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- PDB-4wm8: Crystal Structure of Human Enterovirus D68 -

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Basic information

Entry
Database: PDB / ID: 4wm8
TitleCrystal Structure of Human Enterovirus D68
Components
  • VP1
  • VP2
  • VP3
  • VP4
KeywordsVIRUS / Enterovirus / Capsid / Beta jelly roll
Function / homology
Function and homology information


symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway / 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 / protein sequestering activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell ...symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway / 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 / protein sequestering activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / viral capsid / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / : / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / RNA helicase activity / induction by virus of host autophagy / symbiont entry into host cell / 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 / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding / cytoplasm
Similarity search - Function
Jelly Rolls - #20 / Picornavirus coat protein VP4 superfamily / 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 VP4 superfamily / 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 / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
DECANOIC ACID / Genome polyprotein / VP4 / Genome polyprotein
Similarity search - Component
Biological speciesEnterovirus D68
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsLiu, Y. / Sheng, J. / Fokine, A. / Meng, G. / Long, F. / Kuhn, R.J. / Rossmann, M.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI11219 United States
CitationJournal: Science / Year: 2015
Title: Virus structure. Structure and inhibition of EV-D68, a virus that causes respiratory illness in children.
Authors: Liu, Y. / Sheng, J. / Fokine, A. / Meng, G. / Shin, W.H. / Long, F. / Kuhn, R.J. / Kihara, D. / Rossmann, M.G.
History
DepositionOct 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Other / Refinement description / Source and taxonomy
Category: cell / citation ...cell / citation / entity_src_nat / pdbx_audit_support / pdbx_database_status / software
Item: _cell.Z_PDB / _citation.journal_id_CSD ..._cell.Z_PDB / _citation.journal_id_CSD / _entity_src_nat.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _software.classification
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 27, 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_struct_oper_list / refine_hist
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 / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,2035
Polymers95,0304
Non-polymers1721
Water3,675204
1
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,712,157300
Polymers5,701,821240
Non-polymers10,33660
Water4,324240
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: VP2
C: VP3
D: VP4
hetero molecules
x 5


  • icosahedral pentamer
  • 476 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)476,01325
Polymers475,15220
Non-polymers8615
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 571 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)571,21630
Polymers570,18224
Non-polymers1,0346
Water43224
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: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 15


  • crystal asymmetric unit, crystal frame
  • 1.43 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)1,428,03975
Polymers1,425,45560
Non-polymers2,58415
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation14
Unit cell
Length a, b, c (Å)327.000, 347.800, 357.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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(0.5, -0.80901699, -0.30901699), (0.809017, 0.30901699, 0.5), (-0.30901699, -0.5, 0.809017)
3generate(-0.30901699, -0.5, -0.809017), (0.5, -0.809017, 0.309017), (-0.80901699, -0.309017, 0.5)
4generate(-0.309017, 0.5, -0.809017), (-0.5, -0.80901699, -0.309017), (-0.809017, 0.30901699, 0.5)
5generate(0.5, 0.80901699, -0.309017), (-0.80901699, 0.309017, -0.5), (-0.309017, 0.5, 0.80901699)
6generate(-0.80901699, 0.309017, -0.50000001), (0.30901699, -0.5, -0.80901699), (-0.49999999, -0.809017, 0.30901699)
7generate(1), (-1), (-1)
8generate(0.809017, 0.30901699, 0.5), (0.30901699, 0.5, -0.80901699), (-0.5, 0.809017, 0.30901699)
9generate(0.5, -0.809017, 0.30901699), (0.80901699, 0.30901699, -0.5), (0.309017, 0.5, 0.80901699)
10generate(-0.5, -0.80901699, -0.309017), (0.80901699, -0.309017, -0.5), (0.309017, -0.5, 0.80901699)
11generate(1), (-1), (-1)
12generate(-0.30901699, -0.5, 0.809017), (-0.5, 0.80901699, 0.30901699), (-0.809017, -0.30901699, -0.5)
13generate(-0.80901699, -0.309017, 0.5), (0.30901699, 0.5, 0.809017), (-0.5, 0.809017, -0.309017)
14generate(-0.809017, 0.30901699, 0.5), (0.309017, -0.5, 0.809017), (0.5, 0.80901699, 0.309017)
15generate(-0.309017, 0.5, 0.80901699), (-0.5, -0.80901699, 0.309017), (0.80901699, -0.309017, 0.5)
DetailsThe biological assembly is an icosahedron generated from an icosahedral asymmetric unit, which consists of entities 1 (chain A), 2 (Chain B), 3 (chain C) and 4 (chain D)

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein VP1


Mass: 32784.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Grown in human rhabdosarcoma cells / Source: (natural) Enterovirus D68 / Strain: Fermon CA62-1 / References: UniProt: Q9YLJ3
#2: Protein VP2


Mass: 27706.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Grown in human rhabdosarcoma cells / Source: (natural) Enterovirus D68 / Strain: Fermon CA62-1 / References: UniProt: Q68T42
#3: Protein VP3


Mass: 27202.881 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Grown in human rhabdosarcoma cells / Source: (natural) Enterovirus D68 / Strain: Fermon CA62-1 / References: UniProt: Q68T42
#4: Protein VP4


Mass: 7336.960 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Grown in human rhabdosarcoma cells / Source: (natural) Enterovirus D68 / Strain: Fermon CA62-1 / References: UniProt: Q8QWD4

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Non-polymers , 2 types, 205 molecules

#5: Chemical ChemComp-DKA / DECANOIC ACID / Capric acid


Mass: 172.265 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 3.57 Å3/Da / Density % sol: 65.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Sodium Acetate (pH 4.5), 3.5 M Sodium Formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9787 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 748623 / % possible obs: 55.7 % / Redundancy: 2.1 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.077 / Rrim(I) all: 0.131 / Χ2: 1.607 / Net I/av σ(I): 8.709 / Net I/σ(I): 9.3 / Num. measured all: 1586943
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.0720.754556560.6540.5710.9511.21341.6
2.07-2.151.90.589694450.7360.4490.7441.29651.9
2.15-2.251.90.439729140.8120.3370.5561.3754.5
2.25-2.3720.343762310.8670.2660.4371.44256.9
2.37-2.522.10.269791410.9010.2110.3441.49759
2.52-2.712.10.206807970.9320.1610.2631.6160.3
2.71-2.992.20.15827450.9620.1160.1911.79661.6
2.99-3.422.20.1816800.9810.0760.1262.00460.8
3.42-4.312.30.072784080.9880.0520.091.99258.2
4.31-502.50.061716060.9920.040.0741.42252.5

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Processing

Software
NameVersionClassification
CNS1.3refinement
PDB_EXTRACT3.15data extraction
HKL-3000phasing
HKL-2000data reduction
HKL-2000data scaling
CNS1.3phasing
RefinementResolution: 2→40.25 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 26427736 / 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
Rfree0.279 37376 5 %RANDOM
Rwork0.275 ---
obs-748174 55.6 %-
Solvent computationSolvent model: FLAT MODEL
Displacement parametersBiso max: 89.72 Å2 / Biso mean: 27.5 Å2 / Biso min: 15.92 Å2
Refine analyzeLuzzati sigma a free: 0.37 Å
Refinement stepCycle: final / Resolution: 2→40.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6277 0 12 204 6493
Biso mean--69.16 30.13 -
Num. residues----805
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it1.912
X-RAY DIFFRACTIONc_scbond_it2.192
X-RAY DIFFRACTIONc_scangle_it3.222.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.36 5080 5.1 %
Rwork0.36 95009 -
all-100089 -
obs--44.8 %
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
X-RAY DIFFRACTION6DRGCNS.PARDRGCNS.TOP

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