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(-) Description

Title :  STRUCTURE OF THE HUMAN LINE-1 ORF1P TRIMER
 
Authors :  E. Khazina, O. Weichenrieder
Date :  28 May 11  (Deposition) - 10 Aug 11  (Release) - 14 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Rna-Binding Protein, Genome Evolution, Nucleic Acid Chaperone, Rnp, Coiled-Coil (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Khazina, V. Truffault, R. Buettner, S. Schmidt, M. Coles, O. Weichenrieder
Trimeric Structure And Flexibility Of The L1Orf1P Protein In Human L1 Retrotransposition
Nat. Struct. Mol. Biol. V. 18 1006 2011
PubMed-ID: 21822284  |  Reference-DOI: 10.1038/NSMB.2097

(-) Compounds

Molecule 1 - LINE-1 ORF1P
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 409008
    Expression System Variant: ROSETTA2
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 104-326
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: THE FOLLOWING RESIDUES ARE SELENOMETHIONINES, M226, M230, M302, M323
    Synonym: ORF1 CODES FOR A 40 KDA PRODUCT

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 14)

Asymmetric/Biological Unit (2, 14)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:142 , ASN B:142 , ASN C:142BINDING SITE FOR RESIDUE CL A1324
2AC2SOFTWAREARG A:135 , ARG C:135BINDING SITE FOR RESIDUE CL A1325

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Tyr A:282 -Pro A:283
2Tyr B:282 -Pro B:283
3Tyr C:282 -Pro C:283

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2YKQ)

(-) Sequences/Alignments

Asymmetric/Biological 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:200
 aligned with LORF1_HUMAN | Q9UN81 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:212
                                   121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321  
          LORF1_HUMAN   112 DQLEERVSAMEDEMNEMKREGKFREKRIKRNEQSLQEIWDYVKRPNLRLIGVPESDVENGTKLENTLQDIIQENFPNLARQANVQIQEIQRTPQRYSSRRATPRHIIVRFTKVEMKEKMLRAAREKGRVTLKGKPIRLTADLSAETLQARREWGPIFNILKEKNFQPRISYPAKLSFISEGEIKYFIDKQMLRDFVTTRPALKELLKEALNM 323
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhhhh.....---...eeeeee.---------....eeeee..hhhhhhhhhhhhhh...ee..ee.eeee...hhhhhhhhhhhhhhhhhhh.....eee...eeeee....eeee..hhhhhhhh...hhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ykq A 112 DQLEERVSAAEDEINEIKREGKFREKRIKRNEQSLQEIWDYVKRPNLRLIGVPESDVENGTKLENTLQDIIQENFPNLA---NVQIQEIQRT---------TPRHIIVRFTKVEmKEKmLRAAREKGRVTLKGKPIRLTVDLSAETLQARREWGPIFNILKEKNFQPRISYPAKLSFISEGEIKYFIDKQmLRDFVTTRPALKELLKEALNm 323
                                   121       131       141       151       161       171       181        |-  |    201 |       - |     221    |  231       241       251       261       271       281       291       301|      311       321 |
                                                                                                        190 194      203       213          226-MSE                                                                     302-MSE              323-MSE
                                                                                                                                                230-MSE                                                                                         


Chain B from PDB  Type:PROTEIN  Length:198
 aligned with LORF1_HUMAN | Q9UN81 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:212
                                   121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321  
          LORF1_HUMAN   112 DQLEERVSAMEDEMNEMKREGKFREKRIKRNEQSLQEIWDYVKRPNLRLIGVPESDVENGTKLENTLQDIIQENFPNLARQANVQIQEIQRTPQRYSSRRATPRHIIVRFTKVEMKEKMLRAAREKGRVTLKGKPIRLTADLSAETLQARREWGPIFNILKEKNFQPRISYPAKLSFISEGEIKYFIDKQMLRDFVTTRPALKELLKEALNM 323
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhhhh....-----..eeeeee.---------....eeeee..hhhhhhhhhhhhhh..eee..eeeeee....hhhhhhhhh.hhhhhhhhh............eeee....eeee..hhhhhhhh...hhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ykq B 112 DQLEERVSAAEDEINEIKREGKFREKRIKRNEQSLQEIWDYVKRPNLRLIGVPESDVENGTKLENTLQDIIQENFPNL-----VQIQEIQRT---------TPRHIIVRFTKVEmKEKmLRAAREKGRVTLKGKPIRLTVDLSAETLQARREWGPIFNILKEKNFQPRISYPAKLSFISEGEIKYFIDKQmLRDFVTTRPALKELLKEALNm 323
                                   121       131       141       151       161       171       181       | -   |   201 |       - |     221    |  231       241       251       261       271       281       291       301|      311       321 |
                                                                                                       189   195     203       213          226-MSE                                                                     302-MSE              323-MSE
                                                                                                                                                230-MSE                                                                                         


Chain C from PDB  Type:PROTEIN  Length:200
 aligned with LORF1_HUMAN | Q9UN81 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:213
                                   120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320   
          LORF1_HUMAN   111 CDQLEERVSAMEDEMNEMKREGKFREKRIKRNEQSLQEIWDYVKRPNLRLIGVPESDVENGTKLENTLQDIIQENFPNLARQANVQIQEIQRTPQRYSSRRATPRHIIVRFTKVEMKEKMLRAAREKGRVTLKGKPIRLTADLSAETLQARREWGPIFNILKEKNFQPRISYPAKLSFISEGEIKYFIDKQMLRDFVTTRPALKELLKEALNM 323
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhhhh.hhhh.---..eeeeee.----------...eeeee..hhhhhhhhhhhhhh..eee..eeeeeee...hhhhhhhhh..hhhhhhhh.....eee...eeeeee..eeeee..hhhhhhhh...hhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ykq C 111 CDQLEERVSAAEDEINEIKREGKFREKRIKRNEQSLQEIWDYVKRPNLRLIGVPESDVENGTKLENTLQDIIQENFPNLAR---VQIQEIQRT----------PRHIIVRFTKVEmKEKmLRAAREKGRVTLKGKPIRLTVDLSAETLQARREWGPIFNILKEKNFQPRISYPAKLSFISEGEIKYFIDKQmLRDFVTTRPALKELLKEALNm 323
                                   120       130       140       150       160       170       180       190|   |  200  |      -   |   220     | 230       240       250       260       270       280       290       300 |     310       320  |
                                                                                                          191 195     203        214         226-MSE                                                                     302-MSE              323-MSE
                                                                                                                                                 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 2YKQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (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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  2ykq
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 Related Entries

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

UniProtKB/Swiss-Prot
        LORF1_HUMAN | Q9UN81: 2ldy 2w7a 2yko 2ykp

(-) Related Entries Specified in the PDB File

2jrb C-TERMINAL DOMAIN OF ORF1P FROM MOUSE LINE-1
2ldy SOLUTION STRUCTURE OF THE RRM-CTD DOMAINS OF HUMAN LINE-1 ORF1P
2w7a STRUCTURE OF THE HUMAN LINE-1 ORF1P CENTRAL DOMAIN
2yko STRUCTURE OF THE HUMAN LINE-1 ORF1P TRIMER
2ykq STRUCTURE OF THE HUMAN LINE-1 ORF1P TRIMER