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(-) Description

Title :  MS2-RNA HAIRPIN (G-10) COMPLEX
 
Authors :  C. Helgstrand, E. Grahn, T. Moss, N. J. Stonehouse, K. Tars, P. G. Stockley, L. Liljas
Date :  25 Jul 06  (Deposition) - 27 Jul 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.56
Chains :  Asym. Unit :  A,B,C,R,S
Biol. Unit 1:  A,B,C,R,S  (60x)
Keywords :  Virus/Rna, 3D-Structure, Capsid, Capsid Protein, Complex (Capsid Protein/Rna Hairpin), Hairpin, Levivirus, Rna-Binding, Structural Protein, Virus/Viral Protein/Rna, Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Helgstrand, E. Grahn, T. Moss, N. J. Stonehouse, K. Tars, P. G. Stockley, L. Liljas
Investigating The Structural Basis Of Purine Specificity In The Structures Of Ms2 Coat Protein Rna Translational Operator Complexes
Nucleic Acids Res. V. 30 2678 2002
PubMed-ID: 12060685  |  Reference-DOI: 10.1093/NAR/GKF371

(-) Compounds

Molecule 1 - MS2 COAT PROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: ENTEROBACTERIO PHAGE MS2
    Organism Taxid: 12022
 
Molecule 2 - 5'-R(*AP*CP*AP*UP*CP*GP*CP*GP*AP*UP *UP*AP*CP*GP*GP*AP*UP*GP*U)-3'
    Chains: R, S
    Organism Scientific: ENTEROBACTERIO PHAGE MS2
    Organism Taxid: 12022
    Other Details: COATPROTEIN-BINDING HAIRPIN
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCRS
Biological Unit 1 (60x): ABCRS

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2IZN)

(-) Sites  (0, 0)

(no "Site" information available for 2IZN)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu B:77 -Pro B:78

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2IZN)

(-) 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:129
 aligned with CAPSD_BPMS2 | P03612 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:129
                                    11        21        31        41        51        61        71        81        91       101       111       121         
          CAPSD_BPMS2     2 ASNFTQFVLVDNGGTGDVTVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSAQNRKYTIKVEVPKVATQTVGGVELPVAAWRSYLNMELTIPIFATNSDCELIVKAMQGLLKDGNPIPSAIAANSGIY 130
               SCOP domains d2izna_ A: MS2 virus coat protein                                                                                                 SCOP domains
               CATH domains 2iznA00 A:1-129 MS2 Viral Coat Protein                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee.......eeeeeeehhhhheeee.........eeeeeeeeee..eeeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeeeeee...hhhhhhhhhhhhhhhh...hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2izn A   1 ASNFTQFVLVDNGGTGDVTVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSAQNRKYTIKVEVPKVATQTVGGVELPVAAWRSYLNMELTIPIFATNSDCELIVKAMQGLLKDGNPIPSAIAANSGIY 129
                                    10        20        30        40        50        60        70        80        90       100       110       120         


Chain B from PDB  Type:PROTEIN  Length:129
 aligned with CAPSD_BPMS2 | P03612 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:129
                                    11        21        31        41        51        61        71        81        91       101       111       121         
          CAPSD_BPMS2     2 ASNFTQFVLVDNGGTGDVTVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSAQNRKYTIKVEVPKVATQTVGGVELPVAAWRSYLNMELTIPIFATNSDCELIVKAMQGLLKDGNPIPSAIAANSGIY 130
               SCOP domains d2iznb_ B: MS2 virus coat protein                                                                                                 SCOP domains
               CATH domains 2iznB00 B:1-129 MS2 Viral Coat Protein                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee.......eeeeeeehhhhheeee.........eeeeeee.....eeeeeeeeeee............hhhh.eeeeeeeeeee...hhhhhhhhhhhhhhhh...hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2izn B   1 ASNFTQFVLVDNGGTGDVTVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSAQNRKYTIKVEVPKVATQTVGGVELPVAAWRSYLNMELTIPIFATNSDCELIVKAMQGLLKDGNPIPSAIAANSGIY 129
                                    10        20        30        40        50        60        70        80        90       100       110       120         


Chain C from PDB  Type:PROTEIN  Length:129
 aligned with CAPSD_BPMS2 | P03612 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:129
                                    11        21        31        41        51        61        71        81        91       101       111       121         
          CAPSD_BPMS2     2 ASNFTQFVLVDNGGTGDVTVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSAQNRKYTIKVEVPKVATQTVGGVELPVAAWRSYLNMELTIPIFATNSDCELIVKAMQGLLKDGNPIPSAIAANSGIY 130
               SCOP domains d2iznc_ C: MS2 virus coat protein                                                                                                 SCOP domains
               CATH domains 2iznC00 C:1-129 MS2 Viral Coat Protein                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee.......eeeeeeeee..eeeeee..hhhhh.eeeeeeee....eeeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeeeeee...hhhhhhhhhhhhhhhh...hhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2izn C   1 ASNFTQFVLVDNGGTGDVTVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSAQNRKYTIKVEVPKVATQTVGGVELPVAAWRSYLNMELTIPIFATNSDCELIVKAMQGLLKDGNPIPSAIAANSGIY 129
                                    10        20        30        40        50        60        70        80        90       100       110       120         


Chain R from PDB  Type:RNA  Length:15
                                               
                 2izn R   3 AUCGCGAUUACGGAU  17
                                    12     


Chain S from PDB  Type:RNA  Length:11
                                           
                 2izn S   5 CGCGAUUACGG  15
                                    14
   Legend:   → Mismatch (orange background)
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    → 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  (1, 3)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 3)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (CAPSD_BPMS2 | P03612)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
cellular component
    GO:0039617    T=3 icosahedral viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles where the subunits (capsomeres) are arranged to form an icosahedron with T=3 symmetry. The T=3 capsid is composed of 12 pentameric and 20 hexameric capsomeres.
    GO:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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    Leu B:77 - Pro B:78   [ RasMol ]  
 
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  2izn
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  CAPSD_BPMS2 | P03612
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 Related Entries

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

UniProtKB/Swiss-Prot
        CAPSD_BPMS2 | P03612: 1aq3 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 2ms2 2vtu 2wbh 4bp7 4zor 5msf 5tc1 6msf 7msf

(-) Related Entries Specified in the PDB File

1aq3 STRUCTURE OF A MS2 COAT PROTEIN MUTANT IN COMPLEX WITH ANRNA OPERATOR
1aq4 STRUCTURE OF A MS2 COAT PROTEIN MUTANT IN COMPLEX WITH ANRNA OPERATOR
1bms MOL_ID: 1; MOLECULE: BACTERIOPHAGE MS2 CAPSID ; CHAIN: A, B, C; ENGINEERED: YES; MUTATION : P78N
1msc BACTERIOPHAGE MS2 UNASSEMBLED COAT PROTEIN DIMER (TRANSLATIONAL REPRESSOR, ASSEMBLY-DEFECTIVE) MUTANT WITH TRP 82 REPLACED BY ARG (W82R)
1mst MOL_ID: 1; MOLECULE: BACTERIOPHAGE MS2 CAPSID
1mva STRUCTURE OF A PROTEIN CAPSID OF THE T45A MUTANT OF PHAGEMS2
1mvb STRUCTURE OF A PROTEIN CAPSID OF THE T59S MUTANT OF PHAGEMS2
1u1y CRYSTAL STRUCTURE OF A COMPLEX BETWEEN WT BACTERIOPHAGE MS2COAT PROTEIN AND AN F5 APTAMER RNA STEMLOOP WITH2AMINOPURINE SUBSTITUTED AT THE-10 POSITION
1zdh STRUCTURE OF BACTERIOPHAGE COAT PROTEIN- OPERATOR COMPLEX
1zdi STRUCTURE OF MS2 PROTEIN CAPSID
1zdj STRUCTURE OF BACTERIOPHAGE COAT PROTEIN-LOOP RNA COMPLEX
1zdk STRUCTURE OF BACTERIOPHAGE COAT PROTEIN-LOOP RNA COMPLEX
1zse RNA STEMLOOP FROM BACTERIOPHAGE QBETA COMPLEXED WITH ANN87S MUTANT MS2 CAPSID
2b2d RNA STEMLOOP OPERATOR FROM BACTERIOPHAGE QBETA COMPLEXEDWITH AN N87S,E89K MUTANT MS2 CAPSID
2b2e RNA STEMLOOP FROM BACTERIOPHAGE MS2 COMPLEXED WITH AN N87S,E89K MUTANT MS2 CAPSID
2b2g MS2 WILD-TYPE RNA STEMLOOP COMPLEXED WITH AN N87S MUTANTMS2 CAPSID
2bny MS2 (N87A MUTANT) - RNA HAIRPIN COMPLEX
2bq5 MS2 (N87AE89K MUTANT) - RNA HAIRPIN COMPLEX
2bs0 MS2 (N87AE89K MUTANT) - VARIANT QBETA RNA HAIRPIN COMPLEX
2bs1 MS2 (N87AE89K MUTANT) - QBETA RNA HAIRPIN COMPLEX
2bu1 MS2-RNA HAIRPIN (5BRU -5) COMPLEX
2c4q MS2-RNA HAIRPIN (2ONE -5) COMPLEX
2c4y MS2-RNA HAIRPIN (2THIOURACIL-5) COMPLEX
2c4z MS2-RNA HAIRPIN (2SU -5-6) COMPLEX
2c50 MS2-RNA HAIRPIN (A -5) COMPLEX
2c51 MS2-RNA HAIRPIN (G -5) COMPLEX
2iz8 MS2-RNA HAIRPIN (C-7) COMPLEX
2iz9 MS2-RNA HAIRPIN (4ONE -5) COMPLEX
2izm MS2-RNA HAIRPIN (C-10) COMPLEX
2ms2 MS2 VIRUS (BACTERIOPHAGE)
5msf F5 APTAMER MS2 COAT PROTEIN COMPLEX
6msf F6 APTAMER MS2 COAT PROTEIN COMPLEX
7msf F7 APTAMER MS2 COAT PROTEIN COMPLEX