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(-) Description

Title :  STRUCTURE OF HUMAN SND1 EXTENDED TUDOR DOMAIN IN COMPLEX WITH THE SYMMETRICALLY DIMETHYLATED ARGININE PIWIL1 PEPTIDE R4ME2S
 
Authors :  R. Lam, K. Liu, Y. H. Guo, C. B. Bian, C. Xu, F. Mackenzie, C. Bountra, J. We C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, J. Min, Structural Gen Consortium (Sgc)
Date :  26 Aug 10  (Deposition) - 15 Sep 10  (Release) - 19 Jan 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.77
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Staphylococcal Nuclease Domain-Containing Protein 1, Tdrd11, Snd1, Piwil1/Miwi, Structural Genomics Consortium, Sgc, P100 Extended Tudor Domain, Transcription Regulation, Symmetrically Dimethylated Arginine Peptides Derived From Piwil1, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Liu, C. Chen, Y. Guo, R. Lam, C. Bian, C. Xu, D. Y. Zhao, J. Jin, F. Mackenzie, T. Pawson, J. Min
Structural Basis For Recognition Of Arginine Methylated Piw Proteins By The Extended Tudor Domain.
Proc. Natl. Acad. Sci. Usa V. 107 18398 2010
PubMed-ID: 20937909  |  Reference-DOI: 10.1073/PNAS.1013106107

(-) Compounds

Molecule 1 - STAPHYLOCOCCAL NUCLEASE DOMAIN-CONTAINING PROTEIN 1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28-MHL
    Expression System StrainBL21-(DE3)-V2R-PRARE2
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentTUDOR DOMAIN (UNP RESIDUES 650-910)
    GeneSND1, TDRD11
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymP100 CO-ACTIVATOR, 100 KDA COACTIVATOR, EBNA2 COACTIVATOR P100, TUDOR DOMAIN-CONTAINING PROTEIN 11
 
Molecule 2 - SYNTHETIC PEPTIDE
    ChainsC, D
    EngineeredYES
    Other DetailsSYMMETRICALLY DIMETHYLATED ARGININE PEPTIDE R4ME2S DERIVED FROM PIWIL1
    SyntheticYES

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
12MR2Mod. Amino AcidN3, N4-DIMETHYLARGININE
2CL1Ligand/IonCHLORIDE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
12MR1Mod. Amino AcidN3, N4-DIMETHYLARGININE
2CL-1Ligand/IonCHLORIDE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
12MR1Mod. Amino AcidN3, N4-DIMETHYLARGININE
2CL-1Ligand/IonCHLORIDE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO B:723 , THR B:779BINDING SITE FOR RESIDUE CL B 1000

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3OMC)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3OMC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OMC)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TUDORPS50304 Tudor domain profile.SND1_HUMAN729-787
 
  2A:729-787
B:729-787
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TUDORPS50304 Tudor domain profile.SND1_HUMAN729-787
 
  1A:729-787
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TUDORPS50304 Tudor domain profile.SND1_HUMAN729-787
 
  1-
B:729-787

(-) Exons   (7, 14)

Asymmetric Unit (7, 14)
 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_HUMAN657-704482A:681-704
B:682-704
24
23
1.30bENST0000035472530bENSE00000977914chr7:127724776-127724899124SND1_HUMAN704-745422A:704-745
B:704-745
42
42
1.31ENST0000035472531ENSE00000977915chr7:127725763-12772583270SND1_HUMAN745-768242A:745-768
B:745-768
24
24
1.32bENST0000035472532bENSE00000977916chr7:127726990-127727103114SND1_HUMAN769-806382A:769-806
B:769-806
38
38
1.33aENST0000035472533aENSE00000977917chr7:127729541-127729744204SND1_HUMAN807-874682A:807-874
B:807-874
68
68
1.34ENST0000035472534ENSE00000977918chr7:127731889-12773193345SND1_HUMAN875-889152A:875-889
B:875-889
15
15
1.35cENST0000035472535cENSE00001925952chr7:127732045-127732659615SND1_HUMAN890-910212A:890-897
B:890-897
8
8

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

    Alignment length:217
                                   690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       
           SND1_HUMAN   681 SYKPVFVTEITDDLHFYVQDVETGTQLEKLMENMRNDIASHPPVEGSYAPRRGEFCIAKFVDGEWYRARVEKVESPAKIHVFYIDYGNREVLPSTRLGTLSPAFSTRVLPAQATEYAFAFIQVPQDDDARTDAVDSVVRDIQNTQCLLNVEHLSAGCPHVTLQFADSKGDVGLGLVKEGLVMVEVRKEKQFQKVITEYLNAQESAKSARLNLWRYGD 897
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee....eeeeee..hhhhhhhhhhhhhhhhhhhhhhhh........eeeee.....eeeeeeeeeee..eeeeee.....eeeehhh.ee..hhhhh.......eeeeee..ee...hhhhhhhhhhhhhhhhh.eeeeeeeee......eeeeee.....hhhhhhhhh...ee....hhhhhhhhhhhhhhhhhhhhh.hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------TUDOR  PDB: A:729-787 UniProt: 729-787                     -------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.29b [INCOMPLETE] ----------------------------------------Exon 1.31  PDB: A:745-76Exon 1.32b  PDB: A:769-806            Exon 1.33a  PDB: A:807-874 UniProt: 807-874                         Exon 1.34      1.35c    Transcript 1 (1)
           Transcript 1 (2) -----------------------Exon 1.30b  PDB: A:704-745                -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3omc A 681 SYKPVFVTEITDDLHFYVQDVETGTQLEKLMENMRNDIASHPPVEGSYAPRRGEFCIAKFVDGEWYRARVEKVESPAKIHVFYIDYGNREVLPSTRLGTLSPAFSTRVLPAQATEYAFAFIQVPQDDDARTDAVDSVVRDIQNTQCLLNVEHLSAGCPHVTLQFADSKGDVGLGLVKEGLVMVEVRKEKQFQKVITEYLNAQESAKSARLNLWRYGD 897
                                   690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       

Chain B from PDB  Type:PROTEIN  Length:216
 aligned with SND1_HUMAN | Q7KZF4 from UniProtKB/Swiss-Prot  Length:910

    Alignment length:216
                                   691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891      
           SND1_HUMAN   682 YKPVFVTEITDDLHFYVQDVETGTQLEKLMENMRNDIASHPPVEGSYAPRRGEFCIAKFVDGEWYRARVEKVESPAKIHVFYIDYGNREVLPSTRLGTLSPAFSTRVLPAQATEYAFAFIQVPQDDDARTDAVDSVVRDIQNTQCLLNVEHLSAGCPHVTLQFADSKGDVGLGLVKEGLVMVEVRKEKQFQKVITEYLNAQESAKSARLNLWRYGD 897
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) TUDOR-3omcB01 B:682-799                                                                                               -------------------------------------SNase-3omcB03 B:837-895                                    -- Pfam domains (1)
           Pfam domains (2) TUDOR-3omcB02 B:682-799                                                                                               -------------------------------------SNase-3omcB04 B:837-895                                    -- Pfam domains (2)
         Sec.struct. author .eeeeeeee.....eeeee..hhhhhhhhhhhhhhhhhhh.hhhhh.......eeeee.....eeeeeeeeeee..eeeee......eeeehhh.eee.hhhhh.......eeeeee..ee...hhhhhhhhhhhhhhhhh.eeeeeeeee......eeeeee.....hhhhhhhhh...ee....hhhhhhhhhhhhhhhhhhhhh.hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------TUDOR  PDB: B:729-787 UniProt: 729-787                     -------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.29b [INCOMPLETE]----------------------------------------Exon 1.31  PDB: B:745-76Exon 1.32b  PDB: B:769-806            Exon 1.33a  PDB: B:807-874 UniProt: 807-874                         Exon 1.34      1.35c    Transcript 1 (1)
           Transcript 1 (2) ----------------------Exon 1.30b  PDB: B:704-745                -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3omc B 682 YKPVFVTEITDDLHFYVQDVETGTQLEKLMENMRNDIASHPPVEGSYAPRRGEFCIAKFVDGEWYRARVEKVESPAKIHVFYIDYGNREVLPSTRLGTLSPAFSTRVLPAQATEYAFAFIQVPQDDDARTDAVDSVVRDIQNTQCLLNVEHLSAGCPHVTLQFADSKGDVGLGLVKEGLVMVEVRKEKQFQKVITEYLNAQESAKSARLNLWRYGD 897
                                   691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891      

Chain C from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 3omc C   2 GrARARA   8
                             |     
                             3-2MR 

Chain D from PDB  Type:PROTEIN  Length:1
                                 
               SCOP domains - SCOP domains
               CATH domains - CATH domains
               Pfam domains - Pfam domains
         Sec.struct. author . Sec.struct. author
                 SAPs(SNPs) - SAPs(SNPs)
                    PROSITE - PROSITE
                 Transcript - Transcript
                 3omc D   2 r   3
                                   |
                                   3-2MR

   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 3OMC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OMC)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: Tudor (88)
(-)
Family: SNase (72)

(-) Gene Ontology  (18, 18)

Asymmetric 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

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        SND1_HUMAN | Q7KZF42e6n 2hqe 2hqx 2o4x 3bdl 3omg 4qmg 5m9o

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