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- PDB-1zse: RNA stemloop from bacteriophage Qbeta complexed with an N87S muta... -

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Basic information

Entry
Database: PDB / ID: 1zse
TitleRNA stemloop from bacteriophage Qbeta complexed with an N87S mutant MS2 Capsid
Components
  • Coat protein
  • RNA HAIRPIN
KeywordsRNA/VIRUS/VIRAL PROTEIN / capsid / complex (capsid protein - rna hairpin) / hairpin / levivirus / virus/viral protein/rna / RNA-VIRUS-VIRAL PROTEIN 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: 3 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 24, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 23, 2023Group: Data collection / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _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 HAIRPIN
A: Coat protein
B: Coat protein
C: Coat protein


Theoretical massNumber of molelcules
Total (without water)47,5264
Polymers47,5264
Non-polymers00
Water2,522140
1
R: RNA HAIRPIN
A: Coat protein
B: Coat protein
C: Coat protein
x 60


Theoretical massNumber of molelcules
Total (without water)2,851,571240
Polymers2,851,571240
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: RNA HAIRPIN
A: Coat protein
B: Coat protein
C: Coat protein
x 5


  • icosahedral pentamer
  • 238 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)237,63120
Polymers237,63120
Non-polymers00
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
R: RNA HAIRPIN
A: Coat protein
B: Coat protein
C: Coat protein
x 6


  • icosahedral 23 hexamer
  • 285 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)285,15724
Polymers285,15724
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: RNA HAIRPIN
A: Coat protein
B: Coat protein
C: Coat protein
x 10


  • crystal asymmetric unit, crystal frame
  • 475 kDa, 40 polymers
Theoretical massNumber of molelcules
Total (without water)475,26240
Polymers475,26240
Non-polymers00
Water72140
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation9
Unit cell
Length a, b, c (Å)287.090, 287.090, 651.150
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), (0.64549722, 0.372678, 0.66666667), (-0.57735027, -0.33333333, 0.74535599)
3generate(-0.30901699, -0.75576131, -0.57735027), (0.17841104, -0.64235033, 0.74535599), (-0.93417236, 0.127322, 0.33333333)
4generate(-0.30901699, 0.17841104, -0.93417236), (-0.75576131, -0.64235033, 0.127322), (-0.57735027, 0.74535599, 0.33333333)
5generate(0.5, 0.64549722, -0.57735027), (-0.8660254, 0.372678, -0.33333333), (0.66666667, 0.74535599)
6generate(0.30901699, -0.75576131, -0.57735027), (-0.75576131, -0.563661, 0.33333333), (-0.57735027, 0.33333333, -0.74535599)
7generate(-0.35682209, -0.93417236), (-0.93417236, 0.33333333, -0.127322), (0.35682209, 0.872678, -0.33333333)
8generate(0.30901699, 0.17841104, -0.93417236), (-0.17841104, 0.97568366, 0.127322), (0.93417236, 0.127322, 0.33333333)
9generate(0.80901699, 0.11026409, -0.57735027), (0.46708618, 0.47568366, 0.74535599), (0.35682209, -0.872678, 0.33333333)
10generate(0.80901699, -0.46708618, -0.35682209), (0.11026409, -0.47568366, 0.872678), (-0.57735027, -0.74535599, -0.33333333)

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Components

#1: RNA chain RNA HAIRPIN / BACTERIOPHAGE QBETA STEMLOOP OPERATOR


Mass: 6391.863 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHESISED RNA STEMLOOP
#2: Protein Coat protein / MS2


Mass: 13711.438 Da / Num. of mol.: 3 / Mutation: N87S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacterio phage MS2 (virus) / Genus: Levivirus / Species: Enterobacteria phage MS2 / Production host: Escherichia coli (E. coli) / References: UniProt: P03612
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 4

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Sample preparation

Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: MS2 COATPROTEIN IN 1.25% OR 1.5% PEG 8K, 0.4M SODIUM PHOSPHATE BUFFER, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Components of the solutions
IDNameCrystal-IDSol-ID
1MS211
2PEG11
3SODIUM PHOSPHATE11
4MS212
5SODIUM PHOSPHATE12

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 26, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. all: 200773 / Num. obs: 141000 / % possible obs: 70.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rsym value: 0.205 / Net I/σ(I): 3.1
Reflection shellResolution: 3.02→3.22 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.482 / % possible all: 70.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2MS2

2ms2


Resolution: 3→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The waters listed in remark 525 are ncs symmetry related waters which are in hydrogen bonding distance to protein or RNA when the biological molecule is generated. NCS symmetry related B ...Details: The waters listed in remark 525 are ncs symmetry related waters which are in hydrogen bonding distance to protein or RNA when the biological molecule is generated. NCS symmetry related B chain instead of the chain used for the actual refinement has been included so that the protein-RNA interactions between the AB dimer and the R chain RNA are clear without generating the NCS symmetry related 'B' chain.
RfactorNum. reflectionSelection details
Rfree0.232 5664 RANDOM
Rwork0.225 --
all0.225 200773 -
obs0.225 141000 -
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2886 257 0 140 3283
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5

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