Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asymmetric Unit
(-)Biological Unit 1
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)

(-) Description

Title :  MS2-RNA HAIRPIN (5BRU-5) COMPLEX
 
Authors :  E. Grahn, T. Moss, C. Helgstrand, K. Fridborg, M. Sundaram, K. Tars, H. Lago, N. J. Stonehouse, D. R. Davis, P. G. Stockley, L. Liljas
Date :  08 Jun 05  (Deposition) - 18 Aug 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,R,S
Biol. Unit 1:  A,B,C,R,S  (60x)
Keywords :  Virus/Rna, Complex (Capsid Protein/Rna Hairpin), Hairpin, Capsid, Levivirus, Capsid Protein, Rna-Binding, Structural Protein, Icosahedral Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Grahn, T. Moss, C. Helgstrand, K. Fridborg, M. Sundaram, K. Tars, H. Lago, N. J. Stonehouse, D. R. Davis, P. G. Stockley, L. Liljas
Structural Basis Of Pyrimidine Specificity In The Ms2 Rna Hairpin-Coat-Protein Complex.
Rna V. 7 1616 2001
PubMed-ID: 11720290

(-) Compounds

Molecule 1 - MS2 COAT PROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: BACTERIOPHAGE MS2
    Organism Taxid: 12022
 
Molecule 2 - 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP *5BU*AP*CP*CP*CP*AP*UP*GP*U)-3'
    Chains: R, S
    Fragment: COAT PROTEIN-BINDING HAIRPIN, RESIDUES 2-18
    Organism Scientific: BACTERIOPHAGE MS2
    Organism Taxid: 12022
    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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
15BU2Mod. Nucleotide5-BROMO-URIDINE-5'-MONOPHOSPHATE
Biological Unit 1 (1, 120)
No.NameCountTypeFull Name
15BU120Mod. Nucleotide5-BROMO-URIDINE-5'-MONOPHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 2BU1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2BU1)

(-) 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 2BU1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2BU1)

(-) Exons   (0, 0)

(no "Exon" information available for 2BU1)

(-) 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 d2bu1a_ A: MS2 virus coat protein                                                                                                 SCOP domains
               CATH domains 2bu1A00 A:1-129 MS2 Viral Coat Protein                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee.......eeeeeeehhhhheeee.........eeeeeee.....eeeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeeeeee...hhhhhhhhhhhhhhhhh..hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bu1 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 d2bu1b_ B: MS2 virus coat protein                                                                                                 SCOP domains
               CATH domains 2bu1B00 B:1-129 MS2 Viral Coat Protein                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee.......eeeeeeehhhhheeee.........eeeeeee.....eeeeeeeeeee............hhhh.eeeeeeeeeee...hhhhhhhhhhhhhhhhh..hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bu1 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 d2bu1c_ C: MS2 virus coat protein                                                                                                 SCOP domains
               CATH domains 2bu1C00 C:1-129 MS2 Viral Coat Protein                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee.......eeeeeeeee..eeeeee..hhhhh.eeeeeeee....eeeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeeeeee...hhhhhhhhhhhhhhhhh..hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bu1 C   1 ASNFTQFVLVDNGGTGDVTVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSAQNRKYTIKVEVPKVATQTVGGVELPVAAWRSYLNMELTIPIFATNSDCELIVKAMQGLLKDGNPIPSAIAANSGIY 129
                                    10        20        30        40        50        60        70        80        90       100       110       120         


Chain R from PDB  Type:RNA  Length:17
                                                 
                 2bu1 R   2 CAUGAGGAUuACCCAUG  18
                                    11       
                                    11-5BU   


Chain S from PDB  Type:RNA  Length:17
                                                 
                 2bu1 S   2 CAUGAGGAUuACCCAUG  18
                                    11       
                                    11-5BU
   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  (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 2BU1)

(-) 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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    5BU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 2bu1)
 
  Cis Peptide Bonds
    Leu B:77 - Pro B:78   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2bu1
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  CAPSD_BPMS2 | P03612
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  CAPSD_BPMS2 | P03612
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 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 2c4q 2c4y 2c4z 2c50 2c51 2iz8 2iz9 2izm 2izn 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
1dzs MS2-RNA HAIRPIN (4ONE -5) COMPLEX
1e7x MS2-RNA HAIRPIN (2ONE -5) COMPLEX
1gkv MS2-RNA HAIRPIN (C-7) COMPLEX
1gkw MS2-RNA HAIRPIN (G-10) COMPLEX
1h8j MS2-RNA HAIRPIN (G -5) COMPLEX
1hdw MS2-RNA HAIRPIN (2THIO-U -5-6) COMPLEX
1he0 MS2-RNA HAIRPIN (2THIOURACIL-5) COMPLEX
1he6 MS2-RNA HAIRPIN (ADE -5) COMPLEX
1kuo MS2-RNA HAIRPIN (C-10) COMPLEX
1msc
1mst MOL_ID: 1; MOLECULE: BACTERIOPHAGE MS2 CAPSID; CHAIN: A, B, C; ENGINEERED: YES; MUTATION: E76D
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
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 (SU-5) COMPLEX
2c4z MS2-RNA HAIRPIN (2SU -5-6) COMPLEX
2c50 MS2-RNA HAIRPIN (A -5) COMPLEX
2c51 MS2-RNA HAIRPIN (G -5) 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