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(-) Description

Title :  SOLUTION STRUCTURE OF THE HUMAN SP100B SAND DOMAIN BY HETERONUCLEAR NMR.
 
Authors :  M. J. Bottomley, Z. Liu, M. W. Collard, J. I. Huggenvik, T. J. Gibson, M. Sattler
Date :  24 May 01  (Deposition) - 06 Jul 01  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (10x)
Keywords :  Nmr, Transcription, Dna Binding, Sp100B, Sand Domain, Kdwk, Antigen, Nuclear Protein, Alternative Splicing (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. J. Bottomley, M. W. Collard, J. I. Huggenvik, Z. Liu, T. J. Gibson, M. Sattler
The Sand Domain Structure Defines A Novel Dna Binding Fold In Transcriptional Regulation
Nat. Struct. Biol. V. 8 626 2001
PubMed-ID: 11427895  |  Reference-DOI: 10.1038/89675
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NUCLEAR AUTOANTIGEN SP100-B
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System GeneEXPRESSED AS FUSION PROTEIN WITH N-TERMINAL 6-HISTIDINE TAG AND A TEV PROTEASE CLEAVAGE SITE
    Expression System PlasmidMODIFIED PET-24D
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System VariantDE3
    FragmentRESIDUES 595-688
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSAND DOMAIN, KDWK DOMAIN, SPECKLED 100 KDA, NUCLEAR DOT-ASSOCIATED SP100 PROTEIN, LYSP100B

 Structural Features

(-) Chains, Units

  
NMR Structure (10x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1H5P)

(-) Sites  (0, 0)

(no "Site" information available for 1H5P)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1H5P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1H5P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1H5P)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SANDPS50864 SAND domain profile.SP100_HUMAN595-676  1A:595-676
2HMG_BOX_2PS50118 HMG boxes A and B DNA-binding domains profile.SP100_HUMAN769-837
676-753
  1-
A:676-688

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002640521aENSE00001732316chr2:231280657-231281043387SP100_HUMAN1-11110--
1.3ENST000002640523ENSE00001679502chr2:231282306-23128238075SP100_HUMAN11-36260--
1.5bENST000002640525bENSE00001674559chr2:231307652-231307814163SP100_HUMAN36-90550--
1.6ENST000002640526ENSE00001804000chr2:231308893-231309061169SP100_HUMAN91-147570--
1.7ENST000002640527ENSE00001666814chr2:231311534-23131161784SP100_HUMAN147-175290--
1.8ENST000002640528ENSE00001691735chr2:231313803-23131386563SP100_HUMAN175-196220--
1.9cENST000002640529cENSE00001693714chr2:231314276-231314425150SP100_HUMAN196-246510--
1.10ENST0000026405210ENSE00001676251chr2:231314887-23131497084SP100_HUMAN246-274290--
1.11bENST0000026405211bENSE00001710520chr2:231325977-231326129153SP100_HUMAN274-325520--
1.12aENST0000026405212aENSE00001631613chr2:231327150-23132723384SP100_HUMAN325-353290--
1.13bENST0000026405213bENSE00001745337chr2:231328782-23132886584SP100_HUMAN353-381290--
1.14ENST0000026405214ENSE00001777629chr2:231331016-23133106954SP100_HUMAN381-399190--
1.15bENST0000026405215bENSE00001683594chr2:231331835-23133193096SP100_HUMAN399-431330--
1.16bENST0000026405216bENSE00001593423chr2:231333758-23133381154SP100_HUMAN431-449190--
1.19aENST0000026405219aENSE00001798084chr2:231334730-23133481384SP100_HUMAN449-477290--
1.20bENST0000026405220bENSE00001688140chr2:231338039-231338155117SP100_HUMAN477-516400--
1.21ENST0000026405221ENSE00001682383chr2:231339109-23133916254SP100_HUMAN516-534190--
1.23ENST0000026405223ENSE00002173127chr2:231359131-23135917545SP100_HUMAN534-549160--
1.24bENST0000026405224bENSE00000922441chr2:231363176-23136325075SP100_HUMAN549-574260--
1.25ENST0000026405225ENSE00000843903chr2:231367781-23136782545SP100_HUMAN574-589160--
1.26aENST0000026405226aENSE00000843904chr2:231368901-231369005105SP100_HUMAN589-624361A:594-62431
1.27aENST0000026405227aENSE00000786632chr2:231371018-231371160143SP100_HUMAN624-671481A:624-67148
1.28aENST0000026405228aENSE00000843907chr2:231372708-23137274639SP100_HUMAN672-684131A:672-68413
1.28dENST0000026405228dENSE00001670285chr2:231375840-23137588142SP100_HUMAN685-698140--
1.29ENST0000026405229ENSE00001510520chr2:231379810-2313812421433SP100_HUMAN699-8791811A:685-6884

(-) Sequences/Alignments

NMR Structure
   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:95
 aligned with SP100_HUMAN | P23497 from UniProtKB/Swiss-Prot  Length:879

    Alignment length:118
                                   603       613       623       633       643       653       663       673       683       693       703        
          SP100_HUMAN   594 KDENINFKQSELPVTCGEVKGTLYKERFKQGTSKKCIQSEDKKWFTPREFEIEGDRGASKNWKLSIRCGGYTLKVLMENKFLPEPPSTRKKRILESHNNTLVDPCEEHKKKNPDASVK 711
               SCOP domains d1h5pa_ A: Nuclear autoantigen Sp100b                                                                                  SCOP domains
               CATH domains 1h5pA00 A:594-688 SAND domain                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeee....eeeee.hhhh.......eee...eee..hhhhhhh.......hhhheee...hhhhhhhh............-----------------------.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -SAND  PDB: A:595-676 UniProt: 595-676                                             ----------------------------------- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------HMG_BOX_2  PDB: A:676-688            PROSITE (2)
           Transcript 1 (1) Exon 1.26a  PDB: A:594-624     -----------------------------------------------Exon 1.28a   Exon 1.28d    Exon 1.29     Transcript 1 (1)
           Transcript 1 (2) ------------------------------Exon 1.27a  PDB: A:624-671 UniProt: 624-671     ---------------------------------------- Transcript 1 (2)
                 1h5p A 594 MDENINFKQSELPVTCGEVKGTLYKERFKQGTSKKCIQSEDKKWFTPREFEIEGDRGASKNWKLSIRCGGYTLKVLMENKFLPEPPSTRKK-----------------------VTIK 688
                                   603       613       623       633       643       653       663       673       683|        -         -    |   
                                                                                                                    684                     685   

   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)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1H5P)

(-) Gene Ontology  (47, 47)

NMR Structure(hide GO term definitions)
Chain A   (SP100_HUMAN | P23497)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0070087    chromo shadow domain binding    Interacting selectively and non-covalently with a chromo shadow domain, a protein domain that is distantly related, and found in association with, the chromo domain.
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0019900    kinase binding    Interacting selectively and non-covalently with a kinase, any enzyme that catalyzes the transfer of a phosphate group.
    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:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0003713    transcription coactivator activity    Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
    GO:0003714    transcription corepressor activity    Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
biological process
    GO:0006978    DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator    A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, resulting in the induction of the transcription of p21 (also known as WAF1, CIP1 and SDI1) or any equivalent protein, in response to the detection of DNA damage.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0060333    interferon-gamma-mediated signaling pathway    A series of molecular signals initiated by the binding of interferon-gamma to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Interferon gamma is the only member of the type II interferon found so far.
    GO:0043392    negative regulation of DNA binding    Any process that stops or reduces the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid).
    GO:0051271    negative regulation of cellular component movement    Any process that stops, prevents, or reduces the frequency, rate or extent of the movement of a cellular component.
    GO:0010596    negative regulation of endothelial cell migration    Any process that decreases the rate, frequency, or extent of the orderly movement of an endothelial cell into the extracellular matrix to form an endothelium.
    GO:1903507    negative regulation of nucleic acid-templated transcription    Any process that stops, prevents or reduces the frequency, rate or extent of nucleic acid-templated transcription.
    GO:0046826    negative regulation of protein export from nucleus    Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of proteins from the nucleus into the cytoplasm.
    GO:0043433    negative regulation of sequence-specific DNA binding transcription factor activity    Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0032897    negative regulation of viral transcription    Any process that stops, prevents, or reduces the frequency, rate or extent of viral transcription.
    GO:0051091    positive regulation of sequence-specific DNA binding transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0016925    protein sumoylation    The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein.
    GO:1902044    regulation of Fas signaling pathway    Any process that modulates the frequency, rate or extent of Fas signaling pathway.
    GO:0045765    regulation of angiogenesis    Any process that modulates the frequency, rate or extent of angiogenesis.
    GO:1902041    regulation of extrinsic apoptotic signaling pathway via death domain receptors    Any process that modulates the frequency, rate or extent of extrinsic apoptotic signaling pathway via death domain receptors.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0034097    response to cytokine    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cytokine stimulus.
    GO:0034341    response to interferon-gamma    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interferon-gamma stimulus. Interferon-gamma is also known as type II interferon.
    GO:0032526    response to retinoic acid    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a retinoic acid stimulus.
    GO:0034340    response to type I interferon    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a type I interferon stimulus. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
    GO:0048384    retinoic acid receptor signaling pathway    The series of molecular signals generated as a consequence of a retinoic acid receptor binding to one of its physiological ligands.
    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.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0060337    type I interferon signaling pathway    A series of molecular signals initiated by the binding of a type I interferon to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
    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:0030870    Mre11 complex    Trimeric protein complex that possesses endonuclease activity; involved in meiotic recombination, DNA repair and checkpoint signaling. In Saccharomyces cerevisiae, the complex comprises Mre11p, Rad50p, and Xrs2p; complexes identified in other species generally contain proteins orthologous to the Saccharomyces cerevisiae proteins.
    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:0000784    nuclear chromosome, telomeric region    The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0034399    nuclear periphery    The portion of the nuclear lumen proximal to the inner nuclear membrane.
    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:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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
        SP100_HUMAN | P234974ptb 5fb0 5fb1 5pwc 5pwd 5pwe 5pwf 5pwg 5pwh 5pwi 5pwj 5pwk 5pwl 5pwm 5pwn 5pwo 5pwp 5pwq 5pwr 5pws 5pwt 5pwu 5pwv 5pww 5pwx 5pwy 5pwz 5px0 5px1 5px2 5px3 5px4 5px5 5px6 5px7 5px8 5px9 5pxa 5pxb 5pxc 5pxd 5pxe 5pxf 5pxg 5pxh 5pxi 5pxj 5pxk 5pxl 5pxm 5pxn 5pxo 5pxp 5pxq 5pxr 5pxs 5pxt 5pxu 5pxv 5pxw 5pxx 5pxy 5pxz 5py0 5py1 5py2 5py3 5py4 5py5 5py6 5py7 5py8 5py9 5pya 5pyb 5pyc 5pyd 5pye 5pyf 5pyg 5pyh 5pyi 5pyj 5pyk 5pyl 5pym 5pyn 5pyo 5pyp 5pyq 5pyr 5pys 5pyt 5pyu 5pyv 5pyw 5pyx 5pyy 5pyz 5pz0 5pz1 5pz2 5pz3 5pz4 5pz5 5pz6 5pz7 5pz8 5pz9 5pza 5pzb 5pzc 5pzd 5pze 5pzf 5pzg 5pzh 5pzi 5pzj

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1H5P)