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Basic information

Entry
Database: PDB / ID: 3vbo
TitleCrystal structure of formaldehyde treated empty human Enterovirus 71 particle (cryo at 100K)
Components
  • Genome Polyprotein, capsid protein VP1
  • Genome Polyprotein, capsid protein VP2
  • Genome Polyprotein, capsid protein VP3
KeywordsVIRUS / hand-foot-and-mouth disease / enterovirus uncoating / pocket factor / adaptor-sensor / 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 enterovirus 71
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsWang, X. / Peng, W. / Ren, J. / Hu, Z. / Xu, J. / Lou, Z. / Li, X. / Yin, W. / Shen, X. / Porta, C. ...Wang, X. / Peng, W. / Ren, J. / Hu, Z. / Xu, J. / Lou, Z. / Li, X. / Yin, W. / Shen, X. / Porta, C. / Walter, T.S. / Evans, G. / Axford, D. / Owen, R. / Rowlands, D.J. / Wang, J. / Stuart, D.I. / Fry, E.E. / Rao, Z.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: A sensor-adaptor mechanism for enterovirus uncoating from structures of EV71.
Authors: Wang, X. / Peng, W. / Ren, J. / Hu, Z. / Xu, J. / Lou, Z. / Li, X. / Yin, W. / Shen, X. / Porta, C. / Walter, T.S. / Evans, G. / Axford, D. / Owen, R. / Rowlands, D.J. / Wang, J. / Stuart, D. ...Authors: Wang, X. / Peng, W. / Ren, J. / Hu, Z. / Xu, J. / Lou, Z. / Li, X. / Yin, W. / Shen, X. / Porta, C. / Walter, T.S. / Evans, G. / Axford, D. / Owen, R. / Rowlands, D.J. / Wang, J. / Stuart, D.I. / Fry, E.E. / Rao, Z.
History
DepositionJan 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Apr 18, 2012Group: Database references
Revision 1.3May 2, 2012Group: Database references
Revision 1.4Sep 13, 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 / struct_conn / struct_site
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 / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)84,8644
Polymers84,8413
Non-polymers231
Water1,22568
1
A: Genome Polyprotein, capsid protein VP1
B: Genome Polyprotein, capsid protein VP2
C: Genome Polyprotein, capsid protein VP3
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,091,842240
Polymers5,090,463180
Non-polymers1,37960
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: Genome Polyprotein, capsid protein VP1
B: Genome Polyprotein, capsid protein VP2
C: Genome Polyprotein, capsid protein VP3
hetero molecules
x 5


  • icosahedral pentamer
  • 424 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)424,32020
Polymers424,20515
Non-polymers1155
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Genome Polyprotein, capsid protein VP1
B: Genome Polyprotein, capsid protein VP2
C: Genome Polyprotein, capsid protein VP3
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 509 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)509,18424
Polymers509,04618
Non-polymers1386
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
6
A: Genome Polyprotein, capsid protein VP1
B: Genome Polyprotein, capsid protein VP2
C: Genome Polyprotein, capsid protein VP3
hetero molecules
x 5


  • crystal asymmetric unit, crystal frame
  • 424 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)424,32020
Polymers424,20515
Non-polymers1155
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation4
Unit cell
Length a, b, c (Å)353.100, 353.100, 353.100
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(-0.3032, 0.5087, 0.8058), (-0.4937, -0.8071, 0.3237), (0.815, -0.2997, 0.4959)-0.1237, -2.687, -0.1257
3generate(0.502, 0.807, 0.311), (-0.807, 0.3078, 0.504), (0.311, -0.504, 0.8058)-0.4476, -0.7624, -0.06344
4generate(-0.3166, -0.4869, 0.814), (0.502, -0.8142, -0.2917), (0.8048, 0.3163, 0.5022)-0.1976, -2.702, -0.119
5generate(0.4969, -0.8083, 0.3159), (0.8118, 0.3042, -0.4984), (0.3068, 0.5041, 0.8073)-0.7536, -0.5605, 0.466

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Components

#1: Protein Genome Polyprotein, capsid protein VP1 / EV71


Mass: 32727.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GROWN IN VERO CELLS / Source: (natural) Human enterovirus 71 / Strain: FUYANG, ANHUI. P.R.C/17.08/1 / References: UniProt: B2ZUN0
#2: Protein Genome Polyprotein, capsid protein VP2 / EV71


Mass: 25987.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GROWN IN VERO CELLS / Source: (natural) Human enterovirus 71 / Strain: FUYANG, ANHUI. P.R.C/17.08/1 / References: UniProt: B2ZUN0
#3: Protein Genome Polyprotein, capsid protein VP3 / EV71


Mass: 26125.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GROWN IN VERO CELLS / Source: (natural) Human enterovirus 71 / Strain: FUYANG, ANHUI. P.R.C/17.08/1 / References: UniProt: B2ZUN0
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AUTHORS INDICATE THAT BASED ON ELECTRON DENSITY MAPS, A225 IS MET.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 200 mM Ammonium phosphate monobasic, 24% (v/v) Isopropanol and 100 mM sodium cacodylate (pH 6.5), VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.975 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.88→50 Å / Num. obs: 167672 / % possible obs: 99.6 % / Observed criterion σ(I): -1.5 / Redundancy: 23.5 % / Rsym value: 0.382 / Net I/σ(I): 6
Reflection shellResolution: 2.88→2.98 Å / Redundancy: 20.1 % / Mean I/σ(I) obs: 1.2 / Num. unique all: 16211 / % possible all: 97.7

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Processing

Software
NameVersionClassification
GDAdata collection
MOLREPphasing
CNS1.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: STARTING MODEL 1BEV

1bev


Resolution: 2.88→49.94 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 17128842.62 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED STRICT NCS CONSTRAINTS
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1680 1 %RANDOM
Rwork0.227 ---
obs0.227 167005 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.1333 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 64.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.76 Å0.84 Å
Refinement stepCycle: LAST / Resolution: 2.88→49.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5397 0 1 68 5466
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
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_d26.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it7.498
X-RAY DIFFRACTIONc_mcangle_it10.8916
X-RAY DIFFRACTIONc_scbond_it12.8912
X-RAY DIFFRACTIONc_scangle_it16.120
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.88→3.06 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.385 264 1 %
Rwork0.397 27185 -
obs--99.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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