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3cdu

Crystal structure of coxsackievirus B3 RNA-dependent RNA polymerase (3Dpol) in complex with a pyrophosphate

Method: X-RAY DIFFRACTION Dmax: 71.7 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

RNA-directed RNA polymerase 3D-POL

Coxsackievirus B3

UniProt P03313

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1724–2185 Not recorded CL CHLORIDE ION × 6 SO4 SULFATE ION × 1 ACT ACETATE ION × 6 POP PYROPHOSPHATE 2- × 1 GOL GLYCEROL × 30 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 10；293 K；2M ammonium sulfate, 0.1M CAPS, 0.2M lithium sulfate, pH 10, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.10 Å R-free 0.220

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3CDU Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3CDW Crystal structure of coxsackievirus B3 RNA-dependent RNA polymerase (3Dpol) in complex with protein primer VPg and a pyrophosphate Deposited 2008-02-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1724–2185（462 aa）
Chain H 1519–1540（22 aa）
Not recorded CL CHLORIDE ION × 7 ACT ACETATE ION × 6 POP PYROPHOSPHATE 2- × 1 GOL GLYCEROL × 27 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10；293 K；2M ammonium sulfate, 0.1M CAPS, 0.2M lithium sulfate, pH 10, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.220
4WFX Coxsackievirus B3 Polymerase - F232L Mutant - NaCl Crystal Form Deposited 2014-09-17 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1724–2185（462 aa） Fragment：unp residues 1724-2185
Mutation：F232L NA SODIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289 K；0.085 M HEPES, 3.655 M NaCl, 15% Glycerol
Resolution 1.81 Å R-free 0.233
4WFY Coxsackievirus B3 Polymerase - F232L Mutant - AmSO4 Crystal Form Deposited 2014-09-17 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1724–2185（462 aa） Fragment：unp residues 1724-2185
Mutation：F232L GOL GLYCEROL × 3 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289 K；0.085 M Tris, 1.275 M Ammonium Sulfate , 25% Glycerol
Resolution 2.06 Å R-free 0.220
4WFZ Coxsackievirus B3 3Dpol RNA Dependent RNA Polymerase - NaCl Crystal Form Deposited 2014-09-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1724–2185（462 aa） Fragment：unp residues 1724-2185
Not recorded NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289 K；0.085 M HEPES, 3.6 M NaCl , 15% Glycerol
Resolution 1.80 Å R-free 0.231
4Y2A Crystal Structure of Coxsackie Virus B3 3D polymerase in complex with GPC-N114 inhibitor Deposited 2015-02-09 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1724–2185（462 aa）
Not recorded 1FS 2,2'-[(4-chlorobenzene-1,2-diyl)bis(oxy)]bis(5-nitrobenzonitrile) × 1 SO4 SULFATE ION × 5 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；50 mM Tris pH 7.5, 24.5% (w/v) glycerol, 1.29 M ammonium sulfate.
Resolution 2.90 Å R-free 0.250
6GZV Identification of a druggable VP1-VP3 interprotomer pocket in the capsid of enteroviruses Deposited 2018-07-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 240 PDB declaration: 240-meric
Chain A 571–854（284 aa）
Chain B 70–332（263 aa）
Chain C 333–570（238 aa）
Chain D 1–69（69 aa）
Not recorded FHK 4-[[4-[1,3-bis(oxidanylidene)isoindol-2-yl]phenyl]sulfonylamino]benzoic acid × 60 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6ZCL Coxsackievirus B3 in complex with capsid binder compound 17 Deposited 2020-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 240 PDB declaration: 240-meric
Chain A 583–851（269 aa）
Chain B 79–330（252 aa）
Chain C 333–569（237 aa）
Chain D 2–69（68 aa）
Not recorded FHK 4-[[4-[1,3-bis(oxidanylidene)isoindol-2-yl]phenyl]sulfonylamino]benzoic acid × 60 MYR MYRISTIC ACID × 60 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6ZCL Coxsackievirus B3 in complex with capsid binder compound 17 Deposited 2020-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 583–851（269 aa）
Chain B 79–330（252 aa）
Chain C 333–569（237 aa）
Chain D 2–69（68 aa）
Not recorded FHK 4-[[4-[1,3-bis(oxidanylidene)isoindol-2-yl]phenyl]sulfonylamino]benzoic acid × 1 MYR MYRISTIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6ZCL Coxsackievirus B3 in complex with capsid binder compound 17 Deposited 2020-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 20 PDB declaration: eicosameric
Chain A 583–851（269 aa）
Chain B 79–330（252 aa）
Chain C 333–569（237 aa）
Chain D 2–69（68 aa）
Not recorded FHK 4-[[4-[1,3-bis(oxidanylidene)isoindol-2-yl]phenyl]sulfonylamino]benzoic acid × 5 MYR MYRISTIC ACID × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6ZCL Coxsackievirus B3 in complex with capsid binder compound 17 Deposited 2020-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 24 PDB declaration: 24-meric
Chain A 583–851（269 aa）
Chain B 79–330（252 aa）
Chain C 333–569（237 aa）
Chain D 2–69（68 aa）
Not recorded FHK 4-[[4-[1,3-bis(oxidanylidene)isoindol-2-yl]phenyl]sulfonylamino]benzoic acid × 6 MYR MYRISTIC ACID × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6ZCL Coxsackievirus B3 in complex with capsid binder compound 17 Deposited 2020-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 583–851（269 aa）
Chain B 79–330（252 aa）
Chain C 333–569（237 aa）
Chain D 2–69（68 aa）
Not recorded FHK 4-[[4-[1,3-bis(oxidanylidene)isoindol-2-yl]phenyl]sulfonylamino]benzoic acid × 1 MYR MYRISTIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7LMS Structure of human SetD3 methyl-transferase in complex with 2A protease from Coxsackievirus B3 Deposited 2021-02-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 855–1001（147 aa）
Mutation：C107A ZN ZINC ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7QUW CVB3-3Cpro in complex with inhibitor MG-78 Deposited 2022-01-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 1541–1720（180 aa）
Not recorded I70 (1R,2S,5S)-N-{(2S,3R)-4-amino-3-hydroxy-4-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}-3-[N-(tert-butylcarbamoyl)-3-methyl-L-valyl]-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.6；293 K；0.2 M MgCl2 0.1M Tris-HCl pH 8.6 25% PEG 3350
Resolution 1.65 Å R-free 0.279
7VXH Coxsackievirus B3 full particle at pH7.4 (VP3-234Q) Deposited 2021-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 240 PDB declaration: 240-meric
Chain A 571–854（284 aa）
Chain B 70–332（263 aa）
Chain C 333–570（238 aa）
Chain D 1–69（69 aa）
Not recorded PLM PALMITIC ACID × 60 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
7VXH Coxsackievirus B3 full particle at pH7.4 (VP3-234Q) Deposited 2021-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 571–854（284 aa）
Chain B 70–332（263 aa）
Chain C 333–570（238 aa）
Chain D 1–69（69 aa）
Not recorded PLM PALMITIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
7VXH Coxsackievirus B3 full particle at pH7.4 (VP3-234Q) Deposited 2021-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 20 PDB declaration: eicosameric
Chain A 571–854（284 aa）
Chain B 70–332（263 aa）
Chain C 333–570（238 aa）
Chain D 1–69（69 aa）
Not recorded PLM PALMITIC ACID × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
7VXH Coxsackievirus B3 full particle at pH7.4 (VP3-234Q) Deposited 2021-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 24 PDB declaration: 24-meric
Chain A 571–854（284 aa）
Chain B 70–332（263 aa）
Chain C 333–570（238 aa）
Chain D 1–69（69 aa）
Not recorded PLM PALMITIC ACID × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
7VXH Coxsackievirus B3 full particle at pH7.4 (VP3-234Q) Deposited 2021-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 571–854（284 aa）
Chain B 70–332（263 aa）
Chain C 333–570（238 aa）
Chain D 1–69（69 aa）
Not recorded PLM PALMITIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
7VXL Coxsackievirus B3 A-particle at pH7.4 (VP3-234Q) Deposited 2021-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 180 PDB declaration: 180-meric
Chain A 571–854（284 aa）
Chain B 70–332（263 aa）
Chain C 333–570（238 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7VXL Coxsackievirus B3 A-particle at pH7.4 (VP3-234Q) Deposited 2021-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 571–854（284 aa）
Chain B 70–332（263 aa）
Chain C 333–570（238 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7VXL Coxsackievirus B3 A-particle at pH7.4 (VP3-234Q) Deposited 2021-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 15 PDB declaration: pentadecameric
Chain A 571–854（284 aa）
Chain B 70–332（263 aa）
Chain C 333–570（238 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7VXL Coxsackievirus B3 A-particle at pH7.4 (VP3-234Q) Deposited 2021-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 18 PDB declaration: octadecameric
Chain A 571–854（284 aa）
Chain B 70–332（263 aa）
Chain C 333–570（238 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7VXL Coxsackievirus B3 A-particle at pH7.4 (VP3-234Q) Deposited 2021-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 571–854（284 aa）
Chain B 70–332（263 aa）
Chain C 333–570（238 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7VXN Coxsackievirus B3 Empty particle at pH7.4 (VP3-234Q) Deposited 2021-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 180 PDB declaration: 180-meric
Chain A 571–854（284 aa）
Chain B 70–332（263 aa）
Chain C 333–570（238 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.53 Å
7VXN Coxsackievirus B3 Empty particle at pH7.4 (VP3-234Q) Deposited 2021-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 571–854（284 aa）
Chain B 70–332（263 aa）
Chain C 333–570（238 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.53 Å
7VXN Coxsackievirus B3 Empty particle at pH7.4 (VP3-234Q) Deposited 2021-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 15 PDB declaration: pentadecameric
Chain A 571–854（284 aa）
Chain B 70–332（263 aa）
Chain C 333–570（238 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.53 Å
7VXN Coxsackievirus B3 Empty particle at pH7.4 (VP3-234Q) Deposited 2021-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 18 PDB declaration: octadecameric
Chain A 571–854（284 aa）
Chain B 70–332（263 aa）
Chain C 333–570（238 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.53 Å
7VXN Coxsackievirus B3 Empty particle at pH7.4 (VP3-234Q) Deposited 2021-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 571–854（284 aa）
Chain B 70–332（263 aa）
Chain C 333–570（238 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.53 Å
7VXZ Coxsackievirus B3 at pH7.4 (VP3-234Q) incubation with coxsackievirus and adenovirus receptor for 20min Deposited 2021-11-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 300 PDB declaration: 300-meric
Chain A 571–854（284 aa）
Chain B 70–332（263 aa）
Chain C 333–570（238 aa）
Chain D 1–69（69 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.19 Å
7VXZ Coxsackievirus B3 at pH7.4 (VP3-234Q) incubation with coxsackievirus and adenovirus receptor for 20min Deposited 2021-11-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 571–854（284 aa）
Chain B 70–332（263 aa）
Chain C 333–570（238 aa）
Chain D 1–69（69 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.19 Å
7VXZ Coxsackievirus B3 at pH7.4 (VP3-234Q) incubation with coxsackievirus and adenovirus receptor for 20min Deposited 2021-11-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 25 PDB declaration: 25-meric
Chain A 571–854（284 aa）
Chain B 70–332（263 aa）
Chain C 333–570（238 aa）
Chain D 1–69（69 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.19 Å
7VXZ Coxsackievirus B3 at pH7.4 (VP3-234Q) incubation with coxsackievirus and adenovirus receptor for 20min Deposited 2021-11-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain A 571–854（284 aa）
Chain B 70–332（263 aa）
Chain C 333–570（238 aa）
Chain D 1–69（69 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.19 Å
7VXZ Coxsackievirus B3 at pH7.4 (VP3-234Q) incubation with coxsackievirus and adenovirus receptor for 20min Deposited 2021-11-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 571–854（284 aa）
Chain B 70–332（263 aa）
Chain C 333–570（238 aa）
Chain D 1–69（69 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.19 Å
7VY5 Coxsackievirus B3 (VP3-234Q) incubation with CD55 at pH7.4 Deposited 2021-11-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 300 PDB declaration: 300-meric
Chain A 583–850（268 aa）
Chain B 77–332（256 aa）
Chain C 333–570（238 aa）
Chain D 2–69（68 aa）
Not recorded PLM PALMITIC ACID × 60 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.15 Å
7VY5 Coxsackievirus B3 (VP3-234Q) incubation with CD55 at pH7.4 Deposited 2021-11-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 583–850（268 aa）
Chain B 77–332（256 aa）
Chain C 333–570（238 aa）
Chain D 2–69（68 aa）
Not recorded PLM PALMITIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.15 Å
7VY5 Coxsackievirus B3 (VP3-234Q) incubation with CD55 at pH7.4 Deposited 2021-11-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 25 PDB declaration: 25-meric
Chain A 583–850（268 aa）
Chain B 77–332（256 aa）
Chain C 333–570（238 aa）
Chain D 2–69（68 aa）
Not recorded PLM PALMITIC ACID × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.15 Å
7VY5 Coxsackievirus B3 (VP3-234Q) incubation with CD55 at pH7.4 Deposited 2021-11-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain A 583–850（268 aa）
Chain B 77–332（256 aa）
Chain C 333–570（238 aa）
Chain D 2–69（68 aa）
Not recorded PLM PALMITIC ACID × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.15 Å
7VY5 Coxsackievirus B3 (VP3-234Q) incubation with CD55 at pH7.4 Deposited 2021-11-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 583–850（268 aa）
Chain B 77–332（256 aa）
Chain C 333–570（238 aa）
Chain D 2–69（68 aa）
Not recorded PLM PALMITIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.15 Å
7VYK Coxsackievirus B3 at pH7.4 (VP3-234Q) incubation with coxsackievirus and adenovirus receptor for 10min Deposited 2021-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 300 PDB declaration: 300-meric
Chain A 583–849（267 aa）
Chain B 70–332（263 aa）
Chain C 333–570（238 aa）
Chain D 1–69（69 aa）
Not recorded PLM PALMITIC ACID × 60 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.79 Å
7VYK Coxsackievirus B3 at pH7.4 (VP3-234Q) incubation with coxsackievirus and adenovirus receptor for 10min Deposited 2021-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 583–849（267 aa）
Chain B 70–332（263 aa）
Chain C 333–570（238 aa）
Chain D 1–69（69 aa）
Not recorded PLM PALMITIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.79 Å
7VYK Coxsackievirus B3 at pH7.4 (VP3-234Q) incubation with coxsackievirus and adenovirus receptor for 10min Deposited 2021-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 25 PDB declaration: 25-meric
Chain A 583–849（267 aa）
Chain B 70–332（263 aa）
Chain C 333–570（238 aa）
Chain D 1–69（69 aa）
Not recorded PLM PALMITIC ACID × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.79 Å
7VYK Coxsackievirus B3 at pH7.4 (VP3-234Q) incubation with coxsackievirus and adenovirus receptor for 10min Deposited 2021-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain A 583–849（267 aa）
Chain B 70–332（263 aa）
Chain C 333–570（238 aa）
Chain D 1–69（69 aa）
Not recorded PLM PALMITIC ACID × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.79 Å
7VYK Coxsackievirus B3 at pH7.4 (VP3-234Q) incubation with coxsackievirus and adenovirus receptor for 10min Deposited 2021-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 583–849（267 aa）
Chain B 70–332（263 aa）
Chain C 333–570（238 aa）
Chain D 1–69（69 aa）
Not recorded PLM PALMITIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.79 Å
7VYL Coxsackievirus B3 at pH5.5 (VP3-234Q) incubation with coxsackievirus and adenovirus receptor for 20min Deposited 2021-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 300 PDB declaration: 300-meric
Chain A 571–851（281 aa）
Chain B 70–332（263 aa）
Chain C 333–570（238 aa）
Chain D 1–69（69 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.79 Å
7VYL Coxsackievirus B3 at pH5.5 (VP3-234Q) incubation with coxsackievirus and adenovirus receptor for 20min Deposited 2021-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 571–851（281 aa）
Chain B 70–332（263 aa）
Chain C 333–570（238 aa）
Chain D 1–69（69 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.79 Å
7VYL Coxsackievirus B3 at pH5.5 (VP3-234Q) incubation with coxsackievirus and adenovirus receptor for 20min Deposited 2021-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 25 PDB declaration: 25-meric
Chain A 571–851（281 aa）
Chain B 70–332（263 aa）
Chain C 333–570（238 aa）
Chain D 1–69（69 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.79 Å
7VYL Coxsackievirus B3 at pH5.5 (VP3-234Q) incubation with coxsackievirus and adenovirus receptor for 20min Deposited 2021-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain A 571–851（281 aa）
Chain B 70–332（263 aa）
Chain C 333–570（238 aa）
Chain D 1–69（69 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.79 Å
7VYL Coxsackievirus B3 at pH5.5 (VP3-234Q) incubation with coxsackievirus and adenovirus receptor for 20min Deposited 2021-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 571–851（281 aa）
Chain B 70–332（263 aa）
Chain C 333–570（238 aa）
Chain D 1–69（69 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.79 Å
8S6F A Structural Investigation of the Interaction between a GC-376-Based Peptidomimetic PROTAC and Its Precursor with the Viral Main Protease of Coxsackievirus B3 Deposited 2024-02-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1541–1720（180 aa）
Not recorded VQR methyl (4~{S})-4-[[(2~{S})-4-methyl-2-(phenylmethoxycarbonylamino)pentanoyl]amino]-5-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]pentanoate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Tris-HCl, 0.2 M MgCl2, 26% PEG4000
Resolution 1.93 Å R-free 0.264
9D9O Crystal structure of CVB3 replication-linked RNA stem-loop D in complex with 3C protein Deposited 2024-08-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: trimeric
Chain A 1541–1723（183 aa）
Chain B 1541–1723（183 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；291.15 K；DL-Malic Acid, PEG 3350
Resolution 2.41 Å R-free 0.238
9D9P Crystal structure of CVB3 replication-linked RNA in complex with 3C protein Deposited 2024-08-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: trimeric
Chain A 1541–1723（183 aa）
Chain B 1541–1723（183 aa）
Not recorded PO4 PHOSPHATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；291.15 K；Glycerol, Bis-Tris, Ammonium Sulfate
Resolution 2.69 Å R-free 0.232
9DCF Structure of Coxsackievirus B3 cloverleaf RNA in complex with 3Cpro dimer Deposited 2024-08-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: trimeric
Chain A 1541–1723（183 aa） Fragment：UNP residues 1541-1723
Chain B 1541–1723（183 aa） Fragment：UNP residues 1541-1723
Mutation：C147A,G55A,D58A,V63A Mutation：C147A,G55A,D58A,V63A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293.15 K；8% v/v Tacsimate, pH 6.0, 25% w/v PEG3350
Resolution 2.87 Å R-free 0.273

20 other PDB entries and 52 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name POLG_CXB3N
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–462； UniProt 1724–2185

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 3cdu

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3cdu
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3cdu
Deposition date deposition_date2008-02-27
Structure title titleCrystal structure of coxsackievirus B3 RNA-dependent RNA polymerase (3Dpol) in complex with a pyrophosphate
Keywords keywordscoxsackievirus, RNA-dependent RNA polymerase, VIZIER Viral Enzymes Involved in Replication, Transferase; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier24.09 Å
Radius of gyration Rg (electron density) rg_electron23.05 Å
Forward intensity I(0) i053030000.00
Molecular weight molecular_weight56784.0 kDa
Excluded volume excluded_volume71099 ų
Envelope volume envelope_volume84540 ų
Hydration-shell volume shell_volume29759 ų
Envelope diameter envelope_diameter73.2 Å
Shell Rg shell_rg30.74 Å
Envelope Rg envelope_rg22.83 Å
Shape Rg shape_rg23.06 Å
Total Rg total_rg23.87 Å
Total atoms total_atoms3971
Residues n_residues468
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax71.7 Å
Rg (real space) rg_real23.88 Å
Rg uncertainty (real space) rg_real_error0.28 Å
I(0) (real space) i0_real5.3030e+07
I(0) uncertainty (real space) i0_real_error6.4810e+05
Rg (reciprocal space) rg_reciprocal23.93 Å
I(0) (reciprocal space) i0_reciprocal53030000.0000
Solution quality estimate total_estimate0.9090
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary70.6 Å
Skewness Skewness skewness0.034
Kurtosis Kurtosis kurtosis-0.568
Angular range angular_range— – 0.3300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha14720000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.946; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.994
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3cdua1
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.8 — DNA/RNA polymerases
Superfamily Superfamily superfamilye.8.1 — DNA/RNA polymerases
Family Family familye.8.1.4 — RNA-dependent RNA-polymerase
Domain ID domain_idd3cdua2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id3cduA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily270 — Reverse transcriptase/Diguanylate cyclase domain
Domain ID domain_id3cduA03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology960 — Mitochondrial Import Receptor Subunit Tom20; Chain A
Homologous superfamily homologous superfamily20 —
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8. Citations (1)

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9. Files and Curves (10)