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- PDB-5c8c: Crystal structure of recombinant coxsackievirus A16 capsid -

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Basic information

Entry
Database: PDB / ID: 5c8c
TitleCrystal structure of recombinant coxsackievirus A16 capsid
Components
  • VP0
  • VP1
  • VP3
KeywordsVIRUS / HAND-FOOT-AND-MOUTH DISEASE / IMMUNOGENICITY / PICORNAVIRUS / ICOSAHEDRAL VIRUS
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 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 MDA-5 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 NF-kappaB cascade / 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
Jelly Rolls - #20 / 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 ...Jelly Rolls - #20 / 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 / Jelly Rolls / 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 / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
: / STEARIC ACID / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesCoxsackievirus A16
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsRen, J. / Wang, X. / Zhu, L. / Hu, Z. / Gao, Q. / Yang, P. / Li, X. / Wang, J. / Shen, X. / Fry, E.E. ...Ren, J. / Wang, X. / Zhu, L. / Hu, Z. / Gao, Q. / Yang, P. / Li, X. / Wang, J. / Shen, X. / Fry, E.E. / Rao, Z. / Stuart, D.I.
CitationJournal: J.Virol. / Year: 2015
Title: Structures of Coxsackievirus A16 Capsids with Native Antigenicity: Implications for Particle Expansion, Receptor Binding, and Immunogenicity.
Authors: Ren, J. / Wang, X. / Zhu, L. / Hu, Z. / Gao, Q. / Yang, P. / Li, X. / Wang, J. / Shen, X. / Fry, E.E. / Rao, Z. / Stuart, D.I.
History
DepositionJun 25, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references
Revision 1.2Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VP1
B: VP0
C: VP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,2477
Polymers94,8533
Non-polymers3944
Water9,116506
1
A: VP1
B: VP0
C: VP3
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,714,841420
Polymers5,691,172180
Non-polymers23,669240
Water3,243180
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: VP1
B: VP0
C: VP3
hetero molecules
x 5


  • icosahedral pentamer
  • 476 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)476,23735
Polymers474,26415
Non-polymers1,97220
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: VP1
B: VP0
C: VP3
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 571 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)571,48442
Polymers569,11718
Non-polymers2,36724
Water32418
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
Unit cell
Length a, b, c (Å)347.900, 347.900, 347.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number208
Space group name H-MP4232
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.5026, -0.8058, 0.3131), (0.8081, 0.3092, -0.5014), (0.3072, 0.5051, 0.8066)-0.7729, 0.2684, 0.3928
3generate(-0.3038, -0.4968, 0.8129), (0.4979, -0.8103, -0.3091), (0.8122, 0.3109, 0.4936)-0.9447, 0.1602, 0.5684
4generate(-0.3081, 0.5001, 0.8093), (-0.5004, -0.8087, 0.3092), (0.8091, -0.3097, 0.4994)-0.1132, -0.01624, 0.09768
5generate(0.5005, 0.811, 0.303), (-0.807, 0.3103, 0.5024), (0.3134, -0.496, 0.8098)0.6341, -0.4774, -0.5426

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein VP1


Mass: 33078.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxsackievirus A16 (strain Tainan/5079/98)
Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: I3W9E1, UniProt: Q9QF31*PLUS
#2: Protein VP0


Mass: 35120.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxsackievirus A16 (strain Tainan/5079/98)
Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: I3W9E1, UniProt: Q9QF31*PLUS
#3: Protein VP3


Mass: 26654.295 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxsackievirus A16 (strain Tainan/5079/98)
Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: I3W9E1, UniProt: Q9QF31*PLUS

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Non-polymers , 4 types, 510 molecules

#4: Chemical ChemComp-STE / STEARIC ACID


Mass: 284.477 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H36O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 506 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.8M Ammonium citrate dibasic, 0.1 M Sodium acetate trihydrate (pH 5.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jul 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 244135 / % possible obs: 100 % / Redundancy: 12.7 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.217 / Net I/σ(I): 11.3
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.796 / Mean I/σ(I) obs: 4.1 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementResolution: 2.5→49.7 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 24257248.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.172 12014 4.9 %RANDOM
Rwork0.164 ---
obs0.164 244027 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.2312 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 24.1 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.23 Å
Luzzati d res low-6 Å
Luzzati sigma a0.31 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.5→49.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6113 0 23 506 6642
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.06
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.296
X-RAY DIFFRACTIONc_mcangle_it6.7312
X-RAY DIFFRACTIONc_scbond_it9.168
X-RAY DIFFRACTIONc_scangle_it10.4816
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.28 1240 5.2 %
Rwork0.268 22644 -
obs--98.8 %

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