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

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Basic information

Entry
Database: PDB / ID: 4jgz
TitleCrystal structure of human coxsackievirus A16 uncoating intermediate (space group I222)
Components
  • Polyprotein, capsid protein VP1Proteolysis
  • Polyprotein, capsid protein VP2Proteolysis
  • Polyprotein, capsid protein VP3Proteolysis
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 / endocytosis involved in viral entry into host cell / cytoplasmic vesicle membrane / : ...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 / endocytosis involved in viral entry into host cell / cytoplasmic vesicle membrane / : / 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 / structural molecule activity / virion attachment to host cell / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Jelly Rolls - #20 / 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) ...Jelly Rolls - #20 / 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 / 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 / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / 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

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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
Water0
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 15


  • crystal asymmetric unit, crystal frame
  • 1.31 MDa, 45 polymers
Theoretical massNumber of molelcules
Total (without water)1,309,97745
Polymers1,309,97745
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation14
Unit cell
Length a, b, c (Å)338.400, 360.200, 366.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(-0.809017, 0.309017, 0.5), (-0.309017, 0.5, -0.809017), (-0.5, -0.809017, -0.309017)
3generate(0.309017, 0.5, 0.809017), (-0.5, 0.809017, -0.309017), (-0.809017, -0.309017, 0.5)
4generate(-0.809017, -0.309017, -0.5), (0.309017, 0.5, -0.809017), (0.5, -0.809017, -0.309017)
5generate(0.309017, -0.5, -0.809017), (0.5, 0.809017, -0.309017), (0.809017, -0.309017, 0.5)
6generate(-1), (-1), (1)
7generate(0.309017, -0.5, 0.809017), (0.5, 0.809017, 0.309017), (-0.809017, 0.309017, 0.5)
8generate(0.5, -0.809017, 0.309017), (0.809017, 0.309017, -0.5), (0.309017, 0.5, 0.809017)
9generate(-0.309017, -0.5, 0.809017), (-0.5, 0.809017, 0.309017), (-0.809017, -0.309017, -0.5)
10generate(-0.5, -0.809017, 0.309017), (-0.809017, 0.309017, -0.5), (0.309017, -0.5, -0.809017)
11generate(1), (-1), (-1)
12generate(-0.5, -0.809017, -0.309017), (0.809017, -0.309017, -0.5), (0.309017, -0.5, 0.809017)
13generate(-0.809017, -0.309017, 0.5), (-0.309017, -0.5, -0.809017), (0.5, -0.809017, 0.309017)
14generate(0.5, -0.809017, -0.309017), (0.809017, 0.309017, 0.5), (-0.309017, -0.5, 0.809017)
15generate(0.809017, -0.309017, 0.5), (-0.309017, 0.5, 0.809017), (-0.5, -0.809017, 0.309017)

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Components

#1: Protein Polyprotein, capsid protein VP1 / Proteolysis


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 / Proteolysis


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 / Proteolysis


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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 12

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Sample preparation

CrystalDensity Matthews: 4.32 Å3/Da / Density % sol: 71.55 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.0 M to 0.75 M lithium sulfate monohydrate, 4-6% PEG6000, 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97621
20.96861
ReflectionResolution: 3→50 Å / Num. obs: 110576 / % possible obs: 25.1 % / Observed criterion σ(I): -3 / Redundancy: 1.1 % / Biso Wilson estimate: 38.2 Å2 / Rmerge(I) obs: 0.459 / Net I/σ(I): 1.1
Reflection shellResolution: 3→3.11 Å / Redundancy: 1.1 % / Mean I/σ(I) obs: 0.3 / Num. unique all: 5050 / % possible all: 11.5

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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→49.46 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 11422859.37 / 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
Rfree0.311 5353 5 %RANDOM
Rwork0.286 ---
obs0.286 108008 24.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 23.2649 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 58.9 Å2
Baniso -1Baniso -2Baniso -3
1-2.25 Å20 Å20 Å2
2---0.97 Å20 Å2
3----1.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.58 Å0.52 Å
Luzzati d res low-10 Å
Luzzati sigma a0.69 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 3→49.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5468 0 0 0 5468
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_improper_angle_d0.97
X-RAY DIFFRACTIONc_mcbond_it12.238
X-RAY DIFFRACTIONc_mcangle_it17.4716
X-RAY DIFFRACTIONc_scbond_it19.5312
X-RAY DIFFRACTIONc_scangle_it24.420
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3→3.11 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.38 189 5 %
Rwork0.355 3558 -
obs--8.5 %
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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