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(-) Description

Title :  IN SITU STRUCTURES OF THE GENOME AND GENOME-DELIVERY APPARATUS IN SSRNA BACTERIOPHAGE MS2
 
Authors :  X. H. Dai, Z. H. Li, M. Lai, S. Shu, Y. S. Du, Z. H. Zhou, R. Sun
Date :  13 Sep 16  (Deposition) - 07 Dec 16  (Release) - 25 Jan 17  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  3.60
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H,M,R
Keywords :  Asymmetric Cryoem Reconstruction, Ssrna Genome Structure, Genome- Delivery Apparatus, Genome-Capsid Interactions, Viral Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Dai, Z. Li, M. Lai, S. Shu, Y. Du, Z. H. Zhou, R. Sun
In Situ Structures Of The Genome And Genome-Delivery Apparatus In A Single-Stranded Rna Virus.
Nature V. 541 112 2017
PubMed-ID: 27992877  |  Reference-DOI: 10.1038/NATURE20589

(-) Compounds

Molecule 1 - CAPSID PROTEIN
    Atcc15597-B1
    ChainsA, B, C, D, E, F, G, H
    Organism ScientificENTEROBACTERIA PHAGE MS2
    Organism Taxid329852
    Other DetailsTHE CAPSID OF MS2 CONTAINS 178 COPIES OF THE COAT PROTEIN ARRANGED AS 89 DIMERS IN A T=3 ICOSAHEDRAL LATTICE. STRUCTURE OF THE CAPSID HAS BEEN SOLVED BY CRYSTALLOGRAPHY WITH ICOSAHEDRAL SYMMETRY APPLIED (PDB ID 2MS2, ALSO INCLUDED AS CHAINS A, B, C IN THIS MODEL). CHAINS D, E, F, G, H ARE COAT PROTEINS THAT HAVE SLIGHTLY DIFFERENT STRUCTURES IN THE ASYMMETRIC CRYOEM RECONSTRUCTION COMPARED TO THE CRYSTALLOGRAPHIC STRUCTURE. STRUCTURES OF THE OTHER 170 COPIES OF THE COAT PROTEIN ARE THE SAME WITH 2MS2, AND THUS ARE NOT INCLUDED DUE TO THE LIMITED NUMBER OF CHAIN IDS.
    SynonymCOAT PROTEIN
 
Molecule 2 - MATURATION PROTEIN
    Atcc15597-B1
    ChainsM
    Organism ScientificENTEROBACTERIA PHAGE MS2
    Organism Taxid329852
    Other DetailsTHE CAPSID OF MS2 CONTAINS A SINGLE COPY OF THE MATURATION PROTEIN. OUR STRUCTURE SHOWS THAT IT REPLACES A COAT PROTEIN DIMER AT ONE OF THE 2-FOLD ICOSAHEDRAL SYMMETRY AXES. FUNCTION OF THE MATURATION PROTEIN IS TO ATTACH THE MS2 VIRION TO THE HOST (E. COLI) F-PILI AND DELIVER THE SSRNA VIRAL GENOME INTO THE HOST DURING INFECTION. OF THE ICOSAHEDRAL CAPSID. 178 COPIES OF THE COAT PROTEIN ARRANGED AS 89 DIMERS IN A T=3 ICOSAHEDRAL LATTICE. STRUCTURE OF THE CAPSID HAS BEEN SOLVED BY CRYSTALLOGRAPHY WITH ICOSAHEDRAL SYMMETRY APPLIED (PDB ID 2MS2, ALSO INCLUDED AS CHAINS A, B, C IN THIS MODEL). CHAINS D, E, F, G, H ARE COAT PROTEINS THAT HAVE SLIGHTLY DIFFERENT STRUCTURES IN THE ASYMMETRIC CRYOEM RECONSTRUCTION COMPARED TO THE CRYSTALLOGRAPHIC STRUCTURE. STRUCTURES OF THE OTHER 170 COPIES OF THE COAT PROTEIN ARE THE SAME WITH 2MS2, AND THUS ARE NOT INCLUDED DUE TO THE LIMITED NUMBER OF CHAIN IDS.
    SynonymMP,ASSEMBLY PROTEIN,A PROTEIN
 
Molecule 3 - PHAGE MS2 GENOME
    Atcc15597-B1
    ChainsR
    Organism ScientificENTEROBACTERIA PHAGE MS2
    Organism Taxid329852

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric/Biological Unit ABCDEFGHMR

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5TC1)

(-) Sites  (0, 0)

(no "Site" information available for 5TC1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5TC1)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu B:77 -Pro B:78
2Leu E:77 -Pro E:78

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5TC1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5TC1)

(-) Exons   (0, 0)

(no "Exon" information available for 5TC1)

(-) 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:129
                                                                                                                                                                  
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee.......eeeeeeehhhhheeeee........eeeeeee.....eeeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeeeeee...hhhhhhhhhhhhhhh....hhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                5tc1 A    1 ASNFTQFVLVDNGGTGDVTVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSAQNRKYTIKVEVPKVATQTVGGVELPVAAWRSYLNMELTIPIFATNSDCELIVKAMQGLLKDGNPIPSAIAANSGIY  129
                                    10        20        30        40        50        60        70        80        90       100       110       120         

Chain B from PDB  Type:PROTEIN  Length:129
                                                                                                                                                                  
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee.......eeeeeeehhhhheeee.........eeeeeeee....eeeeeeeee........................eeeeee...hhhhhhhhhhhhhhhh.....hhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                5tc1 B    1 ASNFTQFVLVDNGGTGDVTVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSAQNRKYTIKVEVPKVATQTVGGVELPVAAWRSYLNMELTIPIFATNSDCELIVKAMQGLLKDGNPIPSAIAANSGIY  129
                                    10        20        30        40        50        60        70        80        90       100       110       120         

Chain C from PDB  Type:PROTEIN  Length:129
                                                                                                                                                                  
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee.......eeeeeeehhhhh.eeee..hhhhh.eeeeeeee....eeeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeeeeee...hhhhhhhhhhhhhhhh.....hhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                5tc1 C    1 ASNFTQFVLVDNGGTGDVTVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSAQNRKYTIKVEVPKVATQTVGGVELPVAAWRSYLNMELTIPIFATNSDCELIVKAMQGLLKDGNPIPSAIAANSGIY  129
                                    10        20        30        40        50        60        70        80        90       100       110       120         

Chain D from PDB  Type:PROTEIN  Length:129
                                                                                                                                                                  
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee.......eeeeeeehhh.eeeee.........eeeeeee.....eeeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeeeeee...hhhhhhhhhhhhhhhh...hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                5tc1 D    1 ASNFTQFVLVDNGGTGDVTVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSAQNRKYTIKVEVPKVATQTVGGVELPVAAWRSYLNMELTIPIFATNSDCELIVKAMQGLLKDGNPIPSAIAANSGIY  129
                                    10        20        30        40        50        60        70        80        90       100       110       120         

Chain E from PDB  Type:PROTEIN  Length:129
                                                                                                                                                                  
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee.......eeeeeeeee..eeeeee........eeeeeeee....eeeeeeeeeee............hhhh.eeeeeeeeeee...hhhhhhhhhhhhhhhh.....hhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                5tc1 E    1 ASNFTQFVLVDNGGTGDVTVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSAQNRKYTIKVEVPKVATQTVGGVELPVAAWRSYLNMELTIPIFATNSDCELIVKAMQGLLKDGNPIPSAIAANSGIY  129
                                    10        20        30        40        50        60        70        80        90       100       110       120         

Chain F from PDB  Type:PROTEIN  Length:129
                                                                                                                                                                  
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee.......eeeeeeehhhhheeeee........eeeeeee.....eeeeeeeeeeeeeeeeee..eeeeeeeeeeeeee..eee...hhhhhhhhhhhhhhhh...hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                5tc1 F    1 ASNFTQFVLVDNGGTGDVTVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSAQNRKYTIKVEVPKVATQTVGGVELPVAAWRSYLNMELTIPIFATNSDCELIVKAMQGLLKDGNPIPSAIAANSGIY  129
                                    10        20        30        40        50        60        70        80        90       100       110       120         

Chain G from PDB  Type:PROTEIN  Length:119
                                                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee.......eeeeeeehhhhheeeee..hhhhh.eeeeeeeeee..eeeeeeeee............eeeeeee....hhhhhhhhhhhhhhhh...hhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                5tc1 G    1 ASNFTQFVLVDNGGTGDVTVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSAQNRKYTIKVEVPKVPVAAWRSYLNMELTIPIFATNSDCELIVKAMQGLLKDGNPIPSAIAANSGIY  129
                                    10        20        30        40        50        60      ||80        90       100       110       120         
                                                                                             67|                                                   
                                                                                              78                                                   

Chain H from PDB  Type:PROTEIN  Length:129
                                                                                                                                                                  
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee.......eeeeeeehhhhheeeee........eeeeeee.....eeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeee...hhhhhhhhhhhhhh.....hhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                5tc1 H    1 ASNFTQFVLVDNGGTGDVTVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSAQNRKYTIKVEVPKVATQTVGGVELPVAAWRSYLNMELTIPIFATNSDCELIVKAMQGLLKDGNPIPSAIAANSGIY  129
                                    10        20        30        40        50        60        70        80        90       100       110       120         

Chain M from PDB  Type:PROTEIN  Length:330
                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................ee....ee..............eee..eeeee.....hhhhhhh............hhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeee...eeeeeeeeeeeeeee..........................hhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeeeeeee.....eeeeeeeeee.........eee.......hhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5tc1 M    1 MRAFSTLDRENETFVYRSNWTPGRFNSTGAKTKQWHYPSPYSRGALSVTSIFSLDARSCYSLFPVSQNLTYIEVPQNVANRASTEVLQKVTQGNFNLGVALAEARSTASQLATQTIALVKAYTAARRGNWRQALRYLALNEDRKFRSKHVAGRWLELQFGWLPLMSDIQGAYEMLTKVHLQEFLPMRAVRQVGTNIKLDGQTTCNISRRIVIWFYINDARLAWLSSLGILNPLGIVWEKVPFSFVVDWLLPVGNMLEGLTAPVGCSYMSGTVTDVITGESIIQGTAKAQISAMHRGVQSVWPTTGAYVKSPFSMVHTLDALALIRQRLSR  393
                                    10    ||  39        49        59        69||     102       112       122       132       142       152       162       172       182       192       202       212       222       232       242|      261       271       281       291       301       311       321       331 ||    353       363       373       383       393
                                         15|                                 70|                                                                                                                                                 242|                                                                              333|                                               
                                          35                                  94                                                                                                                                                  252                                                                               346                                               

Chain R from PDB  Type:RNA  Length:242
                                                                                                                                                                                                                                                                                   
                5tc1 R  102 GGAAUUCCAUUCCCCGUUCGCGUUUACGCGGACGGCGCAAACCAUUGCGCGCGACGUAUCGUGCACUAGGUAUAGUGUUACAAAGUAAUCUACUAAUAGAAUGAGGAUUACCCAUGAAGAAGUUCAACUCUUGACAAAUCCUUGUCCUGCCUGUAAGGAGUGAUCAAUCGAUCAGACGAUAUUAUAUGUCCGGUUUUAAACCGAUUCCCUCAGGAGUGUAACUAGCUGCUUGGCUAGUUACC 3564
                                   111  ||   185       195    || 597       902       912  ||   983      1462      1721      1731|     1757     |1779      1789 ||   2047     |2377      2387|     2477   || 2786      2796|     2849  ||  3365      3542      3552      3562  
                                      114|                  200|          606|          915|          990|      1470|       1731|           1763|           1791|         2053|         2387|         2481|           2796|        2852|         3372|                        
                                       179                   593           902           977          1460       1720        1748            1776            2040          2374          2468          2781            2840         3359          3540                        

   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 5TC1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5TC1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5TC1)

(-) Gene Ontology  (9, 10)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Leu B:77 - Pro B:78   [ RasMol ]  
    Leu E:77 - Pro E:78   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        CAPSD_BPMS2 | P036121aq3 1aq4 1bms 1msc 1mst 1mva 1mvb 1u1y 1zdh 1zdi 1zdj 1zdk 1zse 2b2d 2b2e 2b2g 2bny 2bq5 2bs0 2bs1 2bu1 2c4q 2c4y 2c4z 2c50 2c51 2iz8 2iz9 2izm 2izn 2ms2 2vtu 2wbh 4bp7 4zor 5msf 6msf 7msf

(-) Related Entries Specified in the PDB File

2ms2 CRYSTALLOGRAPHIC STRUCTURE OF MS2 CAPSID WITH ICOSAHEDRAL SYMMETRY AT 2.8 ANGSTROMS RESOLUTION. RELATED ID: EMD-8397 RELATED DB: EMDB IN SITU STRUCTURES OF THE GENOME AND GENOME-DELIVERY APPARATUS IN SSRNA BACTERIOPHAGE MS2
5tc1