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(-) Description

Title :  CRYO EM STRUCTURE OF THE CONJUGATIVE RELAXASE TRAI OF THE F/R1 PLASMID SYSTEM
 
Authors :  A. Ilangovan, G. Zanetti, G. Waksman
Date :  23 Feb 17  (Deposition) - 03 May 17  (Release) - 28 Jun 17  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  3.90
Chains :  Asym./Biol. Unit :  A,C
Keywords :  Relaxase, Cryo Em, Helicase, Translocase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Ilangovan, C. W. M. Kay, S. Roier, H. El Mkami, E. Salvadori, E. L. Zechner, G. Zanetti, G. Waksman
Cryo-Em Structure Of A Relaxase Reveals The Molecular Basis Of Dna Unwinding During Bacterial Conjugation
Cell V. 169 708 2017
PubMed-ID: 28457609  |  Reference-DOI: 10.1016/J.CELL.2017.04.010

(-) Compounds

Molecule 1 - DNA HELICASE I
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: TRAI
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
 
Molecule 2 - DNA (5'- D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
    Chains: C
    Engineered: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5N8O)

(-) Sites  (0, 0)

(no "Site" information available for 5N8O)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5N8O)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Ala A:442 -Ala A:443
2Gly A:460 -Arg A:461
3Pro A:501 -Gly A:502
4Thr A:983 -Ser A:984
5Arg A:1118 -Ser A:1119
6Ile A:1204 -Pro A:1205
7Asp A:1291 -Asn A:1292
8Gly A:1418 -Thr A:1419

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5N8O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5N8O)

(-) Exons   (0, 0)

(no "Exon" information available for 5N8O)

(-) 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:1432
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....hhhhhhhh.............eeehhhhhhh......hhhhhhhhhhh..........ee..ee.....eeeee..hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.eeeeee..eeeeee.....eee.........................................hhhhhhhhhhhhhhhhhhhhhhhhhhhh........................hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.......hhhhhhhhhhhh.....hh.hhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhh....................hhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhh............................................ee..hhhhh.hhhhhhhhhhhhh....eeeee..........hhhhhh....eee.........ee.....hhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhhh.......eee.......................eeeeee....eeeeee...ee....eee.........eee.hhh...........eee.....eee............eee.........ee..........ee....hhhhh..eee..ee..........eeee.....................ee....................hhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhh.......hhhhhhhhhh......hhhhhhhhhhhhhh.....................hhhhhhhhhhhhhhhhh....................hhhhhh........eee.........hhhhhhhhhhhhh.........eee..hhhhhhhhhhh...ee.hhhhhhhhhhhhhh..........eee.hhhhh.hhhhhhhhhh.......eee...............hhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhh........................hhhhhhhhhhhhh.............hhhhhhhhh..hhhhh.eeeee....hhhhhhhhhhhhhhhhh........eeeeeee....hhhhhhhhhhh...ee.........eeeeee....eeeee.......ee...........eeeeeeee.....eeee.............eee........eee......eee....hhhhh.ee...eee..........eee.............hhhhhhhhh......ee......hhhhhhhhh.....hhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5n8o A    1 MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGKGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQDGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLVMALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEALGYETEVVGKHGMWEMPGVPVEAFSVDPEIRMAEWMQTLKETGFDIRAYRDAADQRTEIRTQAPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPENGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYSDAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGRRQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRWQGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVTMTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDSSWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVSDSPFTALKLENGWVETPGHSVSDSATVFASVTQMAMNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQIKARAGETLLETAISLQKAGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINAQIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMILETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDTQLQQRSGETPDFSNTLFLLDESSMVGNTEMARAYALIAAGGGRAVASGDTDQLQAIAPGQSFRLQQTRSAADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRLEGAWAPEHSVTEFSHSQEAKLAEAQQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVMVPVLNTANIRDGELRRLSTWEKNPDALALVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVTLYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAITAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVLEPK 1473
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230    || 272       282       292       302   ||  320       330       340       350       360       370       380       390       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       670       680       690       700       710       720       730       740       750       760       770       780       790      |801       811       821       831       841       851       861       871       881       891       901       911       921       931       941       951       961       971       981       991      1001      1011      1021      1031      1041      1051      1061      1071      1081      1091      1101      1111      1121      1131      1141      1151      1161      1171      1181      1191      1201      1211      1221      1231      1241      1251      1261      1271      1281      1291      1301      1311      1321      1331      1341      1351      1361      1371      1381      1391      1401      1411      1421      1431      1441      1451      1461      1471  
                                                                                                                                                                                                                                                                    235|                                   306|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               797|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
                                                                                                                                                                                                                                                                     268                                    315                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                799                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  


Chain C from PDB  Type:DNA  Length:18
                                                   
                5n8o C    5 TTTTTTTTTTTTTTTTTT   22
                                    14
   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 5N8O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5N8O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5N8O)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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  Sites
(no "Sites" information available for 5n8o)
 
  Cis Peptide Bonds
    Ala A:442 - Ala A:443   [ RasMol ]  
    Arg A:1118 - Ser A:1119   [ RasMol ]  
    Asp A:1291 - Asn A:1292   [ RasMol ]  
    Gly A:1418 - Thr A:1419   [ RasMol ]  
    Gly A:460 - Arg A:461   [ RasMol ]  
    Ile A:1204 - Pro A:1205   [ RasMol ]  
    Pro A:501 - Gly A:502   [ RasMol ]  
    Thr A:983 - Ser A:984   [ RasMol ]  
 

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 Related Entries

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UniProtKB/TrEMBL
        Q6TDU5_ECOLX | Q6TDU5: 4l0j

(-) Related Entries Specified in the PDB File

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