Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION STRUCTURE OF THE LEUCINE RICH REPEAT OF HUMAN ACIDIC LEUCINE-RICH NUCLEAR PHOSPHOPROTEIN 32 FAMILY MEMBER B
 
Authors :  N. Tochio, T. Umehara, K. Tsuda, S. Koshiba, T. Harada, S. Watanabe, A. T T. Kigawa, S. Yokoyama
Date :  25 May 10  (Deposition) - 09 Jun 10  (Release) - 25 Aug 10  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Phapi2 Protein, Silver-Stainable Protein Ssp29, Acidic Protein Rich In Leucines, Gene Regulation, Rdc (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Tochio, T. Umehara, Y. Munemasa, T. Suzuki, S. Sato, K. Tsuda, S. Koshiba, T. Kigawa, R. Nagai, S. Yokoyama
Solution Structure Of Histone Chaperone Anp32B: Interaction With Core Histones H3-H4 Through Its Acidic Concave Domain.
J. Mol. Biol. V. 401 97 2010
PubMed-ID: 20538007  |  Reference-DOI: 10.1016/J.JMB.2010.06.005

(-) Compounds

Molecule 1 - ACIDIC LEUCINE-RICH NUCLEAR PHOSPHOPROTEIN 32 FAMILY MEMBER B
    ChainsA
    EngineeredYES
    Expression SystemCELL-FREE SYNTHESIS
    Expression System VectorP060227-01
    Expression System Vector TypeVECTOR
    FragmentRESIDUES IN UNP 1-161
    GeneANP32B
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymACIDIC PROTEIN RICH IN LEUCINES, PUTATIVE HLA-DR-ASSOCIATED PROTEIN I-2, PHAPI2, SILVER-STAINABLE PROTEIN SSP29

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x)A
NMR Structure * (1x)A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2RR6)

(-) Sites  (0, 0)

(no "Site" information available for 2RR6)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2RR6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2RR6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2RR6)

(-) PROSITE Motifs  (1, 4)

NMR Structure (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LRRPS51450 Leucine-rich repeat profile.AN32B_HUMAN43-64
89-110
65-84
114-135
  4A:50-71
A:96-117
A:72-91
A:121-142
NMR Structure * (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LRRPS51450 Leucine-rich repeat profile.AN32B_HUMAN43-64
89-110
65-84
114-135
  4A:50-71
A:96-117
A:72-91
A:121-142

(-) Exons   (0, 0)

(no "Exon" information available for 2RR6)

(-) 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:168
 aligned with AN32B_HUMAN | Q92688 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:168
                                   1                                                                                                                                                                
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153        
          AN32B_HUMAN     - -------MDMKRRIHLELRNRTPAAVRELVLDNCKSNDGKIEGLTAEFVNLEFLSLINVGLISVSNLPKLPKLKKLELSENRIFGGLDMLAEKLPNLTHLNLSGNKLKDISTLEPLKKLECLKSLDLFNCEVTNLNDYRESVFKLLPQLTYLDGYDREDQEAPDSDAE 161
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------LRR_4-2rr6A01 A:95-144                            ------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhhhh..hhhhh.eee......................eee...................eee.........hhhhhhhh....eee.......hhhhhhhhhhh....eee...hhhhhh.hhhhhhhhhh....ee..ee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------LRR  PDB: A:50-71     LRR  PDB: A:72-91   ----LRR  PDB: A:96-117    ---LRR  PDB: A:121-142   -------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2rr6 A   1 GSSGSSGMDMKRRIHLELRNRTPAAVRELVLDNCKSNDGKIEGLTAEFVNLEFLSLINVGLISVSNLPKLPKLKKLELSENRIFGGLDMLAEKLPNLTHLNLSGNKLKDISTLEPLKKLECLKSLDLFNCEVTNLNDYRESVFKLLPQLTYLDGYDREDQEAPDSDAE 168
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160        

   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 2RR6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2RR6)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: LRR (77)

(-) Gene Ontology  (15, 15)

NMR Structure(hide GO term definitions)
Chain A   (AN32B_HUMAN | Q92688)
molecular function
    GO:0070063    RNA polymerase binding    Interacting selectively and non-covalently with an RNA polymerase molecule or complex.
    GO:0042393    histone binding    Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
    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).
biological process
    GO:0006919    activation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that initiates the activity of the inactive enzyme cysteine-type endopeptidase in the context of an apoptotic process.
    GO:0048839    inner ear development    The process whose specific outcome is the progression of the inner ear over time, from its formation to the mature structure.
    GO:0045596    negative regulation of cell differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of cell differentiation.
    GO:0006334    nucleosome assembly    The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
    GO:0060021    palate development    The biological process whose specific outcome is the progression of the palate from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure. The palate is the partition that separates the nasal and oral cavities.
    GO:0046827    positive regulation of protein export from nucleus    Any process that activates or increases the frequency, rate or extent of directed movement of proteins from the nucleus into the cytoplasm.
    GO:0001944    vasculature development    The process whose specific outcome is the progression of the vasculature over time, from its formation to the mature structure. The vasculature is an interconnected tubular multi-tissue structure that contains fluid that is actively transported around the organism.
    GO:0021591    ventricular system development    The process whose specific outcome is the progression of the brain ventricular system over time, from its formation to the mature structure. The brain ventricular system consists of four communicating cavities within the brain that are continuous with the central canal of the spinal cord. These cavities include two lateral ventricles, the third ventricle and the fourth ventricle. Cerebrospinal fluid fills the ventricles and is produced by the choroid plexus.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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: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.

 Visualization

(-) Interactive Views

NMR Structure
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2rr6)
 
  Sites
(no "Sites" information available for 2rr6)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2rr6)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2rr6
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  AN32B_HUMAN | Q92688
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  AN32B_HUMAN | Q92688
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        AN32B_HUMAN | Q926882ell

(-) Related Entries Specified in the PDB File

2ell RELATED ID: 11083 RELATED DB: BMRB