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- PDB-6t48: Bovine enterovirus F3 in complex with glutathione and a Cysteinyl... -

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Basic information

Entry
Database: PDB / ID: 6t48
TitleBovine enterovirus F3 in complex with glutathione and a Cysteinylglycine dipeptide
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 / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / ribonucleoside triphosphate phosphatase activity / 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 / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / ribonucleoside triphosphate phosphatase activity / 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 / symbiont-mediated suppression of host innate immune response / 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 / 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 ...Helicase/polymerase/peptidase polyprotein, Calicivirus-type / 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 / 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
CYSTEINE / GLYCINE / GLUTATHIONE / : / STEARIC ACID / Genome polyprotein
Similarity search - Component
Biological speciesEnterovirus F
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 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 12, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)93,54121
Polymers91,8614
Non-polymers1,68017
Water11,025612
1
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,612,4541260
Polymers5,511,664240
Non-polymers100,7901020
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
Unit cell
Length a, b, c (Å)344, 349.4, 352.7
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 , 9 types, 629 molecules

#5: Chemical ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S
#6: Chemical ChemComp-STE / STEARIC ACID


Mass: 284.477 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H36O2
#7: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#11: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#12: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 612 / 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 / 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: 0.976 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.17→20 Å / Num. obs: 908128 / % possible obs: 82.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.374 / Rpim(I) all: 0.187 / Net I/σ(I): 5.7
Reflection shellResolution: 2.17→2.2 Å / Rmerge(I) obs: 0.798 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 37002 / CC1/2: 0.275 / Rpim(I) all: 0.787 / % possible all: 68

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Processing

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

5osn


Resolution: 2.17→19.98 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 32369612.68 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.203 45420 5 %RANDOM
Rwork0.2 ---
obs-908128 82.6 %-
Solvent computationBsol: 35.72 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 18.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.77 Å2-0 Å20 Å2
2--2.14 Å2-0 Å2
3----0.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.32 Å
Refinement stepCycle: 1 / Resolution: 2.17→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6288 0 94 612 6994
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.748
X-RAY DIFFRACTIONc_mcangle_it5.9316
X-RAY DIFFRACTIONc_scbond_it8.9112
X-RAY DIFFRACTIONc_scangle_it11.3820
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.17→2.25 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.288 3727 4.8 %
Rwork0.288 73416 -
obs--70.5 %

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