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- PDB-4jgy: Crystal structure of human coxsackievirus A16 uncoating intermedi... -

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Basic information

Entry
Database: PDB / ID: 4jgy
TitleCrystal structure of human coxsackievirus A16 uncoating intermediate (space group P4232)
Components
  • Polyprotein, capsid protein VP1
  • Polyprotein, capsid protein VP2
  • Polyprotein, capsid protein VP3
KeywordsVIRUS / hand-foot-and-mouth disease / picornavirus uncoating / pocket factor / 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 / 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
Biological speciesHuman coxsackievirus A16
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsRen, J. / Wang, X. / Hu, Z. / Gao, Q. / Sun, Y. / Li, X. / Porta, C. / Walter, T.S. / Gilbert, R.J. / Zhao, Y. ...Ren, J. / Wang, X. / Hu, Z. / Gao, Q. / Sun, Y. / Li, X. / Porta, C. / Walter, T.S. / Gilbert, R.J. / Zhao, Y. / Axford, D. / Williams, M. / Mcauley, K. / Rowlands, D.J. / Yin, W. / Wang, J. / Stuart, D.I. / Rao, Z. / Fry, E.E.
CitationJournal: Nat Commun / Year: 2013
Title: Picornavirus uncoating intermediate captured in atomic detail.
Authors: Ren, J. / Wang, X. / Hu, Z. / Gao, Q. / Sun, Y. / Li, X. / Porta, C. / Walter, T.S. / Gilbert, R.J. / Zhao, Y. / Axford, D. / Williams, M. / McAuley, K. / Rowlands, D.J. / Yin, W. / Wang, J. ...Authors: Ren, J. / Wang, X. / Hu, Z. / Gao, Q. / Sun, Y. / Li, X. / Porta, C. / Walter, T.S. / Gilbert, R.J. / Zhao, Y. / Axford, D. / Williams, M. / McAuley, K. / Rowlands, D.J. / Yin, W. / Wang, J. / Stuart, D.I. / Rao, Z. / Fry, E.E.
History
DepositionMar 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyprotein, capsid protein VP1
B: Polyprotein, capsid protein VP2
C: Polyprotein, capsid protein VP3


Theoretical massNumber of molelcules
Total (without water)87,3323
Polymers87,3323
Non-polymers00
Water00
1
A: Polyprotein, capsid protein VP1
B: Polyprotein, capsid protein VP2
C: Polyprotein, capsid protein VP3
x 60


Theoretical massNumber of molelcules
Total (without water)5,239,907180
Polymers5,239,907180
Non-polymers00
Water0
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: Polyprotein, capsid protein VP1
B: Polyprotein, capsid protein VP2
C: Polyprotein, capsid protein VP3
x 5


  • icosahedral pentamer
  • 437 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)436,65915
Polymers436,65915
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Polyprotein, capsid protein VP1
B: Polyprotein, capsid protein VP2
C: Polyprotein, capsid protein VP3
x 6


  • icosahedral 23 hexamer
  • 524 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)523,99118
Polymers523,99118
Non-polymers00
Water0
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
6
A: Polyprotein, capsid protein VP1
B: Polyprotein, capsid protein VP2
C: Polyprotein, capsid protein VP3
x 5


  • crystal asymmetric unit, crystal frame
  • 437 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)436,65915
Polymers436,65915
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation4
Unit cell
Length a, b, c (Å)357.000, 357.000, 357.000
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:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.5, -0.809017, 0.309017), (0.809017, 0.309017, -0.5), (0.309017, 0.5, 0.809017)
3generate(-0.309017, -0.5, 0.809017), (0.5, -0.809017, -0.309017), (0.809017, 0.309017, 0.5)
4generate(-0.309017, 0.5, 0.809017), (-0.5, -0.809017, 0.309017), (0.809017, -0.309017, 0.5)
5generate(0.5, 0.809017, 0.309017), (-0.809017, 0.309017, 0.5), (0.309017, -0.5, 0.809017)

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Components

#1: Protein Polyprotein, capsid protein VP1


Mass: 33090.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GROWN IN VERO CELLS / Source: (natural) Human coxsackievirus A16 / Strain: Ningbo.CHN/028-2/2009 / References: UniProt: I3W9E1
#2: Protein Polyprotein, capsid protein VP2


Mass: 27587.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GROWN IN VERO CELLS / Source: (natural) Human coxsackievirus A16 / Strain: Ningbo.CHN/028-2/2009 / References: UniProt: I3W9E1
#3: Protein Polyprotein, capsid protein VP3


Mass: 26654.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GROWN IN VERO CELLS / Source: (natural) Human coxsackievirus A16 / Strain: Ningbo.CHN/028-2/2009 / References: UniProt: I3W9E1
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 32

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Sample preparation

CrystalDensity Matthews: 4.38 Å3/Da / Density % sol: 71.94 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.88 M lithium sulfate monohydrate, 0.1 M BIS-TRIS propane, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12941
22941
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I0310.9762
SYNCHROTRONDiamond I2420.9686
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELApr 30, 2012
DECTRIS PILATUS 6M2PIXELApr 21, 2012
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97621
20.96861
ReflectionResolution: 3→50 Å / Num. obs: 150962 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 61.4 Å2 / Rmerge(I) obs: 0.604 / Net I/σ(I): 2.8
Reflection shellResolution: 3→3.11 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 0.3 / Num. unique all: 13824 / % possible all: 91.1

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Processing

Software
NameClassification
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3VBR

3vbr


Resolution: 3→49.51 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 19783238.46 / 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
Rfree0.233 1480 1 %RANDOM
Rwork0.227 ---
obs0.227 146270 95.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.1135 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 75.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.42 Å
Luzzati d res low-10 Å
Luzzati sigma a0.77 Å0.66 Å
Refinement stepCycle: LAST / Resolution: 3→49.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5468 0 0 0 5468
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_improper_angle_d1.05
X-RAY DIFFRACTIONc_mcbond_it9.398
X-RAY DIFFRACTIONc_mcangle_it13.3316
X-RAY DIFFRACTIONc_scbond_it16.4312
X-RAY DIFFRACTIONc_scangle_it19.5720
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3→3.11 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.405 104 0.9 %
Rwork0.385 11199 -
obs--74.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top

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