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- PDB-4k4y: Coxsackievirus B3 polymerase elongation complex (r2+1_form) -

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Basic information

Entry
Database: PDB / ID: 4k4y
TitleCoxsackievirus B3 polymerase elongation complex (r2+1_form)
Components
  • DNA/RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*AP*(DOC))-3')
  • RNA (5'-R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*UP*CP*GP*AP*AP*A)-3')
  • RNA (5'-R(*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
  • RNA-dependent RNA polymerase
KeywordsTransferase/rna / polymerase / RNA-dependent RNA polymerase / protein-RNA complex / Transferase-rna complex
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / Picornavirus coat protein VP4 superfamily / Reverse transcriptase/Diguanylate cyclase domain / Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein ...Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / Picornavirus coat protein VP4 superfamily / Reverse transcriptase/Diguanylate cyclase domain / Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE / DNA/RNA hybrid / DNA/RNA hybrid (> 10) / RNA / RNA (> 10) / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHuman coxsackievirus B3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å
AuthorsGong, P. / Peersen, O.B.
CitationJournal: Plos One / Year: 2013
Title: Structures of coxsackievirus, rhinovirus, and poliovirus polymerase elongation complexes solved by engineering RNA mediated crystal contacts.
Authors: Gong, P. / Kortus, M.G. / Nix, J.C. / Davis, R.E. / Peersen, O.B.
History
DepositionApr 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2May 20, 2015Group: Structure summary
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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
A: RNA-dependent RNA polymerase
B: RNA (5'-R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*UP*CP*GP*AP*AP*A)-3')
C: DNA/RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*AP*(DOC))-3')
D: RNA (5'-R(*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
E: RNA-dependent RNA polymerase
F: RNA (5'-R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*UP*CP*GP*AP*AP*A)-3')
G: DNA/RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*AP*(DOC))-3')
H: RNA (5'-R(*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
I: RNA-dependent RNA polymerase
J: RNA (5'-R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*UP*CP*GP*AP*AP*A)-3')
K: DNA/RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*AP*(DOC))-3')
L: RNA (5'-R(*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
M: RNA-dependent RNA polymerase
N: RNA (5'-R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*UP*CP*GP*AP*AP*A)-3')
O: DNA/RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*AP*(DOC))-3')
P: RNA (5'-R(*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)279,20135
Polymers276,11416
Non-polymers3,08719
Water6,702372
1
A: RNA-dependent RNA polymerase
B: RNA (5'-R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*UP*CP*GP*AP*AP*A)-3')
C: DNA/RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*AP*(DOC))-3')
D: RNA (5'-R(*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8159
Polymers69,0294
Non-polymers7865
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: RNA-dependent RNA polymerase
F: RNA (5'-R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*UP*CP*GP*AP*AP*A)-3')
G: DNA/RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*AP*(DOC))-3')
H: RNA (5'-R(*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8159
Polymers69,0294
Non-polymers7865
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: RNA-dependent RNA polymerase
J: RNA (5'-R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*UP*CP*GP*AP*AP*A)-3')
K: DNA/RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*AP*(DOC))-3')
L: RNA (5'-R(*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8159
Polymers69,0294
Non-polymers7865
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
M: RNA-dependent RNA polymerase
N: RNA (5'-R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*UP*CP*GP*AP*AP*A)-3')
O: DNA/RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*AP*(DOC))-3')
P: RNA (5'-R(*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7568
Polymers69,0294
Non-polymers7274
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.373, 60.402, 194.026
Angle α, β, γ (deg.)89.92, 89.96, 79.75
Int Tables number1
Space group name H-MP1

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Components

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RNA chain , 2 types, 8 molecules BFJNDHLP

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


Mass: 7629.574 Da / Num. of mol.: 4 / Source method: obtained synthetically
#4: RNA chain
RNA (5'-R(*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')


Mass: 2974.854 Da / Num. of mol.: 4 / Source method: obtained synthetically

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Protein / DNA/RNA hybrid , 2 types, 8 molecules AEIMCGKO

#1: Protein
RNA-dependent RNA polymerase


Mass: 53624.203 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human coxsackievirus B3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q66338, UniProt: Q5UEA2*PLUS
#3: DNA/RNA hybrid
DNA/RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*AP*(DOC))-3')


Mass: 4799.939 Da / Num. of mol.: 4 / Source method: obtained synthetically

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Non-polymers , 4 types, 391 molecules

#5: Chemical
ChemComp-DCT / 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE


Type: DNA linking / Mass: 451.158 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H16N3O12P3
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 2.52 Å3/Da / Density % sol: 51.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.17 M sodium acetate, 0.085 M Tris, 25.5% PEG 4000, and 15% glycerol and directly frozen , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.72→45.06 Å / Num. obs: 70840 / % possible obs: 97.8 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 2 / Redundancy: 1.92 % / Rmerge(I) obs: 0.097 / Χ2: 1.03 / Net I/σ(I): 5 / Scaling rejects: 1027
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.72-2.821.920.4221.61353870131.1797.5
2.82-2.931.920.3571.81362070411.1397.7
2.93-3.061.920.3092.31382871371.197.8
3.06-3.221.920.2442.91372971061.0497.9
3.22-3.431.910.1843.91354270401.0498.1
3.43-3.691.910.1515137807173197.9
3.69-4.061.920.1286.11364770830.9997.7
4.06-4.651.930.1186.61385571560.9498.2
4.65-5.861.920.17.71360770330.9198.4
5.86-45.061.920.06611.61375470580.9397.1

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
d*TREK9.9.8.0Ldata reduction
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.72→43.762 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7546 / SU ML: 0.37 / σ(F): 1.96 / Phase error: 30.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2469 3555 5.03 %
Rwork0.199 --
obs0.2015 70695 97.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 169.4 Å2 / Biso mean: 50.9641 Å2 / Biso min: 22.4 Å2
Refinement stepCycle: LAST / Resolution: 2.72→43.762 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14772 2948 192 372 18284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00818613
X-RAY DIFFRACTIONf_angle_d1.16625837
X-RAY DIFFRACTIONf_chiral_restr0.0482918
X-RAY DIFFRACTIONf_plane_restr0.0072749
X-RAY DIFFRACTIONf_dihedral_angle_d17.757272
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.72-2.75730.40281310.30922673280497
2.7573-2.79660.33991490.28752612276197
2.7966-2.83840.3661460.29422675282198
2.8384-2.88270.37011370.29812767290498
2.8827-2.930.35911470.29062580272797
2.93-2.98050.33541500.27482754290497
2.9805-3.03470.36841410.27292673281498
3.0347-3.0930.33621460.2672655280198
3.093-3.15610.31931430.25252726286998
3.1561-3.22470.30671510.24182685283697
3.2247-3.29970.30771490.2592682283198
3.2997-3.38220.32711320.24852708284098
3.3822-3.47360.30541520.2132638279098
3.4736-3.57580.24881400.20182783292398
3.5758-3.69120.23981590.19112655281498
3.6912-3.8230.21641400.17332659279998
3.823-3.9760.24271290.16682686281597
3.976-4.15680.19321280.1462699282798
4.1568-4.37580.15521470.1512711285898
4.3758-4.64960.17711480.13262783293198
4.6496-5.00820.18441300.15532686281698
5.0082-5.51130.20781490.16452706285598
5.5113-6.30680.23131360.18052648278498
6.3068-7.93810.19131500.18112681283198
7.9381-43.76730.18271250.18252615274094

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