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- PDB-3vbh: Crystal structure of formaldehyde treated human enterovirus 71 (s... -

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Basic information

Entry
Database: PDB / ID: 3vbh
TitleCrystal structure of formaldehyde treated human enterovirus 71 (space group R32)
Components
  • (Genome Polyprotein, capsid protein ...) x 3
  • Genome Polyprotein, vapsid 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 / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase ...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 / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Rhinovirus 14, subunit 4 - #370 / Rhinovirus 14, subunit 4 / 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 ...Rhinovirus 14, subunit 4 - #370 / Rhinovirus 14, subunit 4 / 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 / Few Secondary Structures / Irregular / 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
: / SPHINGOSINE / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHuman enterovirus 71
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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_conn_angle / 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_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_conn.pdbx_dist_value / _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, vapsid protein VP3
D: Genome Polyprotein, capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8879
Polymers92,4514
Non-polymers4365
Water3,513195
1
A: Genome Polyprotein, capsid protein VP1
B: Genome polyprotein, capsid protein VP2
C: Genome Polyprotein, vapsid protein VP3
D: Genome Polyprotein, capsid protein VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,573,247540
Polymers5,547,079240
Non-polymers26,168300
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: Genome Polyprotein, capsid protein VP1
B: Genome polyprotein, capsid protein VP2
C: Genome Polyprotein, vapsid protein VP3
D: Genome Polyprotein, capsid protein VP4
hetero molecules
x 5


  • icosahedral pentamer
  • 464 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)464,43745
Polymers462,25720
Non-polymers2,18125
Water36020
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, vapsid protein VP3
D: Genome Polyprotein, capsid protein VP4
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 557 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)557,32554
Polymers554,70824
Non-polymers2,61730
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: Genome Polyprotein, capsid protein VP1
B: Genome polyprotein, capsid protein VP2
C: Genome Polyprotein, vapsid protein VP3
D: Genome Polyprotein, capsid protein VP4
hetero molecules
x 10


  • crystal asymmetric unit, crystal frame
  • 929 kDa, 40 polymers
Theoretical massNumber of molelcules
Total (without water)928,87490
Polymers924,51340
Non-polymers4,36150
Water72140
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation9
Unit cell
Length a, b, c (Å)330.000, 330.000, 748.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.3086, 0.7561, 0.5771), (-0.756, 0.5632, -0.3336), (-0.5773, -0.3333, 0.7454)
3generate(-0.8091, 0.467, 0.3567), (-0.467, -0.1425, -0.8727), (-0.3567, -0.8727, 0.3334)
4generate(-0.809, -0.4675, -0.3564), (0.4669, -0.1428, -0.8727), (0.3571, -0.8724, 0.3338)
5generate(0.3094, -0.7559, -0.577), (0.7556, 0.5638, -0.3335), (0.5774, -0.3328, 0.7456)
6generate(-0.934, 0.3573), (0.3569, -0.3337, -0.8725), (0.9341, 0.1277, 0.3333)
7generate(0.5, -0.6452, 0.5776), (0.866, 0.3726, -0.3334), (0.6669, 0.7451)
8generate(0.3087, -0.1781, 0.9343), (0.1781, 0.9758, 0.1271), (-0.9343, 0.1272, 0.333)
9generate(-0.3091, -0.1781, 0.9342), (-0.7558, 0.6422, -0.1277), (-0.5772, -0.7456, -0.3331)
10generate(-0.5, -0.6455, 0.5774), (-0.6451, -0.1672, -0.7456), (0.5778, -0.7452, -0.3329)

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Components

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Genome Polyprotein, capsid protein ... , 3 types, 3 molecules ABD

#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: 26874.252 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: B2ZUN1, UniProt: B2ZUN0*PLUS
#4: Protein Genome Polyprotein, capsid protein VP4 / EV71


Mass: 6380.943 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

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Protein , 1 types, 1 molecules C

#3: Protein Genome Polyprotein, vapsid protein VP3 / EV71


Mass: 26468.225 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

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Non-polymers , 5 types, 200 molecules

#5: Chemical ChemComp-SPH / SPHINGOSINE


Mass: 299.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H37NO2
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 45

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Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG400, 0.2 M tri-Sodium Citrate, 0.1 M Tris.HCl pH 8.5 mixed with virus and equilibrated against salt reservoir , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 405370 / % possible obs: 59.1 % / Observed criterion σ(I): -1.5 / Redundancy: 2.2 % / Rmerge(I) obs: 0.377 / Net I/σ(I): 1.9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 1.1 % / Mean I/σ(I) obs: 0.5 / Num. unique all: 10180 / % possible all: 59.1

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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: PDB ENTRY 3VBF

3vbf


Resolution: 2.3→49.5 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 38230274.53 / 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
Rfree0.226 3978 1 %RANDOM
Rwork0.217 ---
obs0.217 393831 57.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 17.7372 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 24.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.52 Å20 Å20 Å2
2--2.52 Å20 Å2
3----5.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.3→49.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6508 0 25 195 6728
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it6.838
X-RAY DIFFRACTIONc_mcangle_it7.7916
X-RAY DIFFRACTIONc_scbond_it11.7612
X-RAY DIFFRACTIONc_scangle_it12.5220
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.379 167 0.9 %
Rwork0.344 17730 -
obs--15.7 %
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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