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(-) Description

Title :  CRYSTAL STRUCTURE OF THE FIRST RRM DOMAIN OF HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN L (HNRNP L)
 
Authors :  W. Zhang, Y. Liu, F. Zeng, L. Niu, M. Teng, X. Li
Date :  14 Mar 11  (Deposition) - 14 Sep 11  (Release) - 14 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.04
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Rbd Fold, Protein Binding, Nucleus (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. Zhang, Y. Liu, F. Zeng, L. Niu, M. Teng, X. Li
Crystal Structure Of The First Rrm Domain Of Heterogeneous Nuclear Ribonucleoprotein L (Hnrnp L)
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN L
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentTHE FIRST RRM DOMAIN
    GeneHNRNPL, HNRPL, P/OKCL.14
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHNRNP L

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:121 , GLU A:124 , TYR A:156 , GLN A:161 , ILE A:162 , TYR A:163 , GLN B:139BINDING SITE FOR RESIDUE GOL A 181
2AC2SOFTWARELEU A:141 , SER A:174 , THR A:175 , LEU B:148BINDING SITE FOR RESIDUE GOL A 182
3AC3SOFTWAREGLN A:139 , ALA B:121 , GLU B:124 , TYR B:156 , GLN B:161 , ILE B:162 , TYR B:163BINDING SITE FOR RESIDUE GOL B 181
4AC4SOFTWARELEU A:148 , HOH B:35 , HIS B:105 , LEU B:141 , SER B:174 , THR B:175BINDING SITE FOR RESIDUE GOL B 182
5AC5SOFTWAREASP B:111 , PRO B:135 , LYS B:136 , ARG B:138 , LYS B:178BINDING SITE FOR RESIDUE GOL B 183

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3R27)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3R27)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3R27)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.HNRPL_HUMAN102-176
 
193-270
382-456
  2A:102-176
B:102-176
-
-
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.HNRPL_HUMAN102-176
 
193-270
382-456
  1A:102-176
-
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.HNRPL_HUMAN102-176
 
193-270
382-456
  1-
B:102-176
-
-

(-) Exons   (0, 0)

(no "Exon" information available for 3R27)

(-) 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:84
 aligned with HNRPL_HUMAN | P14866 from UniProtKB/Swiss-Prot  Length:589

    Alignment length:84
                                   106       116       126       136       146       156       166       176    
          HNRPL_HUMAN    97 KTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQKIS 180
               SCOP domains d3r27a_ A: automated matches                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee......hhhhhhhhhhhhh.eeeeeee....eeeeee.hhhhhhhhhhhhhhh.eee..eeeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----RRM  PDB: A:102-176 UniProt: 102-176                                       ---- PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                 3r27 A  97 KTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQKIS 180
                                   106       116       126       136       146       156       166       176    

Chain B from PDB  Type:PROTEIN  Length:84
 aligned with HNRPL_HUMAN | P14866 from UniProtKB/Swiss-Prot  Length:589

    Alignment length:84
                                   106       116       126       136       146       156       166       176    
          HNRPL_HUMAN    97 KTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQKIS 180
               SCOP domains d3r27b_ B: automated matches                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee......hhhhhhhhhh....eeeeeee....eeeeee.hhhhhhhhhhhhhhh.eee..eeeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----RRM  PDB: B:102-176 UniProt: 102-176                                       ---- PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                 3r27 B  97 KTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQKIS 180
                                   106       116       126       136       146       156       166       176    

   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 Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3R27)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3R27)

(-) Gene Ontology  (19, 19)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (HNRPL_HUMAN | P14866)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0097157    pre-mRNA intronic binding    Interacting selectively and non-covalently with an intronic sequence of a pre-messenger RNA (pre-mRNA).
    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:0044212    transcription regulatory region DNA binding    Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
biological process
    GO:0006396    RNA processing    Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
    GO:0010467    gene expression    The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
    GO:0000398    mRNA splicing, via spliceosome    The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
    GO:0000381    regulation of alternative mRNA splicing, via spliceosome    Any process that modulates the frequency, rate or extent of alternative splicing of nuclear mRNAs.
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:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.
    GO:0045120    pronucleus    The nucleus of either the ovum or the spermatozoon following fertilization. Thus, in the fertilized ovum, there are two pronuclei, one originating from the ovum, the other from the spermatozoon that brought about fertilization; they approach each other, but do not fuse until just before the first cleavage, when each pronucleus loses its membrane to release its contents.
    GO:0035770    ribonucleoprotein granule    A non-membranous macromolecular complex containing proteins and translationally silenced mRNAs. RNA granules contain proteins that control the localization, stability, and translation of their RNA cargo. Different types of RNA granules (RGs) exist, depending on the cell type and cellular conditions.

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