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- PDB-2c4z: MS2-RNA HAIRPIN (2SU -5-6) COMPLEX -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 2c4z
TitleMS2-RNA HAIRPIN (2SU -5-6) COMPLEX
Components
  • 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*SUR *SUR*AP*CP*CP*CP*AP*UP*GP*U)-3'
  • COAT PROTEIN
KeywordsVIRUS/RNA / CAPSID / COMPLEX (CAPSID PROTEIN-RNA HAIRPIN) / HAIRPIN / LEVIVIRUS / VIRUS/VIRAL PROTEIN/RNA / VIRUS COAT PROTEIN / RNA- BINDING / 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: 2.6 Å
AuthorsGrahn, E. / Moss, T. / Helgstrand, C. / Fridborg, K. / Sundaram, M. / Tars, K. / Lago, H. / Stonehouse, N.J. / Davis, D.R. / Stockley, P.G. / Liljas, L.
CitationJournal: Rna / Year: 2001
Title: Structural basis of pyrimidine specificity in the MS2 RNA hairpin-coat-protein complex.
Authors: Grahn, E. / Moss, T. / Helgstrand, C. / Fridborg, K. / Sundaram, M. / Tars, K. / Lago, H. / Stonehouse, N.J. / Davis, D.R. / Stockley, P.G. / Liljas, L.
History
DepositionOct 25, 2005Deposition site: PDBE / Processing site: PDBE
SupersessionJan 5, 2006ID: 1HDW
Revision 1.0Jan 5, 2006Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2012Group: Advisory / Version format compliance
Revision 1.2Oct 9, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: citation / pdbx_database_status / struct_conn
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.title / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 13, 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
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
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
R: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*SUR *SUR*AP*CP*CP*CP*AP*UP*GP*U)-3'
S: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*SUR *SUR*AP*CP*CP*CP*AP*UP*GP*U)-3'


Theoretical massNumber of molelcules
Total (without water)53,4055
Polymers53,4055
Non-polymers00
Water3,297183
1
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
R: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*SUR *SUR*AP*CP*CP*CP*AP*UP*GP*U)-3'
S: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*SUR *SUR*AP*CP*CP*CP*AP*UP*GP*U)-3'
x 60


Theoretical massNumber of molelcules
Total (without water)3,204,298300
Polymers3,204,298300
Non-polymers00
Water3,243180
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: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
R: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*SUR *SUR*AP*CP*CP*CP*AP*UP*GP*U)-3'
S: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*SUR *SUR*AP*CP*CP*CP*AP*UP*GP*U)-3'
x 5


  • icosahedral pentamer
  • 267 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)267,02525
Polymers267,02525
Non-polymers00
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
R: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*SUR *SUR*AP*CP*CP*CP*AP*UP*GP*U)-3'
S: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*SUR *SUR*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)320,43030
Polymers320,43030
Non-polymers00
Water32418
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: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
R: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*SUR *SUR*AP*CP*CP*CP*AP*UP*GP*U)-3'
S: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*SUR *SUR*AP*CP*CP*CP*AP*UP*GP*U)-3'
x 10


  • crystal asymmetric unit, crystal frame
  • 534 kDa, 50 polymers
Theoretical massNumber of molelcules
Total (without water)534,05050
Polymers534,05050
Non-polymers00
Water54030
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(0.809017, 0.110264, -0.57735), (0.467086, 0.475684, 0.745356), (0.356822, -0.872678, 0.333333)
3generate(0.5, 0.645497, -0.57735), (0.866025, -0.372678, 0.333333), (-0.666667, -0.745356)
4generate(0.5, 0.866025), (0.645497, -0.372678, -0.666667), (-0.57735, 0.333333, -0.745356)
5generate(0.809017, 0.467086, 0.356822), (0.110264, 0.475684, -0.872678), (-0.57735, 0.745356, 0.333333)
6generate(0.309017, 0.755761, 0.57735), (0.755761, -0.563661, 0.333333), (0.57735, 0.333333, -0.745356)
7generate(0.809017, -0.110264, 0.57735), (0.467086, -0.475684, -0.745356), (0.356822, 0.872678, -0.333333)
8generate(0.809017, -0.467086, -0.356822), (-0.110264, 0.475684, -0.872678), (0.57735, 0.745356, 0.333333)
9generate(0.309017, 0.178411, -0.934172), (-0.178411, 0.975684, 0.127322), (0.934172, 0.127322, 0.333333)
10generate(0.934172, -0.356822), (0.356822, 0.333333, 0.872678), (0.934172, -0.127322, -0.333333)

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Components

#1: 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) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P03612
#2: RNA chain 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*SUR *SUR*AP*CP*CP*CP*AP*UP*GP*U)-3'


Mass: 6094.789 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ENTEROBACTERIO PHAGE MS2 (virus)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 1

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Sample preparation

CrystalDescription: NONE

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Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.933
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 16, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 239866 / % possible obs: 76 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 48.3 Å2 / Rmerge(I) obs: 0.14
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.28 / % possible all: 10

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2MS2

2ms2


Resolution: 2.6→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.193 2372 1 %RANDOM
Rwork0.191 ---
obs0.191 239802 75.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.68 Å2 / ksol: 0.255382 e/Å3
Displacement parametersBiso mean: 35.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.32 Å
Luzzati d res low-6 Å
Luzzati sigma a0.45 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2895 633 0 183 3711
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.99
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
Refine LS restraints NCSNCS model details: CONSTRAINTS
LS refinement shellResolution: 2.6→2.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.36 1516 -
obs--9.7 %

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