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- PDB-5bno: Crystal structure of human enterovirus D68 in complex with 6'SLN -

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Basic information

Entry
Database: PDB / ID: 5bno
TitleCrystal structure of human enterovirus D68 in complex with 6'SLN
Components(Capsid protein ...Capsid) x 4
KeywordsVIRUS / Enterovirus / Capsid / Beta jelly roll / Receptor
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 / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / : / symbiont-mediated suppression of host toll-like receptor signaling pathway / 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 / 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 / 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 / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
6'-sialyl-N-acetyllactosamine / Genome polyprotein
Similarity search - Component
Biological speciesEnterovirus D68
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsLiu, Y. / Sheng, J. / Meng, G. / Xiao, C. / Rossmann, M.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI011219 United States
CitationJournal: Nat Commun / Year: 2015
Title: Sialic acid-dependent cell entry of human enterovirus D68.
Authors: Liu, Y. / Sheng, J. / Baggen, J. / Meng, G. / Xiao, C. / Thibaut, H.J. / van Kuppeveld, F.J. / Rossmann, M.G.
History
DepositionMay 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Other / Category: cell / pdbx_audit_support
Item: _cell.Z_PDB / _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)95,7055
Polymers95,0304
Non-polymers6751
Water5,350297
1
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,742,297300
Polymers5,701,821240
Non-polymers40,47660
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: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
hetero molecules
x 5


  • icosahedral pentamer
  • 479 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)478,52525
Polymers475,15220
Non-polymers3,3735
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 574 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)574,23030
Polymers570,18224
Non-polymers4,0486
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: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
hetero molecules
x 15


  • crystal asymmetric unit, crystal frame
  • 1.44 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)1,435,57475
Polymers1,425,45560
Non-polymers10,11915
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation14
Unit cell
Length a, b, c (Å)325.700, 347.400, 356.500
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)

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Components

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Capsid protein ... , 4 types, 4 molecules ABCD

#1: Protein Capsid protein VP1 /


Mass: 32784.168 Da / Num. of mol.: 1 / Fragment: UNP residues 565-861 / Source method: isolated from a natural source / Details: Grown in human rhabdosarcoma cells / Source: (natural) Enterovirus D68 / Cell line: human rhabdomyosarcoma cells / References: UniProt: Q68T42
#2: Protein Capsid protein VP2 /


Mass: 27706.336 Da / Num. of mol.: 1 / Fragment: UNP residues 70-317 / Source method: isolated from a natural source / Details: Grown in human rhabdosarcoma cells / Source: (natural) Enterovirus D68 / Cell line: human rhabdomyosarcoma cells / References: UniProt: Q68T42
#3: Protein Capsid protein VP3 /


Mass: 27202.881 Da / Num. of mol.: 1 / Fragment: UNP residues 318-564 / Source method: isolated from a natural source / Details: Grown in human rhabdosarcoma cells / Source: (natural) Enterovirus D68 / Cell line: human rhabdomyosarcoma cells / References: UniProt: Q68T42
#4: Protein Capsid protein VP4 /


Mass: 7336.960 Da / Num. of mol.: 1 / Fragment: UNP residues 2-69 / Source method: isolated from a natural source / Details: Grown in human rhabdosarcoma cells / Source: (natural) Enterovirus D68 / Cell line: human rhabdomyosarcoma cells / References: UniProt: Q68T42

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Sugars / Non-polymers , 2 types, 298 molecules

#5: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 6'-sialyl-N-acetyllactosamine


Type: oligosaccharide, Oligosaccharide / Class: Glycan component / Mass: 674.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 6'-sialyl-N-acetyllactosamine
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a4-b1_b6-c2WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 3.54 Å3/Da / Density % sol: 65.3 %
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: Aug 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 803405 / % possible obs: 74.6 % / Redundancy: 1.8 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.129 / Rrim(I) all: 0.178 / Χ2: 1.241 / Net I/av σ(I): 5.373 / Net I/σ(I): 5 / Num. measured all: 1436142
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allΧ2% possible allRrim(I) all
2.15-2.231.60.865803350.5590.7761.04175
2.23-2.321.70.755826060.610.6711.09177.1
2.32-2.421.70.623830310.6810.551.12577.40.834
2.42-2.551.80.515827070.7460.451.15377.10.687
2.55-2.711.80.395822570.8160.3421.19476.60.525
2.71-2.921.80.289816660.8860.2471.226760.382
2.92-3.211.80.175807170.9520.1481.319750.231
3.21-3.681.90.113792920.9760.0941.39173.60.148
3.68-4.631.90.082774260.9820.0681.49671.70.107
4.63-5020.068733680.9850.0541.26667.10.087

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Processing

Software
NameVersionClassification
HKL-2000data scaling
HKL-2000data reduction
CNS1.3refinement
PDB_EXTRACT3.15data extraction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MW8

4mw8


Resolution: 2.15→38.26 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 27418320 / 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
Rfree0.256 40605 5.1 %RANDOM
Rwork0.254 ---
obs-802817 74.4 %-
Solvent computationSolvent model: FLAT MODEL
Displacement parametersBiso max: 95.42 Å2 / Biso mean: 25.1 Å2 / Biso min: 13.39 Å2
Refine analyzeLuzzati sigma a free: 0.37 Å
Refinement stepCycle: final / Resolution: 2.15→38.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6303 0 46 297 6646
Biso mean--70.71 28.85 -
Num. residues----808
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_d0.85
X-RAY DIFFRACTIONc_mcbond_it1.161.5
X-RAY DIFFRACTIONc_mcangle_it1.892
X-RAY DIFFRACTIONc_scbond_it2.232
X-RAY DIFFRACTIONc_scangle_it3.252.5
LS refinement shellResolution: 2.15→2.28 Å / Rfactor Rfree error: 0.004 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.327 6629 4.9 %
Rwork0.324 128037 -
all-134666 -
obs--75.3 %
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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