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- PDB-2izm: MS2-RNA HAIRPIN (C-10) COMPLEX -

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Basic information

Entry
Database: PDB / ID: 2izm
TitleMS2-RNA HAIRPIN (C-10) COMPLEX
Components
  • 5'-R(*AP*CP*AP*UP*GP*CP*GP*GP*AP*UP *CP*AP*CP*CP*CP*AP*UP*GP*U)-3'
  • Capsid proteinCapsid
KeywordsVIRUS/RNA / VIRUS/VIRAL PROTEIN/RNA / COMPLEX (CAPSID PROTEIN-RNA HAIRPIN) / VIRION PROTEIN / CAPSID PROTEIN / STRUCTURAL PROTEIN / CAPSID / HAIRPIN / LEVIVIRUS / RNA-BINDING / 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 / Capsid protein
Similarity search - Component
Biological speciesEscherichia phage MS2 (virus)
BACTERIOPHAGE MS2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.7 Å
AuthorsHelgstrand, C. / Grahn, E. / Moss, T. / Stonehouse, N.J. / Tars, K. / Stockley, P.G. / Liljas, L.
CitationJournal: Nucleic Acids Res. / Year: 2002
Title: Investigating the Structural Basis of Purine Specificity in the Structures of MS2 Coat Protein RNA Translational Operator Complexes
Authors: Helgstrand, C. / Grahn, E. / Moss, T. / Stonehouse, N.J. / Tars, K. / Stockley, P.G. / Liljas, L.
History
DepositionJul 25, 2006Deposition site: PDBE / Processing site: PDBE
SupersessionJul 3, 2007ID: 1KUO
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Apr 28, 2021Group: Data collection / Other / Category: pdbx_database_status / reflns
Item: _pdbx_database_status.status_code_sf / _reflns.pdbx_redundancy
Revision 1.5Mar 8, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: cell / database_2 ...cell / database_2 / entity / entity_src_gen / pdbx_entity_src_syn / pdbx_struct_oper_list / struct_ncs_oper / struct_ref / struct_ref_seq
Item: _cell.Z_PDB / _database_2.pdbx_DOI ..._cell.Z_PDB / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 1.6Mar 6, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
C: Capsid protein
R: 5'-R(*AP*CP*AP*UP*GP*CP*GP*GP*AP*UP *CP*AP*CP*CP*CP*AP*UP*GP*U)-3'
S: 5'-R(*AP*CP*AP*UP*GP*CP*GP*GP*AP*UP *CP*AP*CP*CP*CP*AP*UP*GP*U)-3'


Theoretical massNumber of molelcules
Total (without water)53,2915
Polymers53,2915
Non-polymers00
Water2,738152
1
A: Capsid protein
B: Capsid protein
C: Capsid protein
R: 5'-R(*AP*CP*AP*UP*GP*CP*GP*GP*AP*UP *CP*AP*CP*CP*CP*AP*UP*GP*U)-3'
S: 5'-R(*AP*CP*AP*UP*GP*CP*GP*GP*AP*UP *CP*AP*CP*CP*CP*AP*UP*GP*U)-3'
x 60


Theoretical massNumber of molelcules
Total (without water)3,197,441300
Polymers3,197,441300
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
A: Capsid protein
B: Capsid protein
C: Capsid protein
R: 5'-R(*AP*CP*AP*UP*GP*CP*GP*GP*AP*UP *CP*AP*CP*CP*CP*AP*UP*GP*U)-3'
S: 5'-R(*AP*CP*AP*UP*GP*CP*GP*GP*AP*UP *CP*AP*CP*CP*CP*AP*UP*GP*U)-3'
x 5


  • icosahedral pentamer
  • 266 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)266,45325
Polymers266,45325
Non-polymers00
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein
B: Capsid protein
C: Capsid protein
R: 5'-R(*AP*CP*AP*UP*GP*CP*GP*GP*AP*UP *CP*AP*CP*CP*CP*AP*UP*GP*U)-3'
S: 5'-R(*AP*CP*AP*UP*GP*CP*GP*GP*AP*UP *CP*AP*CP*CP*CP*AP*UP*GP*U)-3'
x 6


  • icosahedral 23 hexamer
  • 320 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)319,74430
Polymers319,74430
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
A: Capsid protein
B: Capsid protein
C: Capsid protein
R: 5'-R(*AP*CP*AP*UP*GP*CP*GP*GP*AP*UP *CP*AP*CP*CP*CP*AP*UP*GP*U)-3'
S: 5'-R(*AP*CP*AP*UP*GP*CP*GP*GP*AP*UP *CP*AP*CP*CP*CP*AP*UP*GP*U)-3'
x 10


  • crystal asymmetric unit, crystal frame
  • 533 kDa, 50 polymers
Theoretical massNumber of molelcules
Total (without water)532,90750
Polymers532,90750
Non-polymers00
Water72140
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation9
Unit cell
Length a, b, c (Å)288.000, 288.000, 653.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.80901699, 0.11026409, -0.57735027), (0.46708618, 0.47568367, 0.74535599), (0.35682209, -0.87267799, 0.33333333)
3generate(0.5, 0.64549722, -0.57735027), (0.86602541, -0.37267799, 0.33333333), (-0.66666667, -0.74535599)
4generate(0.5, 0.86602541), (0.64549722, -0.372678, -0.66666667), (-0.57735027, 0.33333333, -0.74535599)
5generate(0.80901699, 0.46708618, 0.35682209), (0.11026409, 0.47568366, -0.872678), (-0.57735027, 0.74535599, 0.33333334)
6generate(0.30901699, 0.75576132, 0.57735027), (0.75576132, -0.563661, 0.33333334), (0.57735026, 0.33333333, -0.745356)
7generate(0.809017, -0.11026409, 0.57735027), (0.46708618, -0.47568366, -0.74535599), (0.35682208, 0.87267799, -0.33333333)
8generate(0.80901699, -0.46708618, -0.35682209), (-0.11026409, 0.47568366, -0.872678), (0.57735026, 0.74535599, 0.33333334)
9generate(0.30901699, 0.17841104, -0.93417236), (-0.17841105, 0.97568366, 0.127322), (0.93417235, 0.127322, 0.33333333)
10generate(0.93417236, -0.35682209), (0.35682209, 0.33333334, 0.872678), (0.93417235, -0.12732201, -0.33333334)

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Components

#1: Protein Capsid protein / Capsid


Mass: 13738.464 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage MS2 (virus) / Gene: MS2g2 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: C0M1L4, UniProt: P03612*PLUS
#2: RNA chain 5'-R(*AP*CP*AP*UP*GP*CP*GP*GP*AP*UP *CP*AP*CP*CP*CP*AP*UP*GP*U)-3'


Mass: 6037.649 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: COAT PROTEIN-BINDING HAIRPIN / Source: (synth.) BACTERIOPHAGE MS2 (virus)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 3

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Sample preparation

CrystalDescription: NONE
Crystal growpH: 7.4 / Details: pH 7.4
Crystal grow
*PLUS
Method: other / Details: Valegard, K., (1986) J. Mol. Biol., 190, 587.

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Data collection

DiffractionMean temperature: 280 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.085
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 24, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.085 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. obs: 134487 / % possible obs: 48.3 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 42.9 Å2 / Rmerge(I) obs: 0.21
Reflection shellResolution: 2.7→2.8 Å / % possible all: 9.4

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.7→38.24 Å / Rfactor Rfree error: 0.007 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1316 1 %RANDOM
Rwork0.246 ---
obs0.246 134414 48.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.99 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 43.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.38 Å
Luzzati d res low-6 Å
Luzzati sigma a0.36 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.7→38.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2895 544 0 152 3591
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_d24.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.08
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: 2.7→2.75 Å / Rfactor Rfree error: 0.116 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 6 0.7 %
Rwork0.374 813 -
obs--5.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA-ALL_MULT.PARAMDNA-RNA-ALL.TOP
X-RAY DIFFRACTION3WATER_REP.TMPWATER.TOP

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