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(-) Description

Title :  STRUCTURE A OF GROUP II INTRON COMPLEXED WITH ITS REVERSE TRANSCRIPTASE
 
Authors :  G. Qu, P. S. Kaushal, J. Wang, H. Shigematsu, C. L. Piazza, R. K. Agrawal, M. Belfort, H. W. Wang
Date :  16 Apr 16  (Deposition) - 11 May 16  (Release) - 22 Jun 16  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  3.80
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Transferase, Group Ii Introns, Ribonucleoprotein, Intron-Encoded Protein, Retrotransposons And Spliceosom (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Qu, P. S. Kaushal, J. Wang, H. Shigematsu, C. L. Piazza, R. K. Agrawal M. Belfort, H. Wang
Structure Of A Group Ii Intron In Complex With Its Reverse Transcriptase.
Nat. Struct. Mol. Biol. V. 23 549 2016
PubMed-ID: 27136327  |  Reference-DOI: 10.1038/NSMB.3220

(-) Compounds

Molecule 1 - GROUP II INTRON
    Chains: A
    Engineered: YES
    Expression System: LACTOCOCCUS LACTIS
    Expression System Plasmid: PLNRK
    Expression System Strain: IL1403
    Expression System Taxid: 1358
    Expression System Vector Type: PLASMID
    Organism Scientific: LACTOCOCCUS LACTIS
    Organism Taxid: 1358
 
Molecule 2 - GROUP II INTRON-ENCODED PROTEIN LTRA
    Chains: C
    EC Number: 2.7.7.49, 3.1.-.-
    Engineered: YES
    Expression System: LACTOCOCCUS LACTIS
    Expression System Plasmid: PLNRK
    Expression System Strain: IL1403
    Expression System Taxid: 1358
    Expression System Vector Type: PLASMID
    Gene: LTRA, MATR
    Organism Scientific: LACTOCOCCUS LACTIS SUBSP. CREMORIS
    Organism Taxid: 1359
 
Molecule 3 - 5'-R(*CP*AP*CP*AP*UP*CP*CP*AP*UP*AP*AP*CP)-3'
    Chains: B
    Engineered: YES
    Expression System: LACTOCOCCUS LACTIS
    Expression System Plasmid: PLNRK
    Expression System Strain: IL1403
    Expression System Taxid: 1358
    Expression System Vector Type: PLASMID
    Gene: LTRA, MATR
    Organism Scientific: LACTOCOCCUS LACTIS SUBSP. CREMORIS
    Organism Taxid: 1359

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5G2X)

(-) Sites  (0, 0)

(no "Site" information available for 5G2X)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5G2X)

(-) Cis Peptide Bonds  (26, 26)

Asymmetric/Biological Unit
No.Residues
1Asn C:18 -Ile C:19
2Phe C:23 -Thr C:24
3Tyr C:44 -Ser C:45
4Asn C:46 -Lys C:47
5Gly C:48 -Ala C:49
6Glu C:64 -Glu C:65
7Glu C:65 -Lys C:66
8Asp C:76 -Gly C:77
9Thr C:78 -Tyr C:79
10Glu C:123 -Pro C:124
11Thr C:207 -Tyr C:208
12Gly C:210 -Thr C:211
13Thr C:249 -Pro C:250
14Gly C:316 -Ser C:317
15Lys C:344 -Thr C:345
16His C:349 -Ser C:350
17Val C:375 -Lys C:376
18Lys C:407 -Lys C:408
19Val C:415 -His C:416
20His C:416 -Arg C:417
21Lys C:418 -Tyr C:419
22Asp C:484 -Gly C:485
23Ser C:486 -Gly C:487
24Gly C:487 -Ser C:488
25Tyr C:527 -Gly C:528
26Lys C:541 -Cys C:542

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5G2X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5G2X)

(-) Exons   (0, 0)

(no "Exon" information available for 5G2X)

(-) 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:RNA  Length:692
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
                5g2x A    1 GUGCGCCCAGAUAGGGUGUUAAGUCAAGUAGUUUAAGGUACUACUCUGUAAGAUAACACAGAAAACAGCCAACCUAACCGAAAAGCGAAAGCUGAUACGGGAACAGAGCACGGUUGGAAAGCGAUGAGUUACCUAAAGACAAUCGGGUACGACUGAGUCGCAAUGUUAAUCAGAUAUAAGGUAUAAGUUGUGUUUACUGAACGCAAGUUUCUAAUUUCGGUUAUGUGUCGAUAGAGGAAAGUGUCUGAAACCUCUAGUACAAAGAAAGGUAAGUUAUGGUUGUGGACUUAUCUGUUAUCACCACAUUUGUACAAUCUGUAGGAGAACCUAUGGGAACGAAACGAAAGCGAUGCCGAGAAUCUGAAUUUACCAAGACUUAACACUAACUGGGGAUACCCUAAACAAGAAUGCCUAAAGGAGGAAAAAGGCUAUAGCACUAGAGCUUGAAAAUCUUGCAAGGGUACGGAGUACUCGUAGUAGUCUGAGAAGGGUAACGCCCUUUACAUGGCAAAGGGGUACAGUUAUUGUGUACUAAAAUUAAAAAUUGAUUAGGGAGGAAAACCUCAAACCAACAAUGGCAAUUUUAGACAAUAACAGAGCCGUAUACUCCGAGAGGGGUACGUACGGUUCCCGAAGAGGGUGGUGCAAACCAGUCACAGUAAUGUGAACAAGGCGGUACCUCCCUACUUCAC 2492
                                    10        20        30        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       360       370       380       390       400       410   ||  425       435       445       455       465       475       485       495       505       515       525       535       545       555       565      |581       591      2390      2400      2410      2420      2430      2440      2450      2460      2470      2480      2490  
                                                                                                                                                                                                                                                                                                                                                                                                                                                       414|                                                                                                                                                     572|                598|                                                                                                        
                                                                                                                                                                                                                                                                                                                                                                                                                                                        420                                                                                                                                                      579                2388                                                                                                        


Chain B from PDB  Type:RNA  Length:12
                                             
                5g2x B    1 CACAUCCAUAAC   12
                                    10  


Chain C from PDB  Type:PROTEIN  Length:487
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh................hhhhhhhhhhhh........eee......eee......hhhhhh............eeeeee....eeeeee....hhhhhhhhhhhhhhhh..................hhhhhhhhh.......eeee...........hhhhhhhhh.......hhhhhhhhhhheee...eee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee....eee.....hhhhhhhhhhhhhh.........hhh........eeeee..eeeee...........eeee...hhhhhhhh........................hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh......eeeeee......eeeeee............hhhhhhhhhh.............hh.eeeee....eeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5g2x C    4 TMAILERISKNSQENIDEVFTRLYRYLLRPDIYYVAYQNLYSNKGASTKGILDDTADGFSEEKIKKIIQSLKDGTYYPQPVRRMYIAKKNSKKMRPLGIPTFTDKLIQEAVRIILESIYEPVFEDVSHGFRPQRSCHTALKTIKREFGGARWFVEGDIKGCFDNIDHVTLIGLINLKIKDMKMSQLIYKFLKAGYLENWQYHKTYSGTPQGGILSPLLANIYLHELDKFVLQLKMKFDRESPERITPEKYVRYADDFIISVKGSKEDCQWIKEQLKLFIHNKLKMELSEEKTLITHSSQPARFLGYDIRVVKKRTLNGSVELLIPLQDKIRQFIFDKKIAIQKKDSSWFPVHRKYLIRSTDLEIITIYNSELRGICNYYGLASNFNQLNYFAYLMEYSCLKTIASKHKGTLSKTISMFKDGSGSWGIPYEIKQGKQRRVLYGYARNTLENRLKAKCCELCGTSDENTSYEIHHVNRKTLVVCFHCHR  592
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       303       313       323       333       343       353       363|      384       394       404       414       424       434       444       454       464       474       484       494       526       536       546       556    || 585       
                                                                                                                                                                                                                                                                                 251|                                                          363|                                                                                                                            502|                                 561|           
                                                                                                                                                                                                                                                                                  302                                                           375                                                                                                                             525                                  581
   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 5G2X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5G2X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5G2X)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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Asymmetric/Biological Unit
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  Ligands, Modified Residues, Ions
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  Sites
(no "Sites" information available for 5g2x)
 
  Cis Peptide Bonds
    Asn C:18 - Ile C:19   [ RasMol ]  
    Asn C:46 - Lys C:47   [ RasMol ]  
    Asp C:484 - Gly C:485   [ RasMol ]  
    Asp C:76 - Gly C:77   [ RasMol ]  
    Glu C:123 - Pro C:124   [ RasMol ]  
    Glu C:64 - Glu C:65   [ RasMol ]  
    Glu C:65 - Lys C:66   [ RasMol ]  
    Gly C:210 - Thr C:211   [ RasMol ]  
    Gly C:316 - Ser C:317   [ RasMol ]  
    Gly C:48 - Ala C:49   [ RasMol ]  
    Gly C:487 - Ser C:488   [ RasMol ]  
    His C:349 - Ser C:350   [ RasMol ]  
    His C:416 - Arg C:417   [ RasMol ]  
    Lys C:344 - Thr C:345   [ RasMol ]  
    Lys C:407 - Lys C:408   [ RasMol ]  
    Lys C:418 - Tyr C:419   [ RasMol ]  
    Lys C:541 - Cys C:542   [ RasMol ]  
    Phe C:23 - Thr C:24   [ RasMol ]  
    Ser C:486 - Gly C:487   [ RasMol ]  
    Thr C:207 - Tyr C:208   [ RasMol ]  
    Thr C:249 - Pro C:250   [ RasMol ]  
    Thr C:78 - Tyr C:79   [ RasMol ]  
    Tyr C:44 - Ser C:45   [ RasMol ]  
    Tyr C:527 - Gly C:528   [ RasMol ]  
    Val C:375 - Lys C:376   [ RasMol ]  
    Val C:415 - His C:416   [ RasMol ]  
 

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 Related Entries

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(-) Related Entries Specified in the PDB File

5g2y STRUCTURE A OF GROUP II INTRON COMPLEXED WITH ITS REVERSE TRANSCRIPTASE RELATED ID: EMD-3331 RELATED DB: EMDB