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- PDB-1u1y: Crystal structure of a complex between WT bacteriophage MS2 coat ... -

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Basic information

Entry
Database: PDB / ID: 1u1y
TitleCrystal structure of a complex between WT bacteriophage MS2 coat protein and an F5 aptamer RNA stemloop with 2aminopurine substituted at the-10 position
Components
  • 5'-R(*CP*CP*GP*GP*(2PR)P*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*G)-3'
  • Coat protein
KeywordsVirus/RNA / Complex (Capsid protein-RNA hairpin) / Hairpin / Capsid / Levivirus / 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 / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsHorn, W.T. / Convery, M.A. / Stonehouse, N.J. / Adams, C.J. / Liljas, L. / Phillips, S.E. / Stockley, P.G.
CitationJournal: Rna / Year: 2004
Title: The crystal structure of a high affinity RNA stem-loop complexed with the bacteriophage MS2 capsid: further challenges in the modeling of ligand-RNA interactions.
Authors: Horn, W.T. / Convery, M.A. / Stonehouse, N.J. / Adams, C.J. / Liljas, L. / Phillips, S.E. / Stockley, P.G.
History
DepositionJul 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: 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 / struct_conn
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 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
R: 5'-R(*CP*CP*GP*GP*(2PR)P*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*G)-3'
S: 5'-R(*CP*CP*GP*GP*(2PR)P*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*G)-3'
A: Coat protein
B: Coat protein
C: Coat protein


Theoretical massNumber of molelcules
Total (without water)52,1445
Polymers52,1445
Non-polymers00
Water2,864159
1
R: 5'-R(*CP*CP*GP*GP*(2PR)P*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*G)-3'
S: 5'-R(*CP*CP*GP*GP*(2PR)P*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*G)-3'
A: Coat protein
B: Coat protein
C: Coat protein
x 60


Theoretical massNumber of molelcules
Total (without water)3,128,646300
Polymers3,128,646300
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: 5'-R(*CP*CP*GP*GP*(2PR)P*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*G)-3'
S: 5'-R(*CP*CP*GP*GP*(2PR)P*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*G)-3'
A: Coat protein
B: Coat protein
C: Coat protein
x 5


  • icosahedral pentamer
  • 261 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)260,72125
Polymers260,72125
Non-polymers00
Water45025
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
R: 5'-R(*CP*CP*GP*GP*(2PR)P*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*G)-3'
S: 5'-R(*CP*CP*GP*GP*(2PR)P*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*G)-3'
A: Coat protein
B: Coat protein
C: Coat protein
x 6


  • icosahedral 23 hexamer
  • 313 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)312,86530
Polymers312,86530
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: 5'-R(*CP*CP*GP*GP*(2PR)P*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*G)-3'
S: 5'-R(*CP*CP*GP*GP*(2PR)P*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*G)-3'
A: Coat protein
B: Coat protein
C: Coat protein
x 10


  • crystal asymmetric unit, crystal frame
  • 521 kDa, 50 polymers
Theoretical massNumber of molelcules
Total (without water)521,44150
Polymers521,44150
Non-polymers00
Water90150
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation9
Unit cell
Length a, b, c (Å)288.610, 288.610, 654.680
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)

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Components

#1: RNA chain 5'-R(*CP*CP*GP*GP*(2PR)P*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*G)-3'


Mass: 5464.358 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein 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: LevivirusEmesvirus / Species: Enterobacteria phage MS2Bacteriophage MS2 / Production host: Escherichia coli (E. coli) / References: UniProt: P03612
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 6

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Sample preparation

Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: MS2 coat protein in 1.25% or 1.5% PEG 8K, sodium phosphate buffer., pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 303K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.244 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 12, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.244 Å / Relative weight: 1
ReflectionResolution: 2.85→30 Å / Num. obs: 170082 / % possible obs: 60.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.85→3.02 Å / % possible all: 71.2

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
X-PLORmodel building
X-PLOR3.851refinement
CCP4(SCALA)data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2MS2

2ms2


Resolution: 2.85→30 Å / Isotropic thermal model: Group / Cross valid method: Random / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.196 7130 -Throughout
Rwork0.188 ---
all0.188 ---
obs0.188 170082 71.2 %-
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 2.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2892 704 0 159 3755
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_bond_d0.007
LS refinement shellResolution: 2.85→3.02 Å / Rfactor Rfree error: 0.015
RfactorNum. reflection% reflection
Rfree0.344 380 -
Rwork0.344 --
obs--0.238 %

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