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- PDB-2bs1: MS2 (N87AE89K mutant) - Qbeta RNA hairpin complex -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 2bs1
TitleMS2 (N87AE89K mutant) - Qbeta RNA hairpin complex
Components
  • 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP *UP*AP*CP*CP*CP*AP*UP*GP*U)-3'
  • MS2 COAT PROTEIN
KeywordsVIRUS/RNA / CAPSID / COMPLEX (CAPSID PROTEIN-RNA HAIRPIN) / HAIRPIN / LEVIVIRUS / VIRUS/VIRAL PROTEIN/RNA / 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: 2.8 Å
AuthorsHorn, W.T. / Tars, K. / Grahn, E. / Helgstrand, C. / Baron, A.J. / Lago, H. / Adams, C.J. / Peabody, D.S. / Phillips, S.E.V. / Stonehouse, N.J. ...Horn, W.T. / Tars, K. / Grahn, E. / Helgstrand, C. / Baron, A.J. / Lago, H. / Adams, C.J. / Peabody, D.S. / Phillips, S.E.V. / Stonehouse, N.J. / Liljas, L. / Stockley, P.G.
CitationJournal: Structure / Year: 2006
Title: Structural Basis of RNA Binding Discrimination between Bacteriophages Qbeta and MS2.
Authors: Horn, W.T. / Tars, K. / Grahn, E. / Helgstrand, C. / Baron, A.J. / Lago, H. / Adams, C.J. / Peabody, D.S. / Phillips, S.E.V. / Stonehouse, N.J. / Liljas, L. / Stockley, P.G.
History
DepositionMay 13, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2006Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Other / Refinement description / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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 *UP*AP*CP*CP*CP*AP*UP*GP*U)-3'
S: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP *UP*AP*CP*CP*CP*AP*UP*GP*U)-3'


Theoretical massNumber of molelcules
Total (without water)53,8705
Polymers53,8705
Non-polymers00
Water2,810156
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 *UP*AP*CP*CP*CP*AP*UP*GP*U)-3'
S: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP *UP*AP*CP*CP*CP*AP*UP*GP*U)-3'
x 60


Theoretical massNumber of molelcules
Total (without water)3,232,214300
Polymers3,232,214300
Non-polymers00
Water5,405300
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 *UP*AP*CP*CP*CP*AP*UP*GP*U)-3'
S: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP *UP*AP*CP*CP*CP*AP*UP*GP*U)-3'
x 5


  • icosahedral pentamer
  • 269 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)269,35125
Polymers269,35125
Non-polymers00
Water45025
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 *UP*AP*CP*CP*CP*AP*UP*GP*U)-3'
S: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP *UP*AP*CP*CP*CP*AP*UP*GP*U)-3'
x 6


  • icosahedral 23 hexamer
  • 323 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)323,22130
Polymers323,22130
Non-polymers00
Water54030
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 *UP*AP*CP*CP*CP*AP*UP*GP*U)-3'
S: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP *UP*AP*CP*CP*CP*AP*UP*GP*U)-3'
x 60


  • crystal asymmetric unit, crystal frame
  • 3.23 MDa, 300 polymers
Theoretical massNumber of molelcules
Total (without water)3,232,214300
Polymers3,232,214300
Non-polymers00
Water5,405300
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)273.100, 273.500, 273.400
Angle α, β, γ (deg.)63.26, 63.11, 63.31
Int Tables number1
Space group name H-MP1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.446651, -0.722882, -0.527204), (0.275961, 0.671825, -0.687384), (0.851087, 0.161533, 0.499559)
3generate(-0.448687, -0.893687, -0.001948), (-0.276367, 0.140826, -0.950678), (0.849883, -0.426019, -0.310173)
4generate(-0.448687, -0.276367, 0.849883), (-0.893687, 0.140826, -0.426019), (-0.001948, -0.950678, -0.310173)
5generate(0.446651, 0.275961, 0.851087), (-0.722882, 0.671825, 0.161533), (-0.527204, -0.687384, 0.499559)
6generate(-0.453953, -0.891025, -0.000742), (-0.891025, 0.453952, 0.001211), (-0.000742, 0.001211, -0.999999)
7generate(-0.449279, -0.270578, 0.851432), (-0.271673, 0.949278, 0.158317), (-0.851083, -0.160182, -0.499999)
8generate(0.449302, 0.280529, 0.848193), (0.275363, 0.859709, -0.430203), (-0.849884, 0.426852, 0.309022)
9generate(0.999982, 0.000684, -0.005984), (-0.005902, 0.309027, -0.951035), (0.001198, 0.951053, 0.309025)
10generate(0.441739, -0.723376, -0.530654), (-0.72677, 0.058255, -0.684406), (0.525996, 0.687992, -0.499994)
11generate(-0.999976, 9.0E-6, 0.006935), (9.0E-6, -0.999997, 0.002584), (0.006935, 0.002584, 0.999973)
12generate(-0.440735, 0.723991, 0.53065), (-0.273757, -0.671411, 0.688668), (0.854874, 0.158251, 0.494112)
13generate(0.454568, 0.890712, -0.000212), (0.278559, -0.141934, 0.949874), (0.846034, -0.431841, -0.312634)
14generate(0.448655, 0.269769, -0.852017), (0.893675, -0.143284, 0.425224), (-0.007369, -0.952205, -0.305371)
15generate(-0.450303, -0.280716, -0.8476), (0.721522, -0.673596, -0.160234), (-0.52596, -0.683715, 0.505865)
16generate(0.453929, 0.891016, -0.006193), (0.891016, -0.453956, -0.003795), (-0.006193, -0.003795, -0.999974)
17generate(0.443363, 0.269469, -0.854878), (0.269469, -0.949692, -0.159601), (-0.854878, -0.159601, -0.493672)
18generate(-0.455183, -0.277554, -0.846033), (-0.277554, -0.858601, 0.431008), (-0.846033, 0.431008, 0.313785)
19generate(-0.99995, 0.005914, 0.008118), (0.005914, -0.306568, 0.95183), (0.008118, 0.95183, 0.306518)
20generate(-0.438087, 0.728131, 0.527168), (0.728131, -0.056484, 0.683107), (0.527168, 0.683107, -0.505429)
21generate(0.450278, -0.724483, 0.521894), (0.271168, -0.445938, -0.852999), (0.850716, 0.525607, -0.004339)
22generate(0.445365, -0.727921, 0.521327), (-0.727921, -0.633402, -0.262553), (0.521327, -0.262553, -0.811963)
23generate(0.441739, -0.72677, 0.525996), (-0.723376, 0.058255, 0.687992), (-0.530654, -0.684406, -0.499994)
24generate(0.444411, -0.722622, 0.52945), (0.278521, 0.673186, 0.685016), (-0.851425, -0.156966, 0.500437)
25generate(0.449688, -0.721209, 0.526914), (0.893183, 0.361578, -0.267369), (0.002309, 0.590864, 0.806768)
26generate(0.44074, -0.729457, -0.523106), (0.274878, -0.445085, 0.852257), (-0.854512, -0.519414, 0.004345)
27generate(-0.449653, -0.89317, 0.007735), (0.725292, -0.360056, 0.58678), (-0.521309, 0.269458, 0.809709)
28generate(-0.440735, -0.273757, 0.854874), (0.723991, -0.671411, 0.158251), (0.53065, 0.688668, 0.494112)
29generate(0.455171, 0.272773, 0.847593), (0.272773, -0.948869, 0.158882), (0.847593, 0.158882, -0.506302)
30generate(0.999953, -0.008865, -0.004045), (-0.004795, -0.808991, 0.587801), (-0.008483, -0.587754, -0.808995)
31generate(-0.446654, 0.725834, 0.523131), (-0.277081, 0.443735, -0.852247), (-0.850721, -0.525609, 0.002919)
32generate(0.446034, 0.895014, -0.002114), (-0.726641, 0.360743, -0.584686), (-0.522539, 0.262326, 0.811257)
33generate(0.444411, 0.278521, -0.851425), (-0.722622, 0.673186, -0.156966), (0.52945, 0.685016, 0.500437)
34generate(-0.449279, -0.271673, -0.851083), (-0.270578, 0.949278, -0.160182), (0.851432, 0.158317, -0.499999)
35generate(-0.999987, 0.004782, -0.001561), (0.004782, 0.80747, -0.58989), (-0.001561, -0.58989, -0.807482)
36generate(-0.444364, 0.728107, -0.52192), (-0.268964, 0.447288, 0.85299), (0.854517, 0.519416, -0.002924)
37generate(-0.441745, 0.726076, -0.526948), (0.729269, 0.632715, 0.260459), (0.522521, -0.269231, -0.809004)
38generate(-0.445415, 0.722006, -0.529445), (0.722006, -0.06003, -0.689277), (-0.529445, -0.689277, -0.494555)
39generate(-0.450303, 0.721522, -0.52596), (-0.280716, -0.673596, -0.683715), (-0.8476, -0.160234, 0.505865)
40generate(-0.449653, 0.725292, -0.521309), (-0.89317, -0.360056, 0.269458), (0.007735, 0.58678, 0.809709)
41generate(0.450278, 0.271168, 0.850716), (-0.724483, -0.445938, 0.525607), (0.521894, -0.852999, -0.004339)
42generate(0.999982, -0.005902, 0.001198), (0.000684, 0.309027, 0.951053), (-0.005984, -0.951035, 0.309025)
43generate(0.446034, -0.726641, -0.522539), (0.895014, 0.360743, 0.262326), (-0.002114, -0.584686, 0.811257)
44generate(-0.44603, -0.895012, 0.003292), (0.722572, -0.362259, -0.588777), (0.528155, -0.260233, 0.808289)
45generate(-0.443407, -0.278333, 0.85201), (-0.278333, -0.860816, -0.42606), (0.85201, -0.42606, 0.304222)
46generate(-0.446654, -0.277081, -0.850721), (0.725834, 0.443735, -0.525609), (0.523131, -0.852247, 0.002919)
47generate(-0.999999, -0.000691, 0.000954), (-0.000691, -0.311483, -0.950251), (0.000954, -0.950251, 0.311483)
48generate(-0.44603, 0.722572, 0.528155), (-0.895012, -0.362259, -0.260233), (0.003292, -0.588777, 0.808289)
49generate(0.449688, 0.893183, 0.002309), (-0.721209, 0.361578, 0.590864), (0.526914, -0.267369, 0.806768)
50generate(0.449302, 0.275363, -0.849884), (0.280529, 0.859709, 0.426852), (0.848193, -0.430203, 0.309022)
51generate(-0.444364, -0.268964, 0.854517), (0.728107, 0.447288, 0.519416), (-0.52192, 0.85299, -0.002924)
52generate(0.454568, 0.278559, 0.846034), (0.890712, -0.141934, -0.431841), (-0.000212, 0.949874, -0.312634)
53generate(0.999953, -0.004795, -0.008483), (-0.008865, -0.808991, -0.587754), (-0.004045, 0.587801, -0.808995)
54generate(0.438086, -0.72744, -0.528121), (-0.72744, -0.632033, 0.267144), (-0.528121, 0.267144, -0.806053)
55generate(-0.454551, -0.890705, 0.005242), (-0.271965, 0.144391, 0.951413), (-0.848185, 0.43104, -0.307874)
56generate(0.44074, 0.274878, -0.854512), (-0.729457, -0.445085, -0.519414), (-0.523106, 0.852257, 0.004345)
57generate(-0.454551, -0.271965, -0.848185), (-0.890705, 0.144391, 0.43104), (0.005242, 0.951413, -0.307874)
58generate(-0.999957, 0.008864, 0.002867), (0.008864, 0.810507, 0.585661), (0.002867, 0.585661, -0.810551)
59generate(-0.441745, 0.729269, 0.522521), (0.726076, 0.632715, -0.269231), (-0.526948, 0.260459, -0.809004)
60generate(0.448655, 0.893675, -0.007369), (0.269769, -0.143284, -0.952205), (-0.852017, 0.425224, -0.305371)

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Components

#1: Protein MS2 COAT PROTEIN


Mass: 13695.505 Da / Num. of mol.: 3 / Mutation: YES
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 *UP*AP*CP*CP*CP*AP*UP*GP*U)-3' / MS2 HAIRPIN


Mass: 6391.863 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BACTERIOPHAGE MS2 (virus)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASN 87 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLU 89 TO LYS ...ENGINEERED RESIDUE IN CHAIN A, ASN 87 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLU 89 TO LYS ENGINEERED RESIDUE IN CHAIN B, ASN 87 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 89 TO LYS ENGINEERED RESIDUE IN CHAIN C, ASN 87 TO ALA ENGINEERED RESIDUE IN CHAIN C, GLU 89 TO LYS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDescription: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 1, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 347537 / % possible obs: 23 % / Observed criterion σ(I): 0 / Redundancy: 1.3 % / Biso Wilson estimate: 68.8 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 1 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 10 / % possible all: 10

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2MS2

2ms2


Resolution: 2.8→29.94 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3935053.26 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.248 3495 1 %RANDOM
Rwork0.245 ---
obs0.245 346578 23.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.5762 Å2 / ksol: 0.350874 e/Å3
Displacement parametersBiso mean: 54.9 Å2
Baniso -1Baniso -2Baniso -3
1-14.65 Å2-9.2 Å2-12.3 Å2
2---9.98 Å22.81 Å2
3----4.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2886 485 0 156 3527
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_d26
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.94
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: 2.8→2.85 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 77 1 %
Rwork0.435 7389 -
obs--10.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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