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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PRP43-ADP-BEF3-U7-RNA COMPLEX
 
Authors :  M. J. Tauchert, R. Ficner
Date :  06 Sep 16  (Deposition) - 25 Jan 17  (Release) - 25 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.62
Chains :  Asym./Biol. Unit :  A,E
Keywords :  Rna Helicase, Deah-Box Protein, Dhx15, Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Tauchert, J. B. Fourmann, R. Luhrmann, R. Ficner
Structural Insights Into The Mechanism Of The Deah-Box Rna Helicase Prp43.
Elife V. 6 2017
PubMed-ID: 28092261  |  Reference-DOI: 10.7554/ELIFE.21510

(-) Compounds

Molecule 1 - PRE-MRNA-SPLICING FACTOR ATP-DEPENDENT RNA HELICASE PRP43
    Chains: A
    EC Number: 3.6.4.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA 2
    Expression System Vector: PETM-13
    Expression System Vector Type: PLASMID
    Gene: CTHT_0005780
    Organism Scientific: CHAETOMIUM THERMOPHILUM VAR. THERMOPHILUM DSM 1495
    Organism Taxid: 759272
    Other Details: THE PROTEIN WAS EXPRESSED WITH 2 ADDITIONAL N-TERMINAL AMINO ACIDS (MA) AND A C-TERMINAL STREP-TAG (WSHPQFEK)
 
Molecule 2 - RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*U)-3')
    Chains: E
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 4)

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2BEF1Ligand/IonBERYLLIUM TRIFLUORIDE ION
3CAC1Ligand/IonCACODYLATE ION
4MG1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:120 , GLY A:122 , SER A:123 , GLY A:124 , LYS A:125 , THR A:126 , THR A:127 , ARG A:162 , THR A:389 , ARG A:435 , MG A:802 , BEF A:803 , HOH A:903 , HOH A:904 , HOH A:905 , HOH A:906 , HOH A:909binding site for residue ADP A 801
2AC2SOFTWARETHR A:126 , ADP A:801 , BEF A:803 , HOH A:906 , HOH A:909 , HOH A:915binding site for residue MG A 802
3AC3SOFTWARETHR A:121 , LYS A:125 , GLU A:219 , ALA A:251 , ARG A:432 , ARG A:435 , ADP A:801 , MG A:802 , HOH A:902 , HOH A:909 , HOH A:915binding site for residue BEF A 803
4AC4SOFTWAREGLY A:400 , PRO A:420binding site for residue CAC A 804

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5LTA)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5LTA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5LTA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5LTA)

(-) Exons   (0, 0)

(no "Exon" information available for 5LTA)

(-) 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:698
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh...........hhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhh.......eeeeee.hhhhhhhhhhhhhhhh.......eeeee..eee......eeeeehhhhhhhhh.......eeeeeee.hhhhhhhhhhhhhhhhhhh......eeeeee...hhhhhhhhh....eeee......eeeee......hhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhh.............eeeeee............eeeeee..eeeeeeee....eeeeeeee.hhhhhhhhhh.......eeeee..hhhhhhhhh.....hhhhh..hhhhhhhhhhh..............hhhhhhhhhhhhhhh.........hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhh..eeee......eeee.....eeee...........eeeeeeeee...eeeeeeee.hhhhhhhhh...........hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lta A  61 TTAKQAEAVEDSDINPWTGQRHSERYFKILKARRKLPVNKQRQEFLDLYHNNQILVFVGETGSGKTTQIPQYVLYDELPHQTGKLIACTQPRRVAAMSVAQRVADELDVKLGEEVGYSIRFENKTSSKTLLKYMTDGQLLREAMHDRDMSRYSCIILDEAHERTLATDILMALLKQLSERRKDLKIIVMSATLDAQKFQSYFFNAPLLAVPGRTHPVEIFYTPEAERDYVEAAIRTVLQIHACEPEGDILLFLTGEEEIEDACRRISLEVDEMIRESDAGPMSVYPLYGTLPPHQQQRIFEKAPQPFRPGGRPGRKCIVATNIAETSLTIDGIVYVVDPGFSKQKIYNPRTRVESLLVSPISKASAQQRAGRAGRTRPGKCFRLYTEEAFKKELIEQTYPEILRSNLSNTVLELKKLGVEDLVHFDLMDPPAPETMMRALEELNYLACLDDDGELTPLGNLASEFPLDPALAVMLISSPEFYCSNEILSITSLLSVPQIWVRPANARKRADEMKAQFAHPDGDHLTLLNAYHAYKGAEARGEDMKKWCHEHFLSYRHLSSADNVRAQLKKIMETHGIELVSTPFHDKNYYTNIRRALLAGFFMQVAMRESSNSKVYKTVKDEQLVLIHPSTTVTTPYEWVVYNEFVLTTKQYVRTVTNIRPEWLLEIAPVYYDLSTFQKGEIKNALTRVAEKIRRQQA 758
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750        


Chain E from PDB  Type:DNA/RNA  Length:8
                                        
                 5lta E   1 UUUUUUUU   8
   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 5LTA)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5LTA)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5LTA)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

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  G0RY84_CHATD | G0RY84
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  3.6.4.13
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 Related Entries

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

UniProtKB/TrEMBL
        G0RY84_CHATD | G0RY84: 5d0u 5ltj 5ltk

(-) Related Entries Specified in the PDB File

5d0u 5D0U IS THE SAME MOLECULE BUT CRYSTALLIZED IN COMPLEX WITH ADP.