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- PDB-1knz: Recognition of the rotavirus mRNA 3' consensus by an asymmetric N... -

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Basic information

Entry
Database: PDB / ID: 1knz
TitleRecognition of the rotavirus mRNA 3' consensus by an asymmetric NSP3 homodimer
Components
  • 5'-R(*UP*GP*AP*CP*C)-3'
  • Nonstructural RNA-binding Protein 34
KeywordsViral protein/RNA / Protein-ssRNA complex / Viral protein-RNA COMPLEX
Function / homology
Function and homology information


regulation of translation / host cell cytoplasm / RNA binding
Similarity search - Function
Alpha-Beta Plaits - #1610 / Rotavirus non-structural protein NSP3, N-terminal domain / Rotavirus non-structural protein NSP3 / NSP3 superfamily / Non-structural protein NSP3, N-terminal, rotavirus / Rotavirus non-structural protein NSP3 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix non-globular / Special / Alpha-Beta Plaits ...Alpha-Beta Plaits - #1610 / Rotavirus non-structural protein NSP3, N-terminal domain / Rotavirus non-structural protein NSP3 / NSP3 superfamily / Non-structural protein NSP3, N-terminal, rotavirus / Rotavirus non-structural protein NSP3 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix non-globular / Special / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / Non-structural protein 3
Similarity search - Component
Biological speciesSimian rotavirus A/SA11
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.45 Å
AuthorsDeo, R.C. / Groft, C.M. / Rajashankar, K.R. / Burley, S.K.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2002
Title: Recognition of the rotavirus mRNA 3' consensus by an asymmetric NSP3 homodimer.
Authors: Deo, R.C. / Groft, C.M. / Rajashankar, K.R. / Burley, S.K.
History
DepositionDec 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
W: 5'-R(*UP*GP*AP*CP*C)-3'
X: 5'-R(*UP*GP*AP*CP*C)-3'
Y: 5'-R(*UP*GP*AP*CP*C)-3'
Z: 5'-R(*UP*GP*AP*CP*C)-3'
A: Nonstructural RNA-binding Protein 34
B: Nonstructural RNA-binding Protein 34
C: Nonstructural RNA-binding Protein 34
D: Nonstructural RNA-binding Protein 34
I: Nonstructural RNA-binding Protein 34
J: Nonstructural RNA-binding Protein 34
M: Nonstructural RNA-binding Protein 34
N: Nonstructural RNA-binding Protein 34


Theoretical massNumber of molelcules
Total (without water)153,22412
Polymers153,22412
Non-polymers00
Water10,899605
1
W: 5'-R(*UP*GP*AP*CP*C)-3'
A: Nonstructural RNA-binding Protein 34
B: Nonstructural RNA-binding Protein 34


Theoretical massNumber of molelcules
Total (without water)38,3063
Polymers38,3063
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
X: 5'-R(*UP*GP*AP*CP*C)-3'
C: Nonstructural RNA-binding Protein 34
D: Nonstructural RNA-binding Protein 34


Theoretical massNumber of molelcules
Total (without water)38,3063
Polymers38,3063
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
Y: 5'-R(*UP*GP*AP*CP*C)-3'
I: Nonstructural RNA-binding Protein 34
J: Nonstructural RNA-binding Protein 34


Theoretical massNumber of molelcules
Total (without water)38,3063
Polymers38,3063
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
Z: 5'-R(*UP*GP*AP*CP*C)-3'
M: Nonstructural RNA-binding Protein 34
N: Nonstructural RNA-binding Protein 34


Theoretical massNumber of molelcules
Total (without water)38,3063
Polymers38,3063
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.275, 85.359, 96.051
Angle α, β, γ (deg.)89.99, 90.00, 90.05
Int Tables number1
Space group name H-MP1

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Components

#1: RNA chain
5'-R(*UP*GP*AP*CP*C)-3'


Mass: 1545.984 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Protein
Nonstructural RNA-binding Protein 34 / NS34 / NSP3


Mass: 18380.004 Da / Num. of mol.: 8 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian rotavirus A/SA11 / Species: Rotavirus A / Strain: SA-11 / Plasmid: pGEX6P1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03536
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 605 / 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: 2.15 Å3/Da / Density % sol: 42.92 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: PEG 4000, ammonium sulfate, MES, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2ammonium sulfate11
3MES11
Crystal grow
*PLUS
Temperature: 24 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 %PEG40001reservoir
250 mMMES/NaOH1reservoirpH5.4
3200 mMammonium sulfate1reservoir
45.5 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 11, 2001
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.45→22 Å / Num. all: 46756 / Num. obs: 46429 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Rsym value: 0.045 / Net I/σ(I): 35
Reflection shellResolution: 2.45→2.49 Å / Mean I/σ(I) obs: 14 / Num. unique all: 2378 / Rsym value: 0.149 / % possible all: 99.3
Reflection
*PLUS
Lowest resolution: 23 Å / Num. measured all: 1328873 / Rmerge(I) obs: 0.045
Reflection shell
*PLUS
% possible obs: 99.3 % / Rmerge(I) obs: 0.149

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Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.45→22 Å / σ(F): 2 / Stereochemistry target values: Engh and Huber
RfactorNum. reflectionSelection details
Rfree0.28 3250 random
Rwork0.228 --
all-46756 -
obs-46429 -
Refine analyzeLuzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.17 Å
Refinement stepCycle: LAST / Resolution: 2.45→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8542 408 0 605 9555
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN_REP.TOP
X-RAY DIFFRACTION2DNA-RNA_REP_2.PARAMDNA-RNA_REP_2.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 22 Å / σ(F): 2 / % reflection Rfree: 7 % / Rfactor obs: 0.228 / Rfactor Rfree: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.2

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