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(-) Description

Title :  STRUCTURE OF THE HUMAN LINE-1 ORF1P CENTRAL DOMAIN
 
Authors :  E. Khazina, O. Weichenrieder
Date :  22 Dec 08  (Deposition) - 27 Jan 09  (Release) - 27 Jan 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Rna-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Khazina, O. Weichenrieder
Non-Ltr Retrotransposons Encode Noncanonical Rrm Domains In Their First Open Reading Frame.
Proc. Natl. Acad. Sci. Usa V. 106 731 2009
PubMed-ID: 19139409  |  Reference-DOI: 10.1073/PNAS.0809964106

(-) Compounds

Molecule 1 - LINE-1 ORF1P
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPETM60
    Expression System StrainROSETTA2(DE3)
    Expression System Taxid562
    FragmentRRM DOMAIN, RESIDUES 157-252
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymORF1 CODES FOR A 40 KDA PRODUCT

 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  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1MLI1Ligand/IonMALONATE ION
2MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1MLI-1Ligand/IonMALONATE ION
2MSE3Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1MLI1Ligand/IonMALONATE ION
2MSE3Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:223 , VAL A:224 , GLU A:225 , HOH A:2101 , HOH A:2108 , ARG B:206 , SER B:208 , ARG B:210 , HOH B:2144 , HOH B:2145BINDING SITE FOR RESIDUE MLI B1253

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2W7A)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Thr A:203 -Pro A:204
2Thr B:203 -Pro B:204

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2W7A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2W7A)

(-) Exons   (0, 0)

(no "Exon" information available for 2W7A)

(-) 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:100
 aligned with LORF1_HUMAN | Q9UN81 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:134
                                   128       138       148       158       168       178       188       198       208       218       228       238       248    
          LORF1_HUMAN   119 SAMEDEMNEMKREGKFREKRIKRNEQSLQEIWDYVKRPNLRLIGVPESDVENGTKLENTLQDIIQENFPNLARQANVQIQEIQRTPQRYSSRRATPRHIIVRFTKVEMKEKMLRAAREKGRVTLKGKPIRLTAD 252
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....----------------------------------eeeee.........hhhhhhhhhhhhhhh.hhhhhh....eeeeeee............eeeeee..hhhhhhhhhhhhhh..eee..eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w7a A 153 GAmG----------------------------------NLRLIGVPESDVENGTKLENTLQDIIQENFPNLARQANVQIQEIQRTPQRYSSRRATPRHIIVRFTKVEmKEKmLRAAREKGRVTLKGKPIRLTVD 252
                              ||     -         -         -       158       168       178       188       198       208       218       228 |     238       248    
                              ||                                157                                                                  226-MSE                      
                            155-MSE                                                                                                      230-MSE                  
                             156                                                                                                                                  

Chain B from PDB  Type:PROTEIN  Length:99
 aligned with LORF1_HUMAN | Q9UN81 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:133
                                   129       139       149       159       169       179       189       199       209       219       229       239       249   
          LORF1_HUMAN   120 AMEDEMNEMKREGKFREKRIKRNEQSLQEIWDYVKRPNLRLIGVPESDVENGTKLENTLQDIIQENFPNLARQANVQIQEIQRTPQRYSSRRATPRHIIVRFTKVEMKEKMLRAAREKGRVTLKGKPIRLTAD 252
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..e----------------------------------eeeee.........hhhhhhhhhhhhhhh.hhhhhh....eeeeeee............eeeeee..hhhhhhhhhhhhhh..eee..eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w7a B 154 AmG----------------------------------NLRLIGVPESDVENGTKLENTLQDIIQENFPNLARQANVQIQEIQRTPQRYSSRRATPRHIIVRFTKVEmKEKmLRAAREKGRVTLKGKPIRLTVD 252
                             ||      -         -         -       159       169       179       189       199       209       219      |229|      239       249   
                           155-MSE                             157                                                                  226-MSE                      
                            156                                                                                                         230-MSE                  

   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 2W7A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2W7A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2W7A)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (LORF1_HUMAN | Q9UN81)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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: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:0003697    single-stranded DNA binding    Interacting selectively and non-covalently with single-stranded DNA.
    GO:0003727    single-stranded RNA binding    Interacting selectively and non-covalently with single-stranded RNA.
biological process
    GO:0032197    transposition, RNA-mediated    Any process involved in a type of transpositional recombination which occurs via an RNA intermediate.
cellular component
    GO:0000932    P-body    A focus in the cytoplasm where mRNAs may become inactivated by decapping or some other mechanism. Protein and RNA localized to these foci are involved in mRNA degradation, nonsense-mediated mRNA decay (NMD), translational repression, and RNA-mediated gene silencing.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0010494    cytoplasmic stress granule    A dense aggregation in the cytosol composed of proteins and RNAs that appear when the cell is under stress.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0005764    lysosome    A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        LORF1_HUMAN | Q9UN812ldy 2yko 2ykp 2ykq

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2W7A)