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(-) Description

Title :  STRUCTURAL BASIS OF CO-TRANSLATIONAL QUALITY CONTROL BY ARFA AND RF2 BOUND TO RIBOSOME
 
Authors :  F. Zeng, Y. Chen, J. Remis, M. Shekhar, J. C. Phillips, E. Tajkhorshid, H
Date :  04 Dec 16  (Deposition) - 11 Jan 17  (Release) - 08 Feb 17  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  3.70
Chains :  Asym./Biol. Unit :  A,a,c,d,e,l,v,w,x,z
Keywords :  Ribosome, Arfa, Rf2, Nonstop Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Zeng, Y. Chen, J. Remis, M. Shekhar, J. C. Phillips, E. Tajkhorshid, H. Jin
Structural Basis Of Co-Translational Quality Control By Arf And Rf2 Bound To Ribosome.
Nature V. 541 554 2017
PubMed-ID: 28077875  |  Reference-DOI: 10.1038/NATURE21053

(-) Compounds

Molecule 1 - 16S RRNA
    Chains: a
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: MRE600
 
Molecule 2 - 23S RRNA
    Chains: A
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: MRE600
 
Molecule 3 - 30S RIBOSOMAL PROTEIN S3
    Chains: c
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: GENE NAME(S): RPSC B3314 JW3276
    Strain: MRE600
 
Molecule 4 - 30S RIBOSOMAL PROTEIN S4
    Chains: d
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: GENE NAME(S): RPSD RAMA B3296 JW3258
    Strain: MRE600
 
Molecule 5 - 30S RIBOSOMAL PROTEIN S5
    Chains: e
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: GENE NAME(S): RPSE SPC B3303 JW3265
    Strain: MRE600
 
Molecule 6 - MRNA
    Chains: z
    Engineered: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synthetic: YES
 
Molecule 7 - P-SITE TRNA FMET
    Chains: x
    Engineered: YES
 
Molecule 8 - 30S RIBOSOMAL PROTEIN S12
    Chains: l
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: GENE NAME(S): RPSL STRA B3342 JW3304
    Strain: MRE600
 
Molecule 9 - PEPTIDE CHAIN RELEASE FACTOR 2
    Chains: v
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PRFB, SUPK, B2891, JW5847
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: GENE NAME(S): PRFB ECK2886 JW5847 SUPK
    Strain: MRE600
    Synonym: RF-2
 
Molecule 10 - ALTERNATIVE RIBOSOME-RESCUE FACTOR A
    Chains: w
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: ARFA, YHDL, B4550, JW3253
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: GENE NAME(S): ARFA ECK3278 JW3253 YHDL
    Strain: MRE600

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric/Biological Unit : Aacdelvwxz

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 10)

Asymmetric/Biological Unit (7, 10)
No.NameCountTypeFull Name
12MG1Mod. Nucleotide2N-METHYLGUANOSINE-5'-MONOPHOSPHATE
24OC1Mod. Nucleotide4N,O2'-METHYLCYTIDINE-5'-MONOPHOSPHATE
35MC1Mod. Nucleotide5-METHYLCYTIDINE-5'-MONOPHOSPHATE
4G7M1Mod. NucleotideN7-METHYL-GUANOSINE-5'-MONOPHOSPHATE
5MA62Mod. Nucleotide6N-DIMETHYLADENOSINE-5'-MONOPHOSHATE
6PSU3Mod. NucleotidePSEUDOURIDINE-5'-MONOPHOSPHATE
7UR31Mod. Nucleotide3-METHYLURIDINE-5'-MONOPHOSHATE

(-) Sites  (0, 0)

(no "Site" information available for 5U4J)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5U4J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5U4J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5U4J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5U4J)

(-) Exons   (0, 0)

(no "Exon" information available for 5U4J)

(-) 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:11
                                            
                5u4j A 1910 GuAACUAuAAC 1920
                             |    1919 
                             |     |   
                          1911-PSU |   
                                1917-PSU


Chain a from PDB  Type:RNA  Length:307
                                                                                                                                                                                                                                                                                                                                                    
                5u4j a    6 GAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUACCGGCUAACUCCGuGCCAGCAGCCgCGGUAAUACGGAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGACGUCAAGUCUUCCCGGGCCUUGUACACACCGcCCGUcACACCAUGGGAGUGGGUUCAUGACUGGGGUGAAGUCGuAACAAGGUAACCGUAGGgGaaCCUGCGGUUGGAUCA 1534
                                    15        25        35 ||    509      |519       529       539       549       559       569     ||883       893       903       913       923       933|     1062      1072      1082   || 1195    ||1384      1394      1404  |   1414      1477      1487      1497|     1507      1517||    1527       
                                                          37|           516-PSU    527-G7M                                         575|                                                  933|                             1086|      1200|                  1402-4OC|            1423|                 1498-UR3          1516-2MG              
                                                          502                                                                       880                                                  1053                              1190       1380                       1407-5MC         1477                                     1518-MA6            
                                                                                                                                                                                                                                                                                                                            1519-MA6           


Chain c from PDB  Type:PROTEIN  Length:21
                                                      
               SCOP domains --------------------- SCOP domains
               CATH domains --------------------- CATH domains
               Pfam domains --------------------- Pfam domains
         Sec.struct. author .eeeee........eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------- SAPs(SNPs)
                    PROSITE --------------------- PROSITE
                 Transcript --------------------- Transcript
                5u4j c  150 KVEVSGRLGGAEIARTEWYRE  170
                                   159       169 


Chain d from PDB  Type:PROTEIN  Length:65
                                                                                                  
               SCOP domains ----------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhh..........hhhhhh................hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                5u4j d    2 ARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQKVRRIYG   66
                                    11        21        31        41        51        61     


Chain e from PDB  Type:PROTEIN  Length:136
                                                                                                                                                                         
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeee....eeeeeeeeeeee....eeeeee....hhhhhhhhhhhhhhh..ee...........eeeee..eeeeeee......ee.hhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5u4j e   10 ELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAIQKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGVHNVLAKAYGSTNPINVVRATIDGLE  145
                                    19        29        39        49        59        69        79        89        99       109       119       129       139      


Chain l from PDB  Type:PROTEIN  Length:123
                                                                                                                                                            
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh...................eeeeeeeeeee.........eeeeeeee....eeeee............eeeee...........eee........................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                5u4j l    2 ATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNGFEVTSYIGGEGHNLQEHSVILIRGGRVKDLPGVRYHTVRGALDCSGVKDRKQARSKYGVKRPKA  124
                                    11        21        31        41        51        61        71        81        91       101       111       121   


Chain v from PDB  Type:PROTEIN  Length:132
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee...hhhhhhhhhhhhhhhhhhhhhh...eeeeeee.....eeeeeee....hhhhhh....eeeeeeee........eeeeeeeeeee....hhhhhhhhhhhhhhhhhhhh.....eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5u4j v  127 DCYLDIQAGSGGTEAQDWASMLERMYLRWAESRGFKTEIIEESEGEVAGIKSVTIKISGDYAYGWLRTETGVHRLVRKSPFDSGGRRHTSFSSAFVYPEVYELEMQKKNAEKQAMEDNKSDIGWGSQIRSYV  327
                                   136       146       156       166       176       186       196       206       216       226|      305       315       325  
                                                                                                                             226|                               
                                                                                                                              296                               


Chain w from PDB  Type:PROTEIN  Length:47
                                                                                
               SCOP domains ----------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhh.ee................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------- PROSITE
                 Transcript ----------------------------------------------- Transcript
                5u4j w    2 SRYQHTKGQIKDNAIEALLHDPLFRQRVEKNKKGKGSYMRKGKHGNR   48
                                    11        21        31        41       


Chain x from PDB  Type:RNA  Length:15
                                                
                5u4j x   28 UCGGGCUCAUAACCC   42
                                    37     


Chain z from PDB  Type:RNA  Length:6
                                       
                5u4j z   43 AAAAUG   48
   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 5U4J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5U4J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5U4J)

(-) Gene Ontology  (36, 72)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        ARFA_ECOLI | P36675: 5h5u 5mdv 5mdw 5mdy 5mgp 5u4i 5u9f 5u9g
        RF2_ECOLI | P07012: 1gqe 1mi6 1ml5 5czp 5dfe 5h5u 5mdv 5mdw 5mgp 5u4i 5u9f 5u9g
        RS12_ECOLI | P0A7S3: 1m5g 1mj1 1zn1 2ykr 3deg 3ep2 3eq3 3eq4 3iy8 3j0d 3j0e 3j9y 3j9z 3ja1 3jbu 3jbv 3jcd 3jce 3jcj 3jcn 4a2i 4adv 4u1u 4u1v 4u20 4u24 4u25 4u26 4u27 4v47 4v48 4v4h 4v4q 4v4v 4v4w 4v50 4v52 4v53 4v54 4v55 4v56 4v57 4v5b 4v5h 4v5y 4v64 4v65 4v66 4v69 4v6c 4v6d 4v6e 4v6k 4v6l 4v6m 4v6n 4v6o 4v6p 4v6q 4v6r 4v6s 4v6t 4v6v 4v6y 4v6z 4v70 4v71 4v72 4v73 4v74 4v75 4v76 4v77 4v78 4v79 4v7a 4v7b 4v7c 4v7d 4v7i 4v7s 4v7t 4v7u 4v7v 4v85 4v89 4v9c 4v9d 4v9o 4v9p 4wf1 4woi 4www 4ybb 5afi 5h5u 5iqr 5it8 5j5b 5j7l 5j88 5j8a 5j91 5jc9 5jte 5ju8 5kcr 5kcs 5kps 5kpv 5kpw 5kpx 5l3p 5lza 5lzb 5lzc 5lzd 5lze 5lzf 5mdv 5mdw 5mdy 5mdz 5me0 5me1 5mgp 5my1 5no2 5no3 5no4 5u4i
        RS3_ECOLI | P0A7V3: 1m5g 2ykr 3j9y 3j9z 3ja1 3jbu 3jbv 3jcd 3jce 3jcj 3jcn 4a2i 4adv 4odq 4u1u 4u1v 4u20 4u24 4u25 4u26 4u27 4v47 4v48 4v4h 4v4q 4v4v 4v4w 4v50 4v52 4v53 4v54 4v55 4v56 4v57 4v5b 4v5h 4v5y 4v64 4v65 4v66 4v69 4v6c 4v6d 4v6e 4v6k 4v6l 4v6m 4v6n 4v6o 4v6p 4v6q 4v6r 4v6s 4v6t 4v6v 4v6y 4v6z 4v70 4v71 4v72 4v73 4v74 4v75 4v76 4v77 4v78 4v79 4v7a 4v7b 4v7c 4v7d 4v7i 4v7s 4v7t 4v7u 4v7v 4v85 4v89 4v9c 4v9d 4v9o 4v9p 4wf1 4woi 4www 4ybb 5afi 5h5u 5iqr 5it8 5j5b 5j7l 5j88 5j8a 5j91 5jc9 5jte 5ju8 5kcr 5kcs 5kps 5kpv 5kpw 5kpx 5l3p 5lza 5lzb 5lzc 5lzd 5lze 5lzf 5mdv 5mdw 5mdy 5mdz 5me0 5me1 5mgp 5my1 5no4 5u4i 5u9f 5u9g
        RS4_ECOLI | P0A7V8: 1eg0 1m5g 2ykr 3j9y 3j9z 3ja1 3jbu 3jbv 3jcd 3jce 3jcj 3jcn 4a2i 4adv 4u1u 4u1v 4u20 4u24 4u25 4u26 4u27 4v47 4v48 4v4h 4v4q 4v4v 4v4w 4v50 4v52 4v53 4v54 4v55 4v56 4v57 4v5b 4v5h 4v5y 4v64 4v65 4v66 4v69 4v6c 4v6d 4v6e 4v6k 4v6l 4v6m 4v6n 4v6o 4v6p 4v6q 4v6r 4v6s 4v6t 4v6v 4v6y 4v6z 4v70 4v71 4v72 4v73 4v74 4v75 4v76 4v77 4v78 4v79 4v7a 4v7b 4v7c 4v7d 4v7i 4v7s 4v7t 4v7u 4v7v 4v85 4v89 4v9c 4v9d 4v9o 4v9p 4wf1 4woi 4www 4ybb 5afi 5h5u 5iqr 5it8 5j5b 5j7l 5j88 5j8a 5j91 5jc9 5jte 5ju8 5kcr 5kcs 5kps 5kpv 5kpw 5kpx 5l3p 5lza 5lzb 5lzc 5lzd 5lze 5lzf 5mdv 5mdw 5mdy 5mdz 5me0 5me1 5mgp 5my1 5no2 5no3 5no4 5u4i
        RS5_ECOLI | P0A7W1: 1eg0 1m5g 2ykr 3iy8 3j9y 3j9z 3ja1 3jbu 3jbv 3jcd 3jce 3jcj 3jcn 4a2i 4adv 4u1u 4u1v 4u20 4u24 4u25 4u26 4u27 4v47 4v48 4v4h 4v4q 4v4v 4v4w 4v50 4v52 4v53 4v54 4v55 4v56 4v57 4v5b 4v5h 4v5y 4v64 4v65 4v66 4v69 4v6c 4v6d 4v6e 4v6k 4v6l 4v6m 4v6n 4v6o 4v6p 4v6q 4v6r 4v6s 4v6t 4v6v 4v6y 4v6z 4v70 4v71 4v72 4v73 4v74 4v75 4v76 4v77 4v78 4v79 4v7a 4v7b 4v7c 4v7d 4v7i 4v7s 4v7t 4v7u 4v7v 4v85 4v89 4v9c 4v9d 4v9o 4v9p 4wf1 4woi 4www 4ybb 5afi 5h5u 5iqr 5it8 5j5b 5j7l 5j88 5j8a 5j91 5jc9 5jte 5ju8 5kcr 5kcs 5kps 5kpv 5kpw 5kpx 5l3p 5lza 5lzb 5lzc 5lzd 5lze 5lzf 5mdv 5mdw 5mdy 5mdz 5me0 5me1 5mgp 5my1 5no2 5no3 5no4 5u4i

(-) Related Entries Specified in the PDB File

5u4i