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- PDB-6t4c: Bovine enterovirus F3 in complex with glutathione -

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Basic information

Entry
Database: PDB / ID: 6t4c
TitleBovine enterovirus F3 in complex with glutathione
Components
  • VP1
  • VP2
  • VP3
  • VP4
KeywordsVIRUS / enterovirus F3 / enterovirus capsid assembly / glutathione / Cys-Gly dipeptide
Function / homology
Function and homology information


picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / 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 ...picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / 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 / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host gene expression / 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 / proteolysis / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Helicase/polymerase/peptidase polyprotein, Calicivirus-type / 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 ...Helicase/polymerase/peptidase polyprotein, Calicivirus-type / 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. / 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
GLUTATHIONE / : / STEARIC ACID / Genome polyprotein
Similarity search - Component
Biological speciesEnterovirus F
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDuyvesteyn, H.M.E. / Ren, J. / Walter, T.S. / Fry, E.E. / Stuart, D.I.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/N00065X/1 United Kingdom
Wellcome Trust101122/Z/13/Z United Kingdom
Wellcome TrustALR00750 United Kingdom
CitationJournal: Commun Biol / Year: 2020
Title: Glutathione facilitates enterovirus assembly by binding at a druggable pocket.
Authors: Duyvesteyn, H.M.E. / Ren, J. / Walter, T.S. / Fry, E.E. / Stuart, D.I.
History
DepositionOct 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 1, 2021Group: Database references / Derived calculations / Category: database_2 / pdbx_struct_conn_angle / struct_conn
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 / _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
Revision 1.2Dec 21, 2022Group: Refinement description / Category: struct_ncs_oper / Item: _struct_ncs_oper.code
Revision 1.3Mar 15, 2023Group: Other / Refinement description / Category: cell / struct_ncs_oper / Item: _cell.Z_PDB / _struct_ncs_oper.code
Revision 1.4Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)93,37018
Polymers91,8614
Non-polymers1,50914
Water12,917717
1
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,602,1901080
Polymers5,511,664240
Non-polymers90,525840
Water4,324240
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation56
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)342.75, 348.16, 351.42
Angle α, β, γ (deg.)90, 90, 90
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.809017, -0.5, 0.309017), (0.5, 0.309017, -0.809017), (0.309017, 0.809017, 0.5)
3generate(0.5, -0.309017, 0.809017), (0.309017, -0.809017, -0.5), (0.809017, 0.5, -0.309017)
4generate(0.5, 0.309017, 0.809017), (-0.309017, -0.809017, 0.5), (0.809017, -0.5, -0.309017)
5generate(0.809017, 0.5, 0.309017), (-0.5, 0.309017, 0.809017), (0.309017, -0.809017, 0.5)
6generate(1), (1), (1)
7generate(0.5, 0.309017, -0.809017), (0.309017, 0.809017, 0.5), (0.809017, -0.5, 0.309017)
8generate(0.309017, -0.809017, -0.5), (0.809017, 0.5, -0.309017), (0.5, -0.309017, 0.809017)
9generate(-0.309017, -0.809017, 0.5), (0.809017, -0.5, -0.309017), (0.5, 0.309017, 0.809017)
10generate(-0.5, 0.309017, 0.809017), (0.309017, -0.809017, 0.5), (0.809017, 0.5, 0.309017)
11generate(1), (1), (1)
12generate(0.309017, 0.809017, 0.5), (0.809017, -0.5, 0.309017), (0.5, 0.309017, -0.809017)
13generate(0.809017, 0.5, -0.309017), (0.5, -0.309017, 0.809017), (0.309017, -0.809017, -0.5)
14generate(0.809017, -0.5, -0.309017), (0.5, 0.309017, 0.809017), (-0.309017, -0.809017, 0.5)
15generate(0.309017, -0.809017, 0.5), (0.809017, 0.5, 0.309017), (-0.5, 0.309017, 0.809017)

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein VP1


Mass: 30247.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterovirus F
References: UniProt: Q2LKZ0, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#2: Protein VP2


Mass: 26757.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterovirus F
References: UniProt: Q2LKZ0, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#3: Protein VP3


Mass: 27149.947 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterovirus F
References: UniProt: Q2LKZ0, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#4: Protein VP4


Mass: 7705.456 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterovirus F
References: UniProt: Q2LKZ0, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase

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Non-polymers , 6 types, 731 molecules

#5: Chemical ChemComp-STE / STEARIC ACID


Mass: 284.477 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H36O2
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#9: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 717 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 1.5 M Ammonium Sulfate and 0.1 M Tris at pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.8→19.98 Å / Num. obs: 1902973 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Redundancy: 13.4 % / Biso Wilson estimate: 17.2 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.394 / Rpim(I) all: 0.111 / Net I/σ(I): 6.2
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 0.5 / Num. unique obs: 94026 / CC1/2: 0.2 / % possible all: 99.9

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Processing

Software
NameClassification
CNSrefinement
DIALSdata reduction
Aimlessdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OSN

5osn


Resolution: 1.8→19.98 Å / Rfactor Rfree error: 0.001 / Cross valid method: THROUGHOUT
Details: Cross-validation method: -> "throughout" Free R value test set selection criteria: -> "random" Number of non-hydrogen atoms used in refinement. Polymer 0 Nonpolymer 0 Solvent 0 CNS Parameter ...Details: Cross-validation method: -> "throughout" Free R value test set selection criteria: -> "random" Number of non-hydrogen atoms used in refinement. Polymer 0 Nonpolymer 0 Solvent 0 CNS Parameter files: CNS_TOPPAR/protein_rep.param CNS_TOPPAR/dna-rna_rep.param CNS_TOPPAR/water_rep.param CNS_TOPPAR/ion.param CNS_TOPPAR/carbohydrate.param ../../toppar/STE.par ../../toppar/gsh_1.par ../../toppar/GOL.par CNS Topology files: CNS_TOPPAR/protein.top CNS_TOPPAR/dna-rna.top CNS_TOPPAR/water.top CNS_TOPPAR/ion.top CNS_TOPPAR/carbohydrate.top ../../toppar/STE.top ../../toppar/gsh_1.top ../../toppar/GOL.top
RfactorNum. reflection% reflection
Rfree0.208 95446 5 %
Rwork0.205 --
obs-1902730 100 %
Solvent computationBsol: 57.9837 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 144.32 Å2 / Biso mean: 22.17 Å2 / Biso min: 10.42 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å2-0 Å20 Å2
2--0.98 Å20 Å2
3----1.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.3 Å
Luzzati d res high-1.8
Refinement stepCycle: LAST / Resolution: 1.8→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6291 0 86 717 7094
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_torsion_deg25.4
X-RAY DIFFRACTIONx_torsion_impr_deg0.84
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.8-1.860.347947250.351796360.00419021518910899.4
1.86-1.940.317952150.3161801630.00319026918968499.7
1.94-2.030.275947750.2731803130.00319024718979099.8
2.03-2.130.24596815.10.2441801570.00219023418983899.8
2.13-2.270.22697605.10.2241801220.00219015118988299.9
2.27-2.440.215948850.211805670.00219029119005599.9
2.44-2.690.19893994.90.1931808600.00219042319025999.9
2.69-3.070.182948550.181809880.002190561190473100
3.07-3.870.1798065.10.1681810940.002190955190900100
3.87-19.980.17593574.90.1721833840.002192759192741100

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