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(-) Description

Title :  HUMAN MITOCHONDRIAL HELICASE SUV3
 
Authors :  Z. Dauter, R. Jedrzejczak, M. Dauter, R. Szczesny, P. Stepien
Date :  30 Mar 11  (Deposition) - 11 May 11  (Release) - 28 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.08
Chains :  Asym./Biol. Unit :  A
Keywords :  Helicase, Mitochondria, Suv3, Nucleus, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Jedrzejczak, J. Wang, M. Dauter, R. J. Szczesny, P. P. Stepien, Z. Dauter
Human Suv3 Protein Reveals Unique Features Among Sf2 Helicases.
Acta Crystallogr. , Sect. D V. 67 988 2011
PubMed-ID: 22101826  |  Reference-DOI: 10.1107/S0907444911040248

(-) Compounds

Molecule 1 - ATP-DEPENDENT RNA HELICASE SUPV3L1, MITOCHONDRIAL
    ChainsA
    EC Number3.6.4.13
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPDEST-HISMBP
    Expression System StrainBL21(DE3)RIL
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentRESIDUES 47-722
    GeneSUPV3L1, SUV3
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSUPPRESSOR OF VAR1 3-LIKE PROTEIN 1, SUV3-LIKE PROTEIN 1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 18)

Asymmetric/Biological Unit (5, 18)
No.NameCountTypeFull Name
1ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2AZI1Ligand/IonAZIDE ION
3CL1Ligand/IonCHLORIDE ION
4MSE14Mod. Amino AcidSELENOMETHIONINE
5NA1Ligand/IonSODIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:24 , THR A:209 , ASN A:210 , SER A:211 , GLY A:212 , LYS A:213 , THR A:214 , TYR A:215 , LEU A:348 , ASN A:415 , PRO A:417 , MSE A:429 , GLN A:466 , ARG A:470 , ARG A:473 , PHE A:474 , SER A:475 , HOH A:730 , HOH A:820 , HOH A:839 , HOH A:841 , HOH A:855 , HOH A:859 , HOH A:904 , HOH A:1018 , HOH A:1029 , HOH A:1067 , HOH A:1098 , HOH A:1100BINDING SITE FOR RESIDUE ANP A 801
2AC2SOFTWAREHOH A:1 , HOH A:2 , HOH A:3 , HOH A:4 , SER A:392 , AZI A:902BINDING SITE FOR RESIDUE NA A 901
3AC3SOFTWARESER A:392 , GLN A:407 , LYS A:410 , HIS A:671 , NA A:901BINDING SITE FOR RESIDUE AZI A 902
4AC4SOFTWAREHOH A:18 , LEU A:529BINDING SITE FOR RESIDUE CL A 903

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3RC3)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Trp A:614 -Pro A:615

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3RC3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3RC3)

(-) Exons   (0, 0)

(no "Exon" information available for 3RC3)

(-) 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:607
 aligned with SUV3_HUMAN | Q8IYB8 from UniProtKB/Swiss-Prot  Length:786

    Alignment length:632
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       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       587       597       607       617       627       637       647       657       667       677       687  
           SUV3_HUMAN    58 IPNTSLFVPLTVKPQGPSADGDVGAELTRPLDKNEVKKVLDKFYKRKEIQKLGADYGLDARLFHQAFISFRNYIMQSHSLDVDIHIVLNDICFGAAHADDLFPFFLRHAKQIFPVLDCKDDLRKISDLRIPPNWYPDARAMQRKIIFHSGPTNSGKTYHAIQKYFSAKSGVYCGPLKLLAHEIFEKSNAAGVPCDLVTGEERVTVQPNGKQASHVSCTVEMCSVTTPYEVAVIDEIQMIRDPARGWAWTRALLGLCAEEVHLCGEPAAIDLVMELMYTTGEEVEVRDYKRLTPISVLDHALESLDNLRPGDCIVCFSKNDIYSVSRQIEIRGLESAVIYGSLPPGTKLAQAKKFNDPNDPCKILVATDAIGMGLNLSIRRIIFYSLIKPSINEKGERELEPITTSQALQIAGRAGRFSSRFKEGEVTTMNHEDLSLLKEILKRPVDPIRAAGLHPTAEQIEMFAYHLPDATLSNLIDIFVDFSQVDGQYFVCNMDDFKFSAELIQHIPLSLRVRYVFCTAPINKKQPFVCSSLLQFARQYSRNEPLTFAWLRRYIKWPLLPPKNIKDLMDLEAVHDVLDLYLWLSYRFMDMFPDASLIRDLQKELDGIIQDGVHNITKLIKMSETHKLLNLE 689
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------              --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Helicase_C-3rc3A01 A:383-475                                                                 -----------------------------------------------------------------------------------------------------------------------------------------------------SUV3_C-3rc3A02 A:625-673                         ---------------- Pfam domains
         Sec.struct. author ..hhhhh........--------------..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhh...eeee....ee..........eeeee.hhh.....eeeeee.hhhhhhh..hhhhhhhhhhhh.eeeeeeeehhhhhhhhhhhhhhhh..eeeee......eee......hhhhh...eeee..hhhhhhhhhhhhhhh....eee....hhhhhhhhhhhhhh......eeee.hhhhh.......eeee.....-----------...hhhhhhhhhh...........eeeee...hhhhhhhhhhhh.......eee..hhhhhhhhhhhh...hhhhhhhhhhhhh.....eee..hhhhhhhhhhh.....hhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....hhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rc3 A  58 IPNTSLFVPLTVKPQ--------------PLDKNEVKKVLDKFYKRKEIQKLGADYGLDARLFHQAFISFRNYImQSHSLDVDIHIVLNDICFGAAHADDLFPFFLRHAKQIFPVLDCKDDLRKISDLRIPPNWYPDARAmQRKIIFHSGPTNSGKTYHAIQKYFSAKSGVYCGPLKLLAHEIFEKSNAAGVPCDLVTGEERVTVQPNGKQASHVSCTVEmCSVTTPYEVAVIDEIQmIRDPARGWAWTRALLGLCAEEVHLCGEPAAIDLVmELmYTTGEEVEVRDYKRLTPISVLDHALESLDNLRPGDCIVCFSKNDIYSVSRQIEIRGLESAVIYGSLPPGTKLAQAKKFNDPNDPCKILVATDAIGmGLNLSIRRIIFYSLIK-----------EPITTSQALQIAGRAGRFSSRFKEGEVTTmNHEDLSLLKEILKRPVDPIRAAGLHPTAEQIEmFAYHLPDATLSNLIDIFVDFSQVDGQYFVCNmDDFKFSAELIQHIPLSLRVRYVFCTAPINKKQPFVCSSLLQFARQYSRNEPLTFAWLRRYIKWPLLPPKNIKDLmDLEAVHDVLDLYLWLSYRFmDmFPDASLIRDLQKELDGIIQDGVHNITKLIKmSETHKLLNLE 689
                                    67    |    -        87        97       107       117       127    |  137       147       157       167       177       187       197|      207       217       227       237       247       257       267       277|      287       297       307       317       327  |  | 337       347       357       367       377       387       397       407       417       427 |     437       | -       457       467       477       487       497       507       517 |     527       537       547   |   557       567       577       587       597       607       617       627       637       647|      657       667       677 |     687  
                                         72             87                                          132-MSE                                                           198-MSE                                                                         278-MSE          295-MSE                            330-MSE                                                                                            429-MSE         445         457                          486-MSE                          519-MSE                         551-MSE                                                                    626-MSE             646-MSE                          679-MSE      
                                                                                                                                                                                                                                                                                                             333-MSE                                                                                                                                                                                                                                                                                                                    648-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  (0, 0)

(no "SCOP Domain" information available for 3RC3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3RC3)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (31, 31)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SUV3_HUMAN | Q8IYB8)
molecular function
    GO:0034458    3'-5' RNA helicase activity    Catalysis of the unwinding of an RNA helix in the direction 3' to 5'.
    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:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003678    DNA helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA helix.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003725    double-stranded RNA binding    Interacting selectively and non-covalently with double-stranded RNA.
    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:0016817    hydrolase activity, acting on acid anhydrides    Catalysis of the hydrolysis of any acid anhydride.
    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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0032508    DNA duplex unwinding    The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating a region of unpaired single strands.
    GO:0006310    DNA recombination    Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
    GO:0006401    RNA catabolic process    The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
    GO:0070827    chromatin maintenance    The chromatin organization process that preserves chromatin in a stable functional or structural state.
    GO:0000965    mitochondrial RNA 3'-end processing    Any process involved in forming the mature 3' end of an RNA molecule transcribed from a mitochondrial genome; occurs in the mitochondrion.
    GO:2000827    mitochondrial RNA surveillance    The set of processes involved in identifying and degrading defective or aberrant RNAs that takes place in the mitochondrion.
    GO:0000958    mitochondrial mRNA catabolic process    The chemical reactions and pathways resulting in the breakdown of mRNA transcribed from the mitochondrial genome and occurring in the mitochondrion.
    GO:0035946    mitochondrial mRNA surveillance    The set of processes involved in identifying and degrading messenger RNA (mRNA) within the mitochondrion.
    GO:0035945    mitochondrial ncRNA surveillance    The set of processes involved in identifying and degrading defective or aberrant non-coding RNA transcripts (ncRNAs) within the mitochondrion.
    GO:0070584    mitochondrion morphogenesis    The process in which the anatomical structures of a mitochondrion are generated and organized.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0030307    positive regulation of cell growth    Any process that activates or increases the frequency, rate, extent or direction of cell growth.
    GO:0000962    positive regulation of mitochondrial RNA catabolic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving catabolism in the mitochondrion of RNA transcribed from the mitochondrial genome.
cellular component
    GO:0045025    mitochondrial degradosome    A mitochondrial protein complex with 3' to 5' exoribonuclease activity that participates in intron-independent turnover and processing of mitochondrial transcripts. In humans, the mitochondrial degradosome is a pentameric complex, and in yeast it exists as a heterodimer.
    GO:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    GO:0042645    mitochondrial nucleoid    The region of a mitochondrion to which the DNA is confined.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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        SUV3_HUMAN | Q8IYB83rc8

(-) Related Entries Specified in the PDB File

3rc8 SUV3 IN COMPLEX WITH SHORT RNA FRAGMENT