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- PDB-6msf: F6 APTAMER MS2 COAT PROTEIN COMPLEX -

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Basic information

Entry
Database: PDB / ID: 6msf
TitleF6 APTAMER MS2 COAT PROTEIN COMPLEX
Components
  • PROTEIN (MS2 PROTEIN CAPSID)
  • RNA (5'-R(*CP*AP*GP*UP*CP*AP*CP*UP*GP*G)-3')
  • RNA (5'-R(*CP*CP*AP*CP*AP*GP*UP*CP*AP*CP*UP*GP*GP*G)-3')
KeywordsVirus/RNA / VIRAL COAT PROTEIN-RNA COMPLEX / RNA APTAMER / 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
AuthorsConvery, M.A. / Rowsell, S. / Stonehouse, N.J. / Ellington, A.D. / Hirao, I. / Murray, J.B. / Peabody, D.S. / Phillips, S.E.V. / Stockley, P.G.
Citation
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.
#1: 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.
#2: 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.
#3: 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
DepositionJan 6, 1998Deposition site: BNL / Processing site: NDB
Revision 1.0Jul 8, 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: RNA (5'-R(*CP*CP*AP*CP*AP*GP*UP*CP*AP*CP*UP*GP*GP*G)-3')
S: RNA (5'-R(*CP*AP*GP*UP*CP*AP*CP*UP*GP*G)-3')
A: PROTEIN (MS2 PROTEIN CAPSID)
B: PROTEIN (MS2 PROTEIN CAPSID)
C: PROTEIN (MS2 PROTEIN CAPSID)


Theoretical massNumber of molelcules
Total (without water)48,8545
Polymers48,8545
Non-polymers00
Water1,54986
1
R: RNA (5'-R(*CP*CP*AP*CP*AP*GP*UP*CP*AP*CP*UP*GP*GP*G)-3')
S: RNA (5'-R(*CP*AP*GP*UP*CP*AP*CP*UP*GP*G)-3')
A: PROTEIN (MS2 PROTEIN CAPSID)
B: PROTEIN (MS2 PROTEIN CAPSID)
C: PROTEIN (MS2 PROTEIN CAPSID)
x 60


Theoretical massNumber of molelcules
Total (without water)2,931,244300
Polymers2,931,244300
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
R: RNA (5'-R(*CP*CP*AP*CP*AP*GP*UP*CP*AP*CP*UP*GP*GP*G)-3')
S: RNA (5'-R(*CP*AP*GP*UP*CP*AP*CP*UP*GP*G)-3')
A: PROTEIN (MS2 PROTEIN CAPSID)
B: PROTEIN (MS2 PROTEIN CAPSID)
C: PROTEIN (MS2 PROTEIN CAPSID)
x 5


  • icosahedral pentamer
  • 244 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)244,27025
Polymers244,27025
Non-polymers00
Water45025
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
R: RNA (5'-R(*CP*CP*AP*CP*AP*GP*UP*CP*AP*CP*UP*GP*GP*G)-3')
S: RNA (5'-R(*CP*AP*GP*UP*CP*AP*CP*UP*GP*G)-3')
A: PROTEIN (MS2 PROTEIN CAPSID)
B: PROTEIN (MS2 PROTEIN CAPSID)
C: PROTEIN (MS2 PROTEIN CAPSID)
x 6


  • icosahedral 23 hexamer
  • 293 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)293,12430
Polymers293,12430
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
R: RNA (5'-R(*CP*CP*AP*CP*AP*GP*UP*CP*AP*CP*UP*GP*GP*G)-3')
S: RNA (5'-R(*CP*AP*GP*UP*CP*AP*CP*UP*GP*G)-3')
A: PROTEIN (MS2 PROTEIN CAPSID)
B: PROTEIN (MS2 PROTEIN CAPSID)
C: PROTEIN (MS2 PROTEIN CAPSID)
x 10


  • crystal asymmetric unit, crystal frame
  • 489 kDa, 50 polymers
Theoretical massNumber of molelcules
Total (without water)488,54150
Polymers488,54150
Non-polymers00
Water90150
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation9
Unit cell
Length a, b, c (Å)287.580, 287.580, 652.190
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
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 RNA (5'-R(*CP*CP*AP*CP*AP*GP*UP*CP*AP*CP*UP*GP*GP*G)-3') / F6


Mass: 4461.724 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: FAMILY 6 CONSENSUS SEQUENCE FROM IN VITRO SELECTION
#2: RNA chain RNA (5'-R(*CP*AP*GP*UP*CP*AP*CP*UP*GP*G)-3') / F6


Mass: 3176.948 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: FAMILY 6 CONSENSUS SEQUENCE FROM IN VITRO SELECTION
#3: Protein PROTEIN (MS2 PROTEIN CAPSID) / MS2 COAT PROTEIN


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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 7

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Sample preparation

CrystalDensity % sol: 80 %
Description: ADDITIONAL DATA WERE COLLECTED AT ESRF STATION ID2.
Crystal growpH: 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 30O OR 37O 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 30O OR 37O C. WASHED CRYSTALS WERE SOAKED IN 2MG/ML RNA.
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 30 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
13.75 mg/mlprotein1drop
21.25 %(w/v)PEG80001dropor 1.5%(w/v)
30.1 Msodium phosphate1drop
40.35 Msodium phosphate1reservoiror 0.4M

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Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1997 / Details: MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.8→36 Å / Num. obs: 169875 / % possible obs: 68 % / Redundancy: 1.8 % / Biso Wilson estimate: 45.9 Å2 / Rmerge(I) obs: 0.186 / Net I/σ(I): 3
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.369 / % possible all: 43
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 36 Å / % possible obs: 68 % / Redundancy: 1.8 % / Num. measured all: 313760 / Biso Wilson estimate: 45.9 Å2
Reflection shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.95 Å / % possible obs: 42.8 % / Redundancy: 1.3 %

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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→36 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.201 6829 4 %RANDOM
Rwork0.195 ---
obs0.195 169871 67.1 %-
Displacement parametersBiso mean: 33.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.29 Å
Luzzati d res low-36 Å
Luzzati sigma a0.33 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.8→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2904 505 0 86 3495
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.95
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it6.052
X-RAY DIFFRACTIONx_mcangle_it8.062.5
X-RAY DIFFRACTIONx_scbond_it9.982.5
X-RAY DIFFRACTIONx_scangle_it12.093
Refine LS restraints NCSNCS model details: CONSTRAINED
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.295 697 3.9 %
Rwork0.303 17123 -
obs--42.5 %
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
Highest resolution: 2.8 Å / Lowest resolution: 36 Å / σ(F): 0 / % reflection Rfree: 4 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 33.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.95
X-RAY DIFFRACTIONx_mcbond_it6.052
X-RAY DIFFRACTIONx_scbond_it9.982.5
X-RAY DIFFRACTIONx_mcangle_it8.062.5
X-RAY DIFFRACTIONx_scangle_it3
LS refinement shell
*PLUS
% reflection Rfree: 3.9 %

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