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- PDB-2qux: PP7 coat protein dimer in complex with RNA hairpin -

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Basic information

Entry
Database: PDB / ID: 2qux
TitlePP7 coat protein dimer in complex with RNA hairpin
Components
  • Coat protein
  • RNA (25-MER)
KeywordsStructural PROTEIN/RNA / Bacteriophage coat protein / RNA-protein complex / Capsid protein / Structural PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


T=3 icosahedral viral capsid / regulation of translation / RNA binding / identical protein binding
Similarity search - Function
Bacteriophage PP7, coat / Phage PP7 coat protein / MS2 Viral Coat Protein / MS2 Viral Coat Protein / Bacteriophage RNA-type, capsid / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Capsid protein
Similarity search - Component
Biological speciesPseudomonas phage PP7 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsChao, J.A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Structural basis for the coevolution of a viral RNA-protein complex.
Authors: Chao, J.A. / Patskovsky, Y. / Almo, S.C. / Singer, R.H.
History
DepositionAug 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Aug 30, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: RNA (25-MER)
F: RNA (25-MER)
I: RNA (25-MER)
L: RNA (25-MER)
O: RNA (25-MER)
R: RNA (25-MER)
A: Coat protein
B: Coat protein
D: Coat protein
E: Coat protein
G: Coat protein
H: Coat protein
J: Coat protein
K: Coat protein
M: Coat protein
N: Coat protein
P: Coat protein
Q: Coat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,10233
Polymers211,72118
Non-polymers1,38115
Water9,224512
1
C: RNA (25-MER)
A: Coat protein
B: Coat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6557
Polymers35,2873
Non-polymers3684
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9230 Å2
MethodPISA
2
F: RNA (25-MER)
D: Coat protein
E: Coat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5636
Polymers35,2873
Non-polymers2763
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8550 Å2
MethodPISA
3
I: RNA (25-MER)
G: Coat protein
H: Coat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5636
Polymers35,2873
Non-polymers2763
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8870 Å2
MethodPISA
4
L: RNA (25-MER)
J: Coat protein
K: Coat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6557
Polymers35,2873
Non-polymers3684
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9150 Å2
MethodPISA
5
O: RNA (25-MER)
M: Coat protein
N: Coat protein


Theoretical massNumber of molelcules
Total (without water)35,2873
Polymers35,2873
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8070 Å2
MethodPISA
6
R: RNA (25-MER)
P: Coat protein
Q: Coat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3794
Polymers35,2873
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.970, 145.388, 109.655
Angle α, β, γ (deg.)90.00, 122.94, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain
RNA (25-MER)


Mass: 8053.845 Da / Num. of mol.: 6 / Source method: obtained synthetically
#2: Protein
Coat protein


Mass: 13616.476 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage PP7 (virus) / Genus: LevivirusEmesvirus / Gene: PP7 coat protein / Plasmid: pET22HT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q38062
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 512 / 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

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 15% PEG 3350, 0.1M Na Citrate, 0.01M MES, 0.001M Cobaltous chloride hexahydrate, 0.18M Ammonium sulfate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 335011
2Na Citrate11
3MES11
4Cobaltous chloride hexahydrate11
5Ammonium sulfate11
6PEG 335012
7Na Citrate12
8MES12
9Cobaltous chloride hexahydrate12
10Ammonium sulfate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9797 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 19, 2007 / Details: Mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.44→33.8 Å / Num. all: 86879 / Num. obs: 85663 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 18.7
Reflection shellResolution: 2.44→2.54 Å / Redundancy: 4 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.3 / Num. unique all: 7525 / % possible all: 87.6

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2QUD

2qud


Resolution: 2.44→33.8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0.45 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2545 -random
Rwork0.175 ---
all0.177 82206 --
obs0.177 82944 99.11 %-
Refinement stepCycle: LAST / Resolution: 2.44→33.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11213 3198 90 512 15013
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.596

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