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- PDB-2bu1: MS2-RNA HAIRPIN (5BRU -5) COMPLEX -

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Basic information

Entry
Database: PDB / ID: 2bu1
TitleMS2-RNA HAIRPIN (5BRU -5) COMPLEX
Components
  • 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP *5BU*AP*CP*CP*CP*AP*UP*GP*U)-3'
  • MS2 COAT PROTEIN
KeywordsVIRUS/RNA / COMPLEX (CAPSID PROTEIN-RNA HAIRPIN) / HAIRPIN / CAPSID / LEVIVIRUS / CAPSID PROTEIN / RNA-BINDING / STRUCTURAL PROTEIN / ICOSAHEDRAL VIRUS / VIRUS-RNA complex
Function / homology
Function and homology information


negative regulation of viral translation / T=3 icosahedral viral capsid / regulation of translation / structural molecule activity / RNA binding / identical protein binding
Similarity search - Function
MS2 Viral Coat Protein / MS2 Viral Coat Protein / Levivirus coat protein / Levivirus coat protein / Bacteriophage RNA-type, capsid / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Capsid protein
Similarity search - Component
Biological speciesBACTERIOPHAGE MS2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGrahn, E. / Moss, T. / Helgstrand, C. / Fridborg, K. / Sundaram, M. / Tars, K. / Lago, H. / Stonehouse, N.J. / Davis, D.R. / Stockley, P.G. / Liljas, L.
CitationJournal: Rna / Year: 2001
Title: Structural basis of pyrimidine specificity in the MS2 RNA hairpin-coat-protein complex.
Authors: Grahn, E. / Moss, T. / Helgstrand, C. / Fridborg, K. / Sundaram, M. / Tars, K. / Lago, H. / Stonehouse, N.J. / Davis, D.R. / Stockley, P.G. / Liljas, L.
History
DepositionJun 8, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2005Provider: repository / Type: Initial release
SupersessionNov 18, 2005ID: 1E6T
Revision 1.1Oct 9, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: citation / pdbx_database_status / struct_conn
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.title / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MS2 COAT PROTEIN
B: MS2 COAT PROTEIN
C: MS2 COAT PROTEIN
R: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP *5BU*AP*CP*CP*CP*AP*UP*GP*U)-3'
S: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP *5BU*AP*CP*CP*CP*AP*UP*GP*U)-3'


Theoretical massNumber of molelcules
Total (without water)53,4985
Polymers53,4985
Non-polymers00
Water3,693205
1
A: MS2 COAT PROTEIN
B: MS2 COAT PROTEIN
C: MS2 COAT PROTEIN
R: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP *5BU*AP*CP*CP*CP*AP*UP*GP*U)-3'
S: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP *5BU*AP*CP*CP*CP*AP*UP*GP*U)-3'
x 60


Theoretical massNumber of molelcules
Total (without water)3,209,910300
Polymers3,209,910300
Non-polymers00
Water4,324240
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: MS2 COAT PROTEIN
B: MS2 COAT PROTEIN
C: MS2 COAT PROTEIN
R: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP *5BU*AP*CP*CP*CP*AP*UP*GP*U)-3'
S: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP *5BU*AP*CP*CP*CP*AP*UP*GP*U)-3'
x 5


  • icosahedral pentamer
  • 267 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)267,49225
Polymers267,49225
Non-polymers00
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: MS2 COAT PROTEIN
B: MS2 COAT PROTEIN
C: MS2 COAT PROTEIN
R: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP *5BU*AP*CP*CP*CP*AP*UP*GP*U)-3'
S: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP *5BU*AP*CP*CP*CP*AP*UP*GP*U)-3'
x 6


  • icosahedral 23 hexamer
  • 321 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)320,99130
Polymers320,99130
Non-polymers00
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
A: MS2 COAT PROTEIN
B: MS2 COAT PROTEIN
C: MS2 COAT PROTEIN
R: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP *5BU*AP*CP*CP*CP*AP*UP*GP*U)-3'
S: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP *5BU*AP*CP*CP*CP*AP*UP*GP*U)-3'
x 10


  • crystal asymmetric unit, crystal frame
  • 535 kDa, 50 polymers
Theoretical massNumber of molelcules
Total (without water)534,98550
Polymers534,98550
Non-polymers00
Water72140
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation9
Unit cell
Length a, b, c (Å)288.000, 288.000, 653.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.809017, 0.110264, -0.57735), (0.467086, 0.475684, 0.745356), (0.356822, -0.872678, 0.333333)
3generate(0.5, 0.645497, -0.57735), (0.866025, -0.372678, 0.333333), (-0.666667, -0.745356)
4generate(0.5, 0.866025), (0.645497, -0.372678, -0.666667), (-0.57735, 0.333333, -0.745356)
5generate(0.809017, 0.467086, 0.356822), (0.110264, 0.475684, -0.872678), (-0.57735, 0.745356, 0.333333)
6generate(0.309017, 0.755761, 0.57735), (0.755761, -0.563661, 0.333333), (0.57735, 0.333333, -0.745356)
7generate(0.809017, -0.110264, 0.57735), (0.467086, -0.475684, -0.745356), (0.356822, 0.872678, -0.333333)
8generate(0.809017, -0.467086, -0.356822), (-0.110264, 0.475684, -0.872678), (0.57735, 0.745356, 0.333333)
9generate(0.309017, 0.178411, -0.934172), (-0.178411, 0.975684, 0.127322), (0.934172, 0.127322, 0.333333)
10generate(0.934172, -0.356822), (0.356822, 0.333333, 0.872678), (0.934172, -0.127322, -0.333333)

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Components

#1: Protein MS2 COAT PROTEIN


Mass: 13738.464 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTERIOPHAGE MS2 (virus) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P03612
#2: RNA chain 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP *5BU*AP*CP*CP*CP*AP*UP*GP*U)-3'


Mass: 6141.553 Da / Num. of mol.: 2 / Fragment: COAT PROTEIN-BINDING HAIRPIN, RESIDUES 2-18 / Source method: obtained synthetically / Source: (synth.) BACTERIOPHAGE MS2 (virus)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFORMS THE PHAGE SHELL AND BINDS TO THE PHAGE RNA

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDescription: NONE
Crystal growpH: 7.4 / Details: pH 7.4
Crystal grow
*PLUS
Temperature: 37 ℃ / Method: vapor diffusion, hanging drop / Details: Valegard, K., (1986) J.Mol.Biol., 190, 587.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.0 %(w/v)MS21drop
20.2 Msodium phosphate1drop
31.5 %(w/v)PEG60001drop
40.02 %(w/v)1dropNaN3
50.4 Msodium phospahte1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 28, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.2→47 Å / Num. obs: 374908 / % possible obs: 69 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.16
Reflection shellResolution: 2.18→2.26 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.4 / % possible all: 13
Reflection
*PLUS
Highest resolution: 2.18 Å / Lowest resolution: 47 Å / % possible obs: 69 % / Rmerge(I) obs: 0.16
Reflection shell
*PLUS
% possible obs: 13 % / Rmerge(I) obs: 0.39

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Processing

Software
NameVersionClassification
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MS2 RECOMBINANT CAPSIDS

Resolution: 2.2→47 Å / Rfactor Rfree error: 0.012 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.244 394 0.1 %RANDOM
Rwork0.219 ---
obs0.219 372421 71.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.9223 Å2 / ksol: 0.303283 e/Å3
Displacement parametersBiso mean: 36.1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.31 Å
Luzzati d res low-6 Å
Luzzati sigma a0.29 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.2→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2895 728 0 205 3828
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.2→2.4 Å / Rfactor Rfree error: 0.182 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 4 0.1 %
Rwork0.313 3309 -
obs--12.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA-5BR_MULT.PARAMDNA-RNA-5BR.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.1
LS refinement shell
*PLUS
Rfactor obs: 0.313

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