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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ACTIVE CATALYTIC CORE OF THE HUMAN DEAD-BOX PROTEIN DDX3
 
Authors :  S. N. Floor, K. J. Condon, J. A. Doudna
Date :  12 Oct 15  (Deposition) - 02 Dec 15  (Release) - 10 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.22
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  B  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Dead-Box Protein, Rna Helicase, Reca Fold, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. N. Floor, K. J. Condon, D. Sharma, E. Jankowsky, J. A. Doudna
Autoinhibitory Interdomain Interactions And Subfamily-Specific Extensions Redefine The Catalytic Core O The Human Dead-Box Protein Ddx3.
J. Biol. Chem. V. 291 2412 2016
PubMed-ID: 26598523  |  Reference-DOI: 10.1074/JBC.M115.700625

(-) Compounds

Molecule 1 - ATP-DEPENDENT RNA HELICASE DDX3X
    Chains: B, A, C
    EC Number: 3.6.4.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHMGWA
    Expression System Strain: BL21 STAR (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: DEAD-BOX DOMAINS
    Gene: DDX3X, DBX, DDX3
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DEAD BOX PROTEIN 3,X-CHROMOSOMAL,DEAD BOX,X ISOFORM, HELICASE-LIKE PROTEIN 2,HLP2

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x):  B 
Biological Unit 2 (1x): A  
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5E7I)

(-) Sites  (0, 0)

(no "Site" information available for 5E7I)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5E7I)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5E7I)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5E7I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5E7I)

(-) Exons   (0, 0)

(no "Exon" information available for 5E7I)

(-) 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:430
                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhh......eee...............hhhhhhhhhhhh.....hhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhh.hhhhhh...........eeee..hhhhhhhhhhhhhhhh......eeee....hhhhhhhhhh....eeeehhhhhhhhhhh.........eeee.hhhhhhhh.hhhhhhhhhhh.........eeeee....hhhhhhhhhhhh...eeee..........eeeeeee.hhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhh....eeeehhhhhh........eeee.....hhhhhhhhhh........eeeeeeehhhhhhhhhhhhhhhhhh....hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5e7i A 134 DDWSKPLPPSERLEQELFSGDDIPVEATGNNCPPHIESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKEGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKYLVLDEADRMLDMGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGSTSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVPSWLENMAYE 577
                                   143       153|      173       183       193       203       213       223       233       243       253  ||   267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577
                                             153|                                                                                         256|                                                                                                                                                                                                                                                                                                                            
                                              164                                                                                          261                                                                                                                                                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:418
                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhh....eee.........hhhhh.hhhhhhhhhhhh.....hhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhh..hhhhhhh........eeee..hhhhhhhhhhhhhhhh......eeee....hhhhhhhhhh....eeeehhhhhhhhhhh.........eeee.hhhhhhhh.hhhhhhhhhh..........eeeee....hhhhhhhhhhhh...eeee..........eeeeeee.hhhhhhhhhhhhhhh......eeee..hhhhhhhhhhhhhhh...eeee....hhhhhhh...eeee..............eeee.....hhhhhhhhhh........eeeeeeehhhhhhhhhhhhhhhhhh......hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5e7i B 134 DDWSKPLPPSERLEQELFSGIPVEATGNNCPPHIESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKERKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKYLVLDEADRMLDMGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGSTSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHEEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVPSWLENMAYE 577
                                   143       153|      175       185       195       205       215       225       235       245       255||     271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471||     489       499       509       519       529       539       549       559       569        
                                             153|                                                                                       256|                                                                                                                                                                                                              472|                                                                                                
                                              166                                                                                        263                                                                                                                                                                                                               481                                                                                                


Chain C from PDB  Type:PROTEIN  Length:424
                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhh......eee.........hhhhh..hhhhhhhhhhh.....hhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhh.hhhhhh........eeee..hhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhh...eeeehhhhhhhhhhh.........eeee.hhhhhhhh.hhhhhhhhhhh.........eeeeee...hhhhhhhhhhhh...eeee...........eeeeee.hhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhh....eeeee.............eeee.....hhhhhhhhhh.........eeeeeehhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5e7i C 134 DDWSKPLPPSERLEQELFSGDIPVEATGNNCPPHIESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKYLVLDEADRMLDMGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGSTSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVPSWLENMA 575
                                   143       153|      174       184       194       204       214       224       234       244       254||     271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571    
                                             153|                                                                                       255|                                                                                                                                                                                                                                                                                                                        
                                              165                                                                                        263
   Legend:   → Mismatch (orange background)
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  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 5E7I)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5E7I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5E7I)

(-) Gene Ontology  (69, 69)

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 Related Entries

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

UniProtKB/Swiss-Prot
        DDX3X_HUMAN | O00571: 2i4i 2jgn 3jrv 4o2c 4o2e 4o2f 4px9 4pxa 5e7j 5e7m

(-) Related Entries Specified in the PDB File

5e7j 5e7m