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- PDB-4k4x: Coxsackievirus B3 polymerase elongation complex (r2_form), rna -

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Basic information

Entry
Database: PDB / ID: 4k4x
TitleCoxsackievirus B3 polymerase elongation complex (r2_form), rna
Components
  • 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(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3')
  • RNA (5'-R(P*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 / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase ...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 / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / Picornavirus coat protein VP4 superfamily / Picornavirus coat protein / 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 ...Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / Picornavirus coat protein VP4 superfamily / Picornavirus coat protein / 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) / 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
RNA / RNA (> 10) / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHuman coxsackievirus B3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 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 1.2May 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3')
D: RNA (5'-R(P*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: RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3')
H: RNA (5'-R(P*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: RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3')
L: RNA (5'-R(P*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: RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3')
P: RNA (5'-R(P*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)275,48724
Polymers275,02216
Non-polymers4668
Water13,133729
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: RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3')
D: RNA (5'-R(P*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9647
Polymers68,7554
Non-polymers2083
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: RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3')
H: RNA (5'-R(P*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8726
Polymers68,7554
Non-polymers1162
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: RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3')
L: RNA (5'-R(P*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8726
Polymers68,7554
Non-polymers1162
Water543
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: RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3')
P: RNA (5'-R(P*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7805
Polymers68,7554
Non-polymers241
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.001, 61.013, 195.137
Angle α, β, γ (deg.)90.02, 89.98, 78.36
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules AEIM

#1: Protein
RNA-dependent RNA polymerase


Mass: 53624.203 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 1724-2185
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, RNA-directed RNA polymerase

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RNA chain , 3 types, 12 molecules BFJNCGKODHLP

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


Mass: 4526.756 Da / Num. of mol.: 4 / Source method: obtained synthetically
#4: RNA chain
RNA (5'-R(P*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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Non-polymers , 3 types, 737 molecules

#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 729 / 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: 2.59 Å3/Da / Density % sol: 52.44 %
Crystal growTemperature: 289 K / 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
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: 2.37→48.78 Å / Num. obs: 109647 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 1.99 % / Biso Wilson estimate: 41.68 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 6.8
Reflection shellResolution: 2.37→2.45 Å / Redundancy: 1.94 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 1.5 / % possible all: 96.6

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
d*TREKdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.37→44.01 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.31 / σ(F): 1.96 / Phase error: 29.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.241 5506 5.04 %
Rwork0.204 --
obs0.205 109273 97.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.46 Å2
Refinement stepCycle: LAST / Resolution: 2.37→44.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14772 2668 28 729 18197
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00818140
X-RAY DIFFRACTIONf_angle_d1.125136
X-RAY DIFFRACTIONf_dihedral_angle_d15.4957052
X-RAY DIFFRACTIONf_chiral_restr0.0482852
X-RAY DIFFRACTIONf_plane_restr0.0062728
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-2.39690.38451860.32013389X-RAY DIFFRACTION96
2.3969-2.42510.33221900.29573366X-RAY DIFFRACTION96
2.4251-2.45470.34871900.2973370X-RAY DIFFRACTION96
2.4547-2.48580.35051890.29273432X-RAY DIFFRACTION96
2.4858-2.51850.32821790.28663402X-RAY DIFFRACTION96
2.5185-2.5530.37211720.30773536X-RAY DIFFRACTION97
2.553-2.58940.3111490.28263367X-RAY DIFFRACTION97
2.5894-2.62810.35332050.27143409X-RAY DIFFRACTION97
2.6281-2.66920.32451830.26353483X-RAY DIFFRACTION97
2.6692-2.71290.30061730.26373428X-RAY DIFFRACTION98
2.7129-2.75970.2841940.25623556X-RAY DIFFRACTION97
2.7597-2.80990.30261830.24843331X-RAY DIFFRACTION98
2.8099-2.86390.30321780.25233478X-RAY DIFFRACTION98
2.8639-2.92230.31411830.25183580X-RAY DIFFRACTION98
2.9223-2.98590.28351840.24313333X-RAY DIFFRACTION98
2.9859-3.05530.28432060.23713578X-RAY DIFFRACTION98
3.0553-3.13170.3031860.253387X-RAY DIFFRACTION98
3.1317-3.21630.28051840.23523587X-RAY DIFFRACTION99
3.2163-3.3110.24921920.21693362X-RAY DIFFRACTION98
3.311-3.41780.23361710.20323554X-RAY DIFFRACTION99
3.4178-3.53990.21872010.19733453X-RAY DIFFRACTION98
3.5399-3.68160.21381900.18853505X-RAY DIFFRACTION98
3.6816-3.8490.2241930.18623477X-RAY DIFFRACTION99
3.849-4.05180.20671600.16953539X-RAY DIFFRACTION98
4.0518-4.30550.18021820.1553492X-RAY DIFFRACTION99
4.3055-4.63760.15621860.14593463X-RAY DIFFRACTION99
4.6376-5.10360.18921710.15533550X-RAY DIFFRACTION99
5.1036-5.84070.21411700.17333462X-RAY DIFFRACTION99
5.8407-7.35310.21082090.1853482X-RAY DIFFRACTION99
7.3531-44.01950.20211670.17433416X-RAY DIFFRACTION96

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