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(-) Description

Title :  THE CLOSED RING STRUCTURE OF THE RHO TRANSCRIPTION TERMINATION FACTOR IN COMPLEX WITH NUCLEIC ACID IN THE MOTOR DOMAINS
 
Authors :  E. Skordalakes, J. M. Berger
Date :  24 Jul 06  (Deposition) - 14 Nov 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.51
Chains :  Asym. Unit :  A,B,J,K,M
Biol. Unit 1:  A,B,J,K,M  (3x)
Keywords :  Atpase, Translocase, Hydrolase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Skordalakes, J. M. Berger
Structural Insights Into Rna-Dependent Ring Closure And Atpase Activation By The Rho Termination Factor.
Cell(Cambridge, Mass. ) V. 127 553 2006
PubMed-ID: 17081977  |  Reference-DOI: 10.1016/J.CELL.2006.08.051

(-) Compounds

Molecule 1 - 5'-R(*UP*C)-3'
    ChainsJ, K
    EngineeredYES
    SyntheticYES
 
Molecule 2 - 5'-R(*UP*CP*UP*CP*U)-3'
    ChainsM
    EngineeredYES
    SyntheticYES
 
Molecule 3 - TRANSCRIPTION TERMINATION FACTOR RHO
    ChainsA, B
    EC Number3.6.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28B
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneRHO, NITA, PSUA, RNSC, SBAA, TSU
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymATP-DEPENDENT HELICASE RHO

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit ABJKM
Biological Unit 1 (3x)ABJKM

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:181 , ALA A:182 , GLY A:183 , LYS A:184 , THR A:185BINDING SITE FOR RESIDUE SO4 A 600
2AC2SOFTWARELYS B:181 , ALA B:182 , GLY B:183 , LYS B:184 , THR B:185BINDING SITE FOR RESIDUE SO4 B 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2HT1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2HT1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2HT1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2HT1)

(-) Exons   (0, 0)

(no "Exon" information available for 2HT1)

(-) 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:324
 aligned with RHO_ECOLI | P0AG30 from UniProtKB/Swiss-Prot  Length:419

    Alignment length:324
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350    
            RHO_ECOLI    31 KQDIIFAILKQHAKSGEDIFGDGVLEILQDGFGFLRSADSSYLAGPDDIYVSPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVNEVNFDKPENARNKILFENLTPLHANSRLRMERGNGSTEDLTARVLDLASPIGRGQRGLIVAPPKAGKTMLLQNIAQSIAYNHPDCVLMVLLIDERPEEVTEMQRLVKGEVVASTFDEPASRHVQVAEMVIEKAKRLVEHKKDVIILLDSITRLARAYNTVVPASGKVLTGGVDANALHRPKRFFGAARNVEEGGSLTIIATALIDTGSKMDEVIYEEFKGTGNMELHLSRKIAEKRV 354
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhh..........eee.......eeeehhhhh.......eeehhhhhhhh......ee...ee........eee.........hhhhhh...hhhhh.ee.......ee.....hhhhhh.hhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhhh...eeeeeeeeehhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhhh...............hhhhhhhhhh.eee....eeeeeeeee....hhhhhhhhhhhh....eeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ht1 A  31 KQDIIFAILKQHAKSGEDIFGDGVLEILQDGFGFLRSADSSYLAGPDDIYVSPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVNEVNFDKPENARNKILFENLTPLHANSRLRMERGNGSTEDLTARVLDLASPIGRGQRGLIVAPPKAGKTMLLQNIAQSIAYNHPDCVLMVLLIDERPEEVTEMQRLVKGEVVASTFDEPASRHVQVAEMVIEKAKRLVEHKKDVIILLDSITRLARAYNTVVPASGKVLTGGVDANALHRPKRFFGAARNVEEGGSLTIIATALIDTGSKMDEVIYEEFKGTGNMELHLSRKIAEKRV 354
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350    

Chain B from PDB  Type:PROTEIN  Length:324
 aligned with RHO_ECOLI | P0AG30 from UniProtKB/Swiss-Prot  Length:419

    Alignment length:324
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350    
            RHO_ECOLI    31 KQDIIFAILKQHAKSGEDIFGDGVLEILQDGFGFLRSADSSYLAGPDDIYVSPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVNEVNFDKPENARNKILFENLTPLHANSRLRMERGNGSTEDLTARVLDLASPIGRGQRGLIVAPPKAGKTMLLQNIAQSIAYNHPDCVLMVLLIDERPEEVTEMQRLVKGEVVASTFDEPASRHVQVAEMVIEKAKRLVEHKKDVIILLDSITRLARAYNTVVPASGKVLTGGVDANALHRPKRFFGAARNVEEGGSLTIIATALIDTGSKMDEVIYEEFKGTGNMELHLSRKIAEKRV 354
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhh........ee..eeee.....eeee.............eehhhhhhhh.........ee...............................hhhhh.ee......eee....hhhhhhhhhhhhh.......eeeeee....hhhhhhhhhhhhhhhhh...eeeeeeeeehhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh..eee....eeeeeeeee....hhhhhhhhhhhh....eee....hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ht1 B  31 KQDIIFAILKQHAKSGEDIFGDGVLEILQDGFGFLRSADSSYLAGPDDIYVSPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVNEVNFDKPENARNKILFENLTPLHANSRLRMERGNGSTEDLTARVLDLASPIGRGQRGLIVAPPKAGKTMLLQNIAQSIAYNHPDCVLMVLLIDERPEEVTEMQRLVKGEVVASTFDEPASRHVQVAEMVIEKAKRLVEHKKDVIILLDSITRLARAYNTVVPASGKVLTGGVDANALHRPKRFFGAARNVEEGGSLTIIATALIDTGSKMDEVIYEEFKGTGNMELHLSRKIAEKRV 354
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350    

Chain J from PDB  Type:RNA  Length:2
                                  
                 2ht1 J   1 UC   2

Chain K from PDB  Type:RNA  Length:2
                                  
                 2ht1 K   1 UC   2

Chain M from PDB  Type:RNA  Length:5
                                     
                 2ht1 M   1 UCUCU   5

   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 2HT1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2HT1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2HT1)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (RHO_ECOLI | P0AG30)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0008186    RNA-dependent ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of RNA, and it drives another reaction.
    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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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.
    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).
biological process
    GO:0006353    DNA-templated transcription, termination    The cellular process that completes DNA-templated transcription; the formation of phosphodiester bonds ceases, the RNA-DNA hybrid dissociates, and RNA polymerase releases the DNA.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RHO_ECOLI | P0AG301a62 1a63 1a8v 1pv4 1pvo 1xpo 1xpr 1xpu 2a8v 3ice 5jji 5jjk 5jjl

(-) Related Entries Specified in the PDB File

1pv4 X-RAY CRYSTAL STRUCTURE OF THE RHO TRANSCRIPTION TERMINATION FACTOR IN COMPLEX WITH SINGLE STRANDED DNA
1pvo X-RAY CRYSTAL STRUCTURE OF RHO TRANSCRIPTION TERMINATION FACTOR IN COMPLEX WITH SSRNA SUBSTRATE AND ANPPNP