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- PDB-4k4u: Poliovirus polymerase elongation complex (r5_form) -

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Basic information

Entry
Database: PDB / ID: 4k4u
TitlePoliovirus polymerase elongation complex (r5_form)
Components
  • RNA (5'-R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*UP*CP*GP*UP*CP*GP*AP*AP*A)-3')
  • RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*AP*GP*A)-3')
  • RNA (5'-R(P*GP*GP*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
  • RNA-directed RNA polymerase 3D-POL
KeywordsTransferase/rna / polymerase / RNA-dependent RNA polymerase / protein-RNA complex / Transferase-rna complex
Function / homology
Function and homology information


symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid ...symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / Reverse transcriptase/Diguanylate cyclase domain / 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 ...Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / Reverse transcriptase/Diguanylate cyclase domain / 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) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / 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 / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Alpha-Beta Plaits / 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
RNA / RNA (> 10) / Genome polyprotein
Similarity search - Component
Biological speciesHuman poliovirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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 22, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
A: RNA-directed RNA polymerase 3D-POL
B: RNA (5'-R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*UP*CP*GP*UP*CP*GP*AP*AP*A)-3')
C: RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*AP*GP*A)-3')
E: RNA-directed RNA polymerase 3D-POL
F: RNA (5'-R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*UP*CP*GP*UP*CP*GP*AP*AP*A)-3')
G: RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*AP*GP*A)-3')
H: RNA (5'-R(P*GP*GP*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
D: RNA (5'-R(P*GP*GP*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,17712
Polymers141,7938
Non-polymers3844
Water1,02757
1
A: RNA-directed RNA polymerase 3D-POL
B: RNA (5'-R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*UP*CP*GP*UP*CP*GP*AP*AP*A)-3')
C: RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*AP*GP*A)-3')
D: RNA (5'-R(P*GP*GP*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0896
Polymers70,8974
Non-polymers1922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: RNA-directed RNA polymerase 3D-POL
F: RNA (5'-R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*UP*CP*GP*UP*CP*GP*AP*AP*A)-3')
G: RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*AP*GP*A)-3')
H: RNA (5'-R(P*GP*GP*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0896
Polymers70,8974
Non-polymers1922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.654, 63.870, 105.095
Angle α, β, γ (deg.)101.080, 106.220, 103.030
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AE

#1: Protein RNA-directed RNA polymerase 3D-POL


Mass: 53789.250 Da / Num. of mol.: 2 / Fragment: unp residues 1749-2209 / Mutation: L446D, C290M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 1 / Strain: Mahoney / Production host: Escherichia coli (E. coli) / References: UniProt: P03300, RNA-directed RNA polymerase

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RNA chain , 3 types, 6 molecules BFCGHD

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


Mass: 8240.921 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: RNA chain RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*AP*GP*A)-3')


Mass: 5201.168 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: RNA chain RNA (5'-R(P*GP*GP*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')


Mass: 3665.266 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Non-polymers , 2 types, 61 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.71 Å3/Da / Density % sol: 54.65 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 4.8%(v/v) isopropanol, 0.096 M tacsimate (Hampton Research), pH 8.5-9.0, 1.92-1.95 M ammonium sulfate, and 10-11%(v/v) glycerol and then gradually exchanged into a cryo stabilizer solution ...Details: 4.8%(v/v) isopropanol, 0.096 M tacsimate (Hampton Research), pH 8.5-9.0, 1.92-1.95 M ammonium sulfate, and 10-11%(v/v) glycerol and then gradually exchanged into a cryo stabilizer solution containing 4.8%(v/v) isopropanol, 0.096 M tacsimate, 1.95 M ammonium sulfate and 19-27%(v/v) xylitol prior to freezing, VAPOR DIFFUSION, SITTING DROP, temperature 289K
PH range: 8.5-9.0

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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: 2.85→45.69 Å / Num. obs: 34198 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.5 / Redundancy: 2.01 % / Rmerge(I) obs: 0.047 / Χ2: 1.17 / Net I/σ(I): 9 / Scaling rejects: 520
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.85-2.952.020.4421.8689334031.398.1
2.95-3.072.010.3462.3690034141.2798.2
3.07-3.212.010.2762.7695534431.2198.4
3.21-3.3820.2113.8683133921.2398.5
3.38-3.592.020.184700434581.1998.5
3.59-3.872.020.1485.3690834001.2298.6
3.87-4.2620.0839.4701734691.1398.5
4.26-4.8720.05913690034020.9898.4
4.87-6.142.010.05116.6696034231.0398.6
6.14-45.692.010.02930.9692233941.1397.4

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
d*TREK9.9.9.4Ddata reduction
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→43.263 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7091 / SU ML: 0.42 / σ(F): 1.97 / Phase error: 34.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2757 1743 5.11 %
Rwork0.2186 --
obs0.2216 34099 98.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 223.58 Å2 / Biso mean: 96.6887 Å2 / Biso min: 57.01 Å2
Refinement stepCycle: LAST / Resolution: 2.85→43.263 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7406 1544 20 57 9027
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099324
X-RAY DIFFRACTIONf_angle_d1.25312954
X-RAY DIFFRACTIONf_chiral_restr0.0491470
X-RAY DIFFRACTIONf_plane_restr0.0071376
X-RAY DIFFRACTIONf_dihedral_angle_d16.7813674
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.85-2.93380.37881500.35822692284298
2.9338-3.02850.37751440.32332701284598
3.0285-3.13670.37781450.29822644278998
3.1367-3.26230.31641360.28152699283598
3.2623-3.41070.38071400.27782742288298
3.4107-3.59040.35321390.28032713285298
3.5904-3.81530.39451490.29342688283798
3.8153-4.10960.2761470.21342659280698
4.1096-4.52280.21951450.17532754289998
4.5228-5.17630.23941460.16972688283498
5.1763-6.51810.27261610.19252723288499
6.5181-43.26750.21121410.19252653279497

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