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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DDX41 DEAD DOMAIN IN AN APO OPEN FORM
 
Authors :  H. Omura, D. Oikawa, T. Nakane, M. Kato, R. Ishii, Y. Goto, H. Suga, R. Ish F. Tokunaga, O. Nureki
Date :  06 Sep 16  (Deposition) - 19 Oct 16  (Release) - 19 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Atpase, Dead Box Protein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Omura, D. Oikawa, T. Nakane, M. Kato, R. Ishii, R. Ishitani, F. Tokunaga, O. Nureki
Structural And Functional Analysis Of Ddx41: A Bispecific Immune Receptor For Dna And Cyclic Dinucleotide
Sci Rep V. 6 34756 2016
PubMed-ID: 27721487  |  Reference-DOI: 10.1038/SREP34756

(-) Compounds

Molecule 1 - PROBABLE ATP-DEPENDENT RNA HELICASE DDX41
    ChainsA, B, C, D
    EC Number3.6.4.13
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 169-399
    GeneDDX41, ABS
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDEAD BOX PROTEIN 41,DEAD BOX PROTEIN ABSTRAKT HOMOLOG

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 5GVS)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Gly A:257 -Pro A:258
2Gly B:257 -Pro B:258
3Leu C:193 -Arg C:194
4Arg C:194 -Gly C:195
5Gly C:195 -Leu C:196
6Gly C:257 -Pro C:258
7Glu C:286 -Asp C:287
8Leu D:193 -Arg D:194
9Arg D:194 -Gly D:195
10Gly D:195 -Leu D:196
11Gly D:257 -Pro D:258
12Glu D:286 -Asp D:287

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5GVS)

(-) 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:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhh........ee..ee.hhhh..eeee..hhhhhhhhhhhhhhhhhhhhhh...........eeee..hhhhhhhhhhhhhhhhhhhhh.......eeee....hhhhhhhhhh....eeeehhhhhhhhhhh.........eeee.hhhhhhhh.hhhhhhhhhh......eeeeee...hhhhhhhhhhhh...eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5gvs A 184 KEMKFPAAILRGLKKKGIHHPTPIQIQGIPTILSGRDMIGIAFTGSGKTLVFTLPVIMFCLEQEKRLPFSKREGPYGLIICPSRELARQTHGILEYYCRLLQEDSSPLLRCALCIGGMSVKEQMETIRHGVHMMVATPGRLMDLLQKKMVSLDICRYLALDEADRMIDMGFEGDIRTIFSYFKGQRQTLLFSATMPKKIQNFAKSALVKPVTINVG 399
                                   193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393      

Chain B from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh.........ee..ee.......eeee..hhhhhhhhhhhhhhhhhhhhhhhh.........eeee..hhhhhhhhhhhhhhhhhhhhh.......eeee....hhhhhhhh......eeeehhhhhhhhhhh.........eeee.hhhhhhhh.hhhhhhhhhh......eeeeee...hhhhhhhhhhhh...eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gvs B 185 EMKFPAAILRGLKKKGIHHPTPIQIQGIPTILSGRDMIGIAFTGSGKTLVFTLPVIMFCLEQEKRLPFSKREGPYGLIICPSRELARQTHGILEYYCRLLQEDSSPLLRCALCIGGMSVKEQMETIRHGVHMMVATPGRLMDLLQKKMVSLDICRYLALDEADRMIDMGFEGDIRTIFSYFKGQRQTLLFSATMPKKIQNFAKSALVKPVTINVG 399
                                   194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394     

Chain C from PDB  Type:PROTEIN  Length:198
                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............hhhhh..eeee..hhhhhhhhhhhhhhhhhhhhhhhh.........eeee..hhhhhhhhhhhhhhhhhhhhh.......eeee....hhhhhhh.......eeeehhhhhhhhhhh.........eeee.hhhhhhhh.hhhhhhhhhh......eeeeee...hhhhhhhhhhhh...eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5gvs C 191 AILRGLKKKGIPTILSGRDMIGIAFTGSGKTLVFTLPVIMFCLEQEKRLPFSKREGPYGLIICPSRELARQTHGILEYYCRLLQEDSSPLLRCALCIGGMSVKEQMETIRHGVHMMVATPGRLMDLLQKKMVSLDICRYLALDEADRMIDMGFEGDIRTIFSYFKGQRQTLLFSATMPKKIQNFAKSALVKPVTINVG 399
                                   211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391        
                                  199|                                                                                                                                                                                            
                                   211                                                                                                                                                                                            

Chain D from PDB  Type:PROTEIN  Length:197
                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhh..eeee..hhhhhhhhhhhhhhhhhhhhhhhh.........eeee..hhhhhhhhhhhhhhhhhhhhh.......eeee....hhhhhhh.......eeeehhhhhhhhhhh.........eeee.hhhhhhhh.hhhhhhhhhhh.....eeeeee...hhhhhhhhhhhh...eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gvs D 191 AILRGLKKKIPTILSGRDMIGIAFTGSGKTLVFTLPVIMFCLEQEKRLPFSKREGPYGLIICPSRELARQTHGILEYYCRLLQEDSSPLLRCALCIGGMSVKEQMETIRHGVHMMVATPGRLMDLLQKKMVSLDICRYLALDEADRMIDMGFEGDIRTIFSYFKGQRQTLLFSATMPKKIQNFAKSALVKPVTINVG 399
                                   212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       
                                  199|                                                                                                                                                                                           
                                   212                                                                                                                                                                                           

   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 5GVS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (28, 28)

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  Cis Peptide Bonds
    Arg C:194 - Gly C:195   [ RasMol ]  
    Arg D:194 - Gly D:195   [ RasMol ]  
    Glu C:286 - Asp C:287   [ RasMol ]  
    Glu D:286 - Asp D:287   [ RasMol ]  
    Gly A:257 - Pro A:258   [ RasMol ]  
    Gly B:257 - Pro B:258   [ RasMol ]  
    Gly C:195 - Leu C:196   [ RasMol ]  
    Gly C:257 - Pro C:258   [ RasMol ]  
    Gly D:195 - Leu D:196   [ RasMol ]  
    Gly D:257 - Pro D:258   [ RasMol ]  
    Leu C:193 - Arg C:194   [ RasMol ]  
    Leu D:193 - Arg D:194   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/Swiss-Prot
        DDX41_HUMAN | Q9UJV92p6n 5gvr 5h1y

(-) Related Entries Specified in the PDB File

5gvr