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(-) Description

Title :  DECH BOX HELICASE DOMAIN
 
Authors :  T. Deimling, G. Witte, K. P. Hopfner
Date :  28 Jan 14  (Deposition) - 02 Jul 14  (Release) - 11 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.71
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Pattern Recognition Receptor, Cytosol, Atpase, Dech Box Domain, Rna, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Deimling, S. Cui, K. Lammens, K. P. Hopfner, G. Witte
Crystal And Solution Structure Of The Human Rig-I Sf2 Domai
Acta Crystallogr. , Sect. F V. 70 1027 2014
PubMed-ID: 25084375  |  Reference-DOI: 10.1107/S2053230X14012230

(-) Compounds

Molecule 1 - PROBABLE ATP-DEPENDENT RNA HELICASE DDX58
    Chains: A, B
    EC Number: 3.6.4.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 230-793
    Gene: DDX58
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DEAD BOX PROTEIN 58, RIG-I-LIKE RECEPTOR 1, RLR-1, RETINOIC ACID-INDUCIBLE GENE 1 PROTEIN, RIG-1, RETINOIC ACID-INDUCIBLE GENE I PROTEIN, RIG-I

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2SO44Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2SO42Ligand/IonSULFATE ION
Biological Unit 3 (1, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2SO44Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:265 , THR A:266 , GLY A:267 , CYS A:268 , GLY A:269 , LYS A:270 , THR A:271 , ARG B:488BINDING SITE FOR RESIDUE SO4 A 801
2AC2SOFTWARETHR A:506 , GLN A:507 , LYS A:508 , LYS A:635BINDING SITE FOR RESIDUE SO4 A 802
3AC3SOFTWAREARG A:488 , THR B:266 , GLY B:267 , CYS B:268 , GLY B:269 , LYS B:270BINDING SITE FOR RESIDUE SO4 B 801
4AC4SOFTWARETHR B:506 , GLN B:507 , LYS B:508BINDING SITE FOR RESIDUE SO4 B 802
5AC5SOFTWAREASN B:744 , HOH B:914 , HOH B:918BINDING SITE FOR RESIDUE CL B 803

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4ON9)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:397 -Ser A:398
2Phe A:685 -Lys A:686

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ON9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ON9)

(-) Exons   (0, 0)

(no "Exon" information available for 4ON9)

(-) 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:514
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhh........eeee..hhhhhhhhhhhhhhhhhh....eeee........hhhhhhhhh.eeeehhhhhhhhhhhh.........eeee.hhhhh...hhhhhhhhhhhhhhhh.......eeeeee.........hhhhhhhhhhhhhhhh...eee....hhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhhhhhhh...eee.........eeee........eeee..eeeee......eeee...eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4on9 A 241 FKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPVYEQQKSVFSKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIPSLSIFTLMIFDECHNTSKQHPYNMIMFNYLDQKLGGSSGPLPQVIGLTASVGVGDAKNTDEALDYICKLCASLDASVIATVKHNLEELEQVVYKPQKFFRKVESRISDKFKYIIAQLMRDTESLAKRICKDLESQIQNREFGTQKYEQWIVTVQKACMVKDEESRICKALFLYTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRAAGFDEIEQDLTQRFEEKLQELESVSRDPSNENPKLEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGILFKASGDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQGSKCFLLTSNAGVIEKEQINMYKEKMMNDSILRLQTWDEAVFREKILHIQTHEKFIRD 792
                                   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   ||  502       512       522|      537       547       557       567       577       587       597       607       617       627       637       647       657   ||  690       700       710       720     ||738       748       758       768       778       788    
                                                                                                                                                                                                                                                                                       494|                      522|                                                                                                                                  661|                                      726|                                                         
                                                                                                                                                                                                                                                                                        497                       528                                                                                                                                   685                                       735                                                         


Chain B from PDB  Type:PROTEIN  Length:495
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhh......eeee..hhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhh.eeeehhhhhhhhhhhh...hhhhh.eeeee.hhhh...hhhhhhhhhhhhhhh......eeeeee.........hhhhhhhhhhhhhhhh...eee....hhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhhhhhhh...ee......eeee......eeeee........eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4on9 B 242 KPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPKGKVVFFANQIPVYEQQKSVFSKYFERHGYRVTGISGNVPVEQIVENNDIIILTPQILVNNLKKGTIPSLSIFTLMIFDECHNTSKQHPYNMIMFNYLDQKLGSGPLPQVIGLTASVGVGDAKNTDEALDYICKLCASLDASVIATVKHNLEELEQVVYKPQKFFRKVESRISDKFKYIIAQLMRDTESLAKRICKDLENLSQIQNREFGTQKYEQWIVTVQKACMVFQMPDKDEESRICKALFLYTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRAAGFDEIEQDLTQRFEEKLQELESVSRDPSNENPKLEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGISGDHNILIATIAQCNLVILYEYVGNVGSKCFLLTSNAGVIEKEQINMYKEKMMNDSILRLQTWDEAVFREKILHIQTHEKFIRDS 793
                                   251       261       271       281    || 294       304       314       324 ||    338       348       358       368       378       388       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|      697|      715     ||738       748       758       768       778       788     
                                                                      286|                                 326|                                                              396|                                                                                                                                                                                                                                                                  660|      697|            721|                                                          
                                                                       290                                  331                                                               399                                                                                                                                                                                                                                                                   688       706             735
   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 4ON9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ON9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ON9)

(-) Gene Ontology  (46, 46)

Asymmetric Unit(hide GO term definitions)

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  4on9
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  DDX58_HUMAN | O95786
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  3.6.4.13
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 Related Entries

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

UniProtKB/Swiss-Prot
        DDX58_HUMAN | O95786: 2lwd 2lwe 2qfb 2qfd 2rmj 2ykg 3lrn 3lrr 3ncu 3og8 3zd6 3zd7 4ay2 4bpb 4nqk 4p4h 5e3h 5f98 5f9f 5f9h

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4ON9)