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- PDB-1zdk: STRUCTURE OF BACTERIOPHAGE COAT PROTEIN-LOOP RNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1zdk
TitleSTRUCTURE OF BACTERIOPHAGE COAT PROTEIN-LOOP RNA COMPLEX
Components
  • PROTEIN (MS2 PROTEIN CAPSID)
  • RNA (5'-R(P*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP*CP*AP*CP*CP*CP*AP*UP*GP*U)-3')
KeywordsVirus/RNA / COMPLEX (COAT PROTEIN-RNA) / COAT PROTEIN / RNA-BINDING / VIRAL PROTEIN CAPSID / RNA FRAGMENT / 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: 2.86 Å
AuthorsGrahn, E. / Stonehouse, N.J. / Valegard, K. / Vandenworm, S. / Liljas, L.
Citation
Journal: RNA / Year: 1999
Title: Crystallographic studies of RNA hairpins in complexes with recombinant MS2 capsids: implications for binding requirements.
Authors: Grahn, E. / Stonehouse, N.J. / Murray, J.B. / van den Worm, S. / Valegard, K. / Fridborg, K. / Stockley, P.G. / Liljas, L.
#1: 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.
#2: 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
DepositionDec 4, 1998Deposition site: PDBE / Processing site: RCSB
Revision 1.0Dec 7, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Apr 19, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / cell ...atom_site / cell / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_struct_oper_list / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_ncs_oper
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _cell.Z_PDB / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[2][3] / _database_PDB_matrix.origx[3][2] / _database_PDB_matrix.origx[3][3] / _pdbx_struct_oper_list.id / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[1][3] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.matrix[2][3] / _pdbx_struct_oper_list.matrix[3][1] / _pdbx_struct_oper_list.matrix[3][2] / _pdbx_struct_oper_list.matrix[3][3] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi
Details: Coordinates and associated matrices have been transformed from the icosahedral point symmetry frame to the crystallographic frame
Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
R: RNA (5'-R(P*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP*CP*AP*CP*CP*CP*AP*UP*GP*U)-3')
S: RNA (5'-R(P*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP*CP*AP*CP*CP*CP*AP*UP*GP*U)-3')
A: PROTEIN (MS2 PROTEIN CAPSID)
B: PROTEIN (MS2 PROTEIN CAPSID)
C: PROTEIN (MS2 PROTEIN CAPSID)


Theoretical massNumber of molelcules
Total (without water)53,3395
Polymers53,3395
Non-polymers00
Water2,792155
1
R: RNA (5'-R(P*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP*CP*AP*CP*CP*CP*AP*UP*GP*U)-3')
S: RNA (5'-R(P*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP*CP*AP*CP*CP*CP*AP*UP*GP*U)-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)3,200,324300
Polymers3,200,324300
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 (5'-R(P*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP*CP*AP*CP*CP*CP*AP*UP*GP*U)-3')
S: RNA (5'-R(P*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP*CP*AP*CP*CP*CP*AP*UP*GP*U)-3')
A: PROTEIN (MS2 PROTEIN CAPSID)
B: PROTEIN (MS2 PROTEIN CAPSID)
C: PROTEIN (MS2 PROTEIN CAPSID)
x 5


  • icosahedral pentamer
  • 267 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)266,69425
Polymers266,69425
Non-polymers00
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
R: RNA (5'-R(P*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP*CP*AP*CP*CP*CP*AP*UP*GP*U)-3')
S: RNA (5'-R(P*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP*CP*AP*CP*CP*CP*AP*UP*GP*U)-3')
A: PROTEIN (MS2 PROTEIN CAPSID)
B: PROTEIN (MS2 PROTEIN CAPSID)
C: PROTEIN (MS2 PROTEIN CAPSID)
x 6


  • icosahedral 23 hexamer
  • 320 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)320,03230
Polymers320,03230
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 (5'-R(P*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP*CP*AP*CP*CP*CP*AP*UP*GP*U)-3')
S: RNA (5'-R(P*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP*CP*AP*CP*CP*CP*AP*UP*GP*U)-3')
A: PROTEIN (MS2 PROTEIN CAPSID)
B: PROTEIN (MS2 PROTEIN CAPSID)
C: PROTEIN (MS2 PROTEIN CAPSID)
x 10


  • crystal asymmetric unit, crystal frame
  • 533 kDa, 50 polymers
Theoretical massNumber of molelcules
Total (without water)533,38750
Polymers533,38750
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
Cell settinghexagonal
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(0.30901699, -0.75576191, -0.57734954), (0.75576185, 0.56366034, -0.33333315), (0.5773495, -0.33333315, 0.74535665)
3generate(-0.80901699, -0.46708655, -0.35682164), (0.46708651, -0.14235205, -0.87267752), (0.35682162, -0.87267752, 0.33333506)
4generate(-0.80901699, 0.46708655, 0.35682164), (-0.46708651, -0.14235205, -0.87267752), (-0.35682162, -0.87267752, 0.33333506)
5generate(0.30901699, 0.75576191, 0.57734954), (-0.75576185, 0.56366034, -0.33333315), (-0.5773495, -0.33333315, 0.74535665)
6generate(-1), (0.74535467, -0.66666814), (-0.66666814, -0.74535467)
7generate(-0.30901699, 0.75576191, 0.57734954), (0.17841012, 0.64234946, -0.74535695), (-0.9341725, -0.12732297, -0.33333247)
8generate(0.80901699, 0.46708655, 0.35682164), (0.11026351, 0.47568353, -0.87267813), (-0.57735035, 0.74535585, 0.33333345)
9generate(0.80901699, -0.46708655, -0.35682164), (-0.11026351, 0.47568353, -0.87267813), (0.57735035, 0.74535585, 0.33333345)
10generate(-0.30901699, -0.75576191, -0.57734954), (-0.17841012, 0.64234946, -0.74535695), (0.9341725, -0.12732297, -0.33333247)

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Components

#1: RNA chain RNA (5'-R(P*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP*CP*AP*CP*CP*CP*AP*UP*GP*U)-3') / 23-NT MS2 VARIANT (CLAMP) RNA FRAGMENT


Mass: 6061.673 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: NON-BIOLOGICAL SEQUENCE
#2: Protein PROTEIN (MS2 PROTEIN CAPSID)


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.: 155 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE RNA MOLECULE IS NUMBERED FROM 1 - 23 IN THE ENTRY. IN PUBLICATIONS, THE NUMBERING IS RELATED TO ...THE RNA MOLECULE IS NUMBERED FROM 1 - 23 IN THE ENTRY. IN PUBLICATIONS, THE NUMBERING IS RELATED TO THE BEGINNING OF THE INITIATION CODON OF THE REPLICASE GENE (+1). THUS, RESIDUES 1 - 23 IN THE ENTRY CORRESPOND TO -17 - +6.

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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 growpH: 7.4 / Details: pH 7.4
Crystal grow
*PLUS
Temperature: 37 ℃ / Method: vapor diffusion, hanging drop / Details: Valegard, K., (1986) J. Mol. Biol., 190, 587.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.0 %(w/v)MS21drop
20.2 Msodium phosphate1drop
31.5 %(w/v)PEG60001drop
40.02 %(w/v)1dropNaN3
50.4 Msodium phospahte1reservoir

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Data collection

DiffractionMean temperature: 280 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 12, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→25 Å / Num. obs: 149789 / % possible obs: 47.4 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.13
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 1.07 % / Rmerge(I) obs: 0.247 / % possible all: 6.5
Reflection
*PLUS
Rmerge(I) obs: 0.13

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.86→10 Å / σ(F): 2 / Details: PARKINSON ET AL. FOR RNA
RfactorNum. reflection% reflection
Rwork0.207 --
obs-111186 47 %
Displacement parametersBiso mean: 21.6 Å2
Refinement stepCycle: LAST / Resolution: 2.86→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2895 810 0 155 3860
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
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_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellHighest resolution: 2.86 Å / Rfactor Rwork: 0.3
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / σ(F): 2 / Rfactor obs: 0.207
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21.6 Å2
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.8

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