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- PDB-5msf: MS2 PROTEIN CAPSID/RNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 5msf
TitleMS2 PROTEIN CAPSID/RNA COMPLEX
Components
  • 5'-R(*CP*CP*GP*GP*AP*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*GP*G)-3'
  • MS2 PROTEIN CAPSID
KeywordsVirus/RNA / CAPSID PROTEIN MS2-RNA APTAMER COMPLEX / RNA-PROTEIN COMPLEX / RNA STEM LOOP / BACTERIOPHAGE MS2 / 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 speciesEnterobacterio phage MS2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 2.8 Å
AuthorsRowsell, S. / Stonehouse, N.J. / Convery, M.A. / Adams, C.J. / Ellington, A.D. / Hirao, I. / Peabody, D.S. / Stockley, P.G. / Phillips, S.E.V.
Citation
Journal: Nat.Struct.Biol. / Year: 1998
Title: Crystal structures of a series of RNA aptamers complexed to the same protein target.
Authors: Rowsell, S. / Stonehouse, N.J. / Convery, M.A. / Adams, C.J. / Ellington, A.D. / Hirao, I. / Peabody, D.S. / Stockley, P.G. / Phillips, S.E.
#1: Journal: Nat.Struct.Biol. / Year: 1998
Title: Crystal Structure of an RNA Aptamer-Protein Complex at 2.8 A Resolution
Authors: Convery, M.A. / Rowsell, S. / Stonehouse, N.J. / Ellington, A.D. / Hirao, I. / Murray, J.B. / Peabody, D.S. / Phillips, S.E. / Stockley, P.G.
#2: Journal: J.Mol.Biol. / Year: 1997
Title: The Three-Dimensional Structures of Two Complexes between Recombinant MS2 Capsids and RNA Operator Fragments Reveal Sequence-Specific Protein-RNA Interactions
Authors: Valegard, K. / Murray, J.B. / Stonehouse, N.J. / Van Den Worm, S. / Stockley, P.G. / Liljas, L.
#3: Journal: Nature / Year: 1994
Title: Crystal Structure of an RNA Bacteriophage Coat Protein-Operator Complex
Authors: Valegard, K. / Murray, J.B. / Stockley, P.G. / Stonehouse, N.J. / Liljas, L.
#4: Journal: J.Mol.Biol. / Year: 1993
Title: The Refined Structure of Bacteriophage MS2 at 2.8 A Resolution
Authors: Golmohammadi, R. / Valegard, K. / Fridborg, K. / Liljas, L.
History
DepositionMay 15, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0Nov 11, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: 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
R: 5'-R(*CP*CP*GP*GP*AP*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*GP*G)-3'
S: 5'-R(*CP*CP*GP*GP*AP*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*GP*G)-3'
A: MS2 PROTEIN CAPSID
B: MS2 PROTEIN CAPSID
C: MS2 PROTEIN CAPSID


Theoretical massNumber of molelcules
Total (without water)52,8675
Polymers52,8675
Non-polymers00
Water1,820101
1
R: 5'-R(*CP*CP*GP*GP*AP*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*GP*G)-3'
S: 5'-R(*CP*CP*GP*GP*AP*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*GP*G)-3'
A: MS2 PROTEIN CAPSID
B: MS2 PROTEIN CAPSID
C: MS2 PROTEIN CAPSID
x 60


Theoretical massNumber of molelcules
Total (without water)3,171,991300
Polymers3,171,991300
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
R: 5'-R(*CP*CP*GP*GP*AP*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*GP*G)-3'
S: 5'-R(*CP*CP*GP*GP*AP*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*GP*G)-3'
A: MS2 PROTEIN CAPSID
B: MS2 PROTEIN CAPSID
C: MS2 PROTEIN CAPSID
x 5


  • icosahedral pentamer
  • 264 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)264,33325
Polymers264,33325
Non-polymers00
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
R: 5'-R(*CP*CP*GP*GP*AP*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*GP*G)-3'
S: 5'-R(*CP*CP*GP*GP*AP*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*GP*G)-3'
A: MS2 PROTEIN CAPSID
B: MS2 PROTEIN CAPSID
C: MS2 PROTEIN CAPSID
x 6


  • icosahedral 23 hexamer
  • 317 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)317,19930
Polymers317,19930
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
R: 5'-R(*CP*CP*GP*GP*AP*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*GP*G)-3'
S: 5'-R(*CP*CP*GP*GP*AP*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*GP*G)-3'
A: MS2 PROTEIN CAPSID
B: MS2 PROTEIN CAPSID
C: MS2 PROTEIN CAPSID
x 10


  • crystal asymmetric unit, crystal frame
  • 529 kDa, 50 polymers
Theoretical massNumber of molelcules
Total (without water)528,66550
Polymers528,66550
Non-polymers00
Water72140
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation9
Unit cell
Length a, b, c (Å)287.300, 287.300, 651.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Cell settingtrigonal
Space group name H-MH32
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.5, -0.8660254, 7.9E-7), (0.6454967, 0.3726783, 0.66666701), (-0.57735086, -0.33333299, 0.74535569)
3generate(-0.30901699, -0.75576184, -0.57734958), (0.17841019, -0.64234953, 0.74535688), (-0.93417252, 0.12732289, 0.33333254)
4generate(-0.30901699, 0.17841019, -0.93417252), (-0.75576184, -0.64234953, 0.12732289), (-0.57734958, 0.74535688, 0.33333254)
5generate(0.5, 0.6454967, -0.57735086), (-0.8660254, 0.3726783, -0.33333299), (7.9E-7, 0.66666701, 0.74535569)
6generate(0.30901699, -0.75576184, -0.57734958), (-0.75576184, -0.5636604, 0.33333317), (-0.57734958, 0.33333317, -0.7453566)
7generate(-0.35682294, -0.93417203), (-0.93417203, 0.33333401, -0.12732261), (0.35682294, 0.87267739, -0.33333401)
8generate(0.30901699, 0.17841019, -0.93417252), (-0.17841019, 0.97568389, 0.12732142), (0.93417252, 0.12732142, 0.3333331)
9generate(0.80901699, 0.11026356, -0.57735037), (0.4670865, 0.47568355, 0.74535586), (0.35682166, -0.87267813, 0.33333345)
10generate(0.80901699, -0.4670865, -0.35682166), (0.11026356, -0.47568355, 0.87267813), (-0.57735037, -0.74535586, -0.33333345)
DetailsTHE COMPLETE PARTICLE CAN BE GENERATED BY APPLYING THE NCS MATRICES TO THE COORDINATES AND THEN APPLYING THE CRYSTALLOGRAPHIC SYMMETRY OPERATORS.

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Components

#1: RNA chain 5'-R(*CP*CP*GP*GP*AP*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*GP*G)-3' / F5 / 18-NT RNA APTAMER


Mass: 5825.563 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: FAMILY 5 CONSENSUS SEQUENCE FROM IN VITRO SELECTION
#2: Protein MS2 PROTEIN CAPSID


Mass: 13738.464 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacterio phage MS2 (virus) / Genus: Levivirus / Species: Enterobacteria phage MS2 / Gene: COAT PROTEIN / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: P03612
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 8

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Sample preparation

CrystalDensity % sol: 80 %
Crystal growTemperature: 300 K / pH: 7.4
Details: PROTEIN IN 1.25% OR 1.5% PEG 8000, 0.1M NA PHOSPHATE PH 7.4 AND 0.02% NA AZIDE WAS EQUILIBRATED AGAINST 0.35M OR 0.4M NA PHOSPHATE PH 7.4, 0.02% NA AZIDE AT 300 OR 370 C. WASHED CRYSTALS ...Details: PROTEIN IN 1.25% OR 1.5% PEG 8000, 0.1M NA PHOSPHATE PH 7.4 AND 0.02% NA AZIDE WAS EQUILIBRATED AGAINST 0.35M OR 0.4M NA PHOSPHATE PH 7.4, 0.02% NA AZIDE AT 300 OR 370 C. WASHED CRYSTALS WERE SOAKED IN 2MG/ML RNA.
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2NA3PO411
3NAN311
4NA3PO412
5NAN312
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 37 ℃ / Method: vapor diffusion, hanging drop / Details: Valegard, K., (1997) J.Mol.Biol., 270, 724.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.6 mg/mlcapsid1drop
21.25 %(w/v)PEG80001drop
30.1 Msodium phosphate1drop
40.02 %(w/v)sodium azide1drop
50.4 Msodium phosphate1reservoir
60.02 %(w/v)sodium azide1reservoir

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Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 172487 / % possible obs: 69 % / Redundancy: 2 % / Biso Wilson estimate: 44.7 Å2 / Rmerge(I) obs: 0.185 / Net I/σ(I): 3
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 1.9 / % possible all: 34
Reflection
*PLUS
Num. measured all: 337020
Reflection shell
*PLUS
% possible obs: 33.5 %

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Processing

Software
NameVersionClassification
CCP4model building
X-PLOR3.86refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CCP4phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: PDB ENTRY 2MS2

2ms2


Resolution: 2.8→30 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.197 6927 4 %RANDOM
Rwork0.188 ---
all-172479 --
obs-172479 68.3 %-
Displacement parametersBiso mean: 37.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.29 Å
Luzzati d res low-30 Å
Luzzati sigma a0.37 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2908 729 0 101 3738
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.38
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it5.642
X-RAY DIFFRACTIONx_mcangle_it7.692.5
X-RAY DIFFRACTIONx_scbond_it8.872.5
X-RAY DIFFRACTIONx_scangle_it10.693
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.318 557 3.9 %
Rwork0.298 13699 -
obs--34.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMTOPH19.SOL
X-RAY DIFFRACTION3DNA-RNA.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.86 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS

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