915chr7:127725763-12772583270SND1_HUMAN745-768242A:48-71
B:48-71
24
24
1.32bENST0000035472532bENSE00000977916chr7:127726990-127727103114SND1_HUMAN769-806382A:72-97
B:72-97
26
26
1.33aENST0000035472533aENSE00000977917chr7:127729541-127729744204SND1_HUMAN807-874680--
1.34ENST0000035472534ENSE00000977918chr7:127731889-12773193345SND1_HUMAN875-889150--
1.35cENST0000035472535cENSE00001925952chr7:127732045-127732659615SND1_HUMAN890-910210--

(-) 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:90
 aligned with SND1_HUMAN | Q7KZF4 from UniProtKB/Swiss-Prot  Length:910

    Alignment length:90
                                   714       724       734       744       754       764       774       784       794
           SND1_HUMAN   705 TQLEKLMENMRNDIASHPPVEGSYAPRRGEFCIAKFVDGEWYRARVEKVESPAKIHVFYIDYGNREVLPSTRLGTLSPAFSTRVLPAQAT 794
               SCOP domains d2hqxa1 A:8-97 P100 co-activator, SND1                                                     SCOP domains
               CATH domains 2hqxA01 A:8-88  [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: A:32-90 UniProt: 729-787                       ------- PROSITE
           Transcript 1 (1) Exon 1.30b  PDB: A:8-48 UniProt: 704-745 -----------------------Exon 1.32b  PDB: A:72-97   Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------Exon 1.31  PDB: A:48-71 -------------------------- Transcript 1 (2)
                 2hqx A   8 TQFQKLMENMRNDIASHPPVEGSYAPRRGEFCIAKFVDGEWYRARVEKVESPAKIHVFYIDYGNREVLPSTRLGTLSPAFSTRVLPAQAT  97
                                    17        27        37        47        57        67        77        87        97

Chain B from PDB  Type:PROTEIN  Length:90
 aligned with SND1_HUMAN | Q7KZF4 from UniProtKB/Swiss-Prot  Length:910

    Alignment length:90
                                   714       724       734       744       754       764       774       784       794
           SND1_HUMAN   705 TQLEKLMENMRNDIASHPPVEGSYAPRRGEFCIAKFVDGEWYRARVEKVESPAKIHVFYIDYGNREVLPSTRLGTLSPAFSTRVLPAQAT 794
               SCOP domains d2hqxb_ B: P100 co-activator, SND1                                                         SCOP domains
               CATH domains 2hqxB01 B:8-88  [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:32-90 UniProt: 729-787                       ------- PROSITE
           Transcript 1 (1) Exon 1.30b  PDB: B:8-48 UniProt: 704-745 -----------------------Exon 1.32b  PDB: B:72-97   Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------Exon 1.31  PDB: B:48-71 -------------------------- Transcript 1 (2)
                 2hqx B   8 TQFQKLMENMRNDIASHPPVEGSYAPRRGEFCIAKFVDGEWYRARVEKVESPAKIHVFYIDYGNREVLPSTRLGTLSPAFSTRVLPAQAT  97
                                    17        27        37        47        57        67        77        87        97

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) 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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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

2hqe P100 TUDOR DOMAIN LARGE FRAGMENT RELATED ID: P100-TDL RELATED DB: TARGETDB RELATED ID: HSA-P100-TDL RELATED DB: TARGETDB