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(-) Description

Title :  CRYSTAL STRUCTURE OF A DEAD BOX PROTEIN FROM THE HYPERTHERMOPHILE METHANOCOCCUS JANNASCHII
 
Authors :  R. M. Story, H. Li, J. N. Abelson
Date :  08 Jan 01  (Deposition) - 21 Feb 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Helicase, Rna-Binding Protein, Atpase, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. M. Story, H. Li, J. N. Abelson
Crystal Structure Of A Dead Box Protein From The Hyperthermophile Methanococcus Jannaschii.
Proc. Natl. Acad. Sci. Usa V. 98 1465 2001
PubMed-ID: 11171974  |  Reference-DOI: 10.1073/PNAS.98.4.1465
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE ATP-DEPENDENT RNA HELICASE MJ0669
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism ScientificMETHANOCALDOCOCCUS JANNASCHII
    Organism Taxid2190
    SynonymDEAD BOX HELICASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 26)

Asymmetric/Biological Unit (2, 26)
No.NameCountTypeFull Name
1MSE20Mod. Amino AcidSELENOMETHIONINE
2SO46Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:197 , GLN B:50 , THR B:187 , MSE B:188 , LYS B:358BINDING SITE FOR RESIDUE SO4 B 801
2AC2SOFTWARETHR B:53 , GLY B:54 , SER B:55 , GLY B:56 , LYS B:57 , THR B:58BINDING SITE FOR RESIDUE SO4 B 802
3AC3SOFTWAREGLY A:54 , SER A:55 , GLY A:56 , LYS A:57 , THR A:58BINDING SITE FOR RESIDUE SO4 A 803
4AC4SOFTWARELYS A:246 , HIS A:314 , GLN A:317BINDING SITE FOR RESIDUE SO4 A 804
5AC5SOFTWAREGLN A:50 , THR A:187 , MSE A:188 , LYS A:358 , LYS B:197BINDING SITE FOR RESIDUE SO4 A 805
6AC6SOFTWAREASN A:222 , GLU A:223 , ARG A:345BINDING SITE FOR RESIDUE SO4 A 806

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1HV8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1HV8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1HV8)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1Q_MOTIFPS51195 DEAD-box RNA helicase Q motif profile.H669_METJA6-34
 
  2A:6-34
B:6-34
2DEAD_ATP_HELICASEPS00039 DEAD-box subfamily ATP-dependent helicases signature.H669_METJA152-160
 
  2A:152-160
B:152-160

(-) Exons   (0, 0)

(no "Exon" information available for 1HV8)

(-) 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:363
 aligned with H669_METJA | Q58083 from UniProtKB/Swiss-Prot  Length:367

    Alignment length:363
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362   
           H669_METJA     3 VEYMNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNENNGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALKNANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNMGFIKDVEKILNACNKDKRILLFSATMPREILNLAKKYMGDYSFIKAKINANIEQSYVEVNENERFEALCRLLKNKEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIINRREYKKLRYIERAMKLKIKKLK 365
               SCOP domains d1hv8a1 A:3-210 Putative DEAD box RNA helicase                                                                                                                                                                  d1hv8a2 A:211-365 Putative DEAD box RNA helicase                                                                                                            SCOP domains
               CATH domains 1hv8A01 A:3-210 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                            ---1hv8A02 A:214-364 P-loop containing nucleotide triphosphate hydrolases                                                                                 - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh..hhhhhhhhhhhh....hhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhh.......eeee..hhhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhh..eeeehhhhhhhhhhh.........eeeeehhhhhhh..hhhhhhhhhhh.....eeeee....hhhhhhhhhhhh..eeeee.......eeeeee.hhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhh....eeee..hhhhhh......eeee.....hhhhhhhhh..........eeeeee...hhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---Q_MOTIF  PDB: A:6-34         ---------------------------------------------------------------------------------------------------------------------DEAD_ATP_------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hv8 A   3 VEYmNFNELNLSDNILNAIRNKGFEKPTDIQmKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNENNGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALKNANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEmLNmGFIKDVEKILNACNKDKRILLFSATmPREILNLAKKYmGDYSFIKAKINANIEQSYVEVNENERFEALCRLLKNKEFYGLVFCKTKRDTKELASmLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVmSRGIDVNDLNCVINYHLPQNPESYmHRIGRTGRAGKKGKAISIINRREYKKLRYIERAmKLKIKKLK 365
                               |    12        22        32 |      42        52        62        72        82        92       102       112       122       132       142       152      |162       172       182     | 192       202       212       222       232       242       252    |  262       272       282       292     | 302       312       322|      332       342       352    |  362   
                               |                          34-MSE                                                                                                                      159-MSE                      188-MSE     200-MSE                                                  257-MSE                                  298-MSE                  323-MSE                           357-MSE    
                               6-MSE                                                                                                                                                     162-MSE                                                                                                                                                                                                       

Chain B from PDB  Type:PROTEIN  Length:363
 aligned with H669_METJA | Q58083 from UniProtKB/Swiss-Prot  Length:367

    Alignment length:363
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362   
           H669_METJA     3 VEYMNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNENNGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALKNANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNMGFIKDVEKILNACNKDKRILLFSATMPREILNLAKKYMGDYSFIKAKINANIEQSYVEVNENERFEALCRLLKNKEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIINRREYKKLRYIERAMKLKIKKLK 365
               SCOP domains d1hv8b1 B:3-210 Putative DEAD box RNA helicase                                                                                                                                                                  d1hv8b2 B:211-365 Putative DEAD box RNA helicase                                                                                                            SCOP domains
               CATH domains 1hv8B01 B:3-210 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                            ---1hv8B02 B:214-355 P-loop containing nucleotide triphosphate hydrolases                                                                        ---------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh..hhhhhhhhhhhh....hhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhh.......eeee..hhhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhh..eeeehhhhhhhhhhh...hhhhh.eeeeehhhhhhh..hhhhhhhhhhh.....eeeeee...hhhhhhhhhhhh..eeeee.......eeeeeeehhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhh....eeee..hhhhhh......eeee.....hhhhhhhhh..........eeeeeee..hhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---Q_MOTIF  PDB: B:6-34         ---------------------------------------------------------------------------------------------------------------------DEAD_ATP_------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hv8 B   3 VEYmNFNELNLSDNILNAIRNKGFEKPTDIQmKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNENNGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALKNANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEmLNmGFIKDVEKILNACNKDKRILLFSATmPREILNLAKKYmGDYSFIKAKINANIEQSYVEVNENERFEALCRLLKNKEFYGLVFCKTKRDTKELASmLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVmSRGIDVNDLNCVINYHLPQNPESYmHRIGRTGRAGKKGKAISIINRREYKKLRYIERAmKLKIKKLK 365
                               |    12        22        32 |      42        52        62        72        82        92       102       112       122       132       142       152      |162       172       182     | 192       202       212       222       232       242       252    |  262       272       282       292     | 302       312       322|      332       342       352    |  362   
                               6-MSE                      34-MSE                                                                                                                      159-MSE                      188-MSE     200-MSE                                                  257-MSE                                  298-MSE                  323-MSE                           357-MSE    
                                                                                                                                                                                         162-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  (1, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1HV8)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (H669_METJA | Q58083)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004004    ATP-dependent RNA helicase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of an RNA helix.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    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.
biological process
    GO:0010501    RNA secondary structure unwinding    The process in which a secondary structure of RNA are broken or 'melted'.

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