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- PDB-7oj7: Crystal structure of human coxsackievirus A24v in complex with a ... -

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Basic information

Entry
Database: PDB / ID: 7oj7
TitleCrystal structure of human coxsackievirus A24v in complex with a pentavalent N-acetylneuraminic acid conjugate
Components(Capsid protein ...) x 4
KeywordsVIRUS / human Coxsackievirus A24v / starfish-like inhibitor / corannulene
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / ribonucleoside triphosphate phosphatase 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 / nucleoside-triphosphate phosphatase / channel activity ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / ribonucleoside triphosphate phosphatase 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 / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
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 ...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 / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-0H0 / Genome polyprotein
Similarity search - Component
Biological speciesCoxsackievirus A24
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsZocher, G. / Stehle, T.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)FOR2327 Germany
German Federal Ministry for Education and ResearchBW-Stiftung - Glykobiologie Germany
CitationJournal: Int J Mol Sci / Year: 2021
Title: Exploring the Effect of Structure-Based Scaffold Hopping on the Inhibition of Coxsackievirus A24v Transduction by Pentavalent N-Acetylneuraminic Acid Conjugates.
Authors: Emil Johansson / Rémi Caraballo / Daniel L Hurdiss / Nitesh Mistry / C David Andersson / Rebecca F Thompson / Neil A Ranson / Georg Zocher / Thilo Stehle / Niklas Arnberg / Mikael Elofsson /
Abstract: Coxsackievirus A24 variant (CVA24v) is the primary causative agent of the highly contagious eye infection designated acute hemorrhagic conjunctivitis (AHC). It is solely responsible for two pandemics ...Coxsackievirus A24 variant (CVA24v) is the primary causative agent of the highly contagious eye infection designated acute hemorrhagic conjunctivitis (AHC). It is solely responsible for two pandemics and several recurring outbreaks of the disease over the last decades, thus affecting millions of individuals throughout the world. To date, no antiviral agents or vaccines are available for combating this disease, and treatment is mainly supportive. CVA24v utilizes Neu5Ac-containing glycans as attachment receptors facilitating entry into host cells. We have previously reported that pentavalent Neu5Ac conjugates based on a glucose-scaffold inhibit CVA24v infection of human corneal epithelial cells. In this study, we report on the design and synthesis of scaffold-replaced pentavalent Neu5Ac conjugates and their effect on CVA24v cell transduction and the use of cryogenic electron microscopy (cryo-EM) to study the binding of these multivalent conjugates to CVA24v. The results presented here provide insights into the development of Neu5Ac-based inhibitors of CVA24v and, most significantly, the first application of cryo-EM to study the binding of a multivalent ligand to a lectin.
History
DepositionMay 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Data collection / Derived calculations / Refinement description
Category: diffrn_source / pdbx_struct_oper_list / struct_ncs_oper
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.name ..._diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_ncs_oper.vector[1] / _struct_ncs_oper.vector[3]
Revision 1.2Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
111: Capsid protein VP1
222: Capsid protein VP2
333: Capsid protein VP3
444: Capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,88615
Polymers98,1534
Non-polymers73411
Water14,700816
1
111: Capsid protein VP1
222: Capsid protein VP2
333: Capsid protein VP3
444: Capsid protein VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,933,181900
Polymers5,889,154240
Non-polymers44,027660
Water4,324240
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
Unit cell
Length a, b, c (Å)305.520, 365.550, 366.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.498934, -0.809029, 0.310705), (0.81071, 0.308999, -0.497261), (0.306291, 0.499992, 0.810058)167.4508, 93.0468
3generate(-0.308416, -0.499378, 0.80963), (0.501034, -0.80877, -0.307987), (0.808606, 0.310664, 0.499644)142.7764, 310.2665, -88.6127
4generate(-0.308216, 0.499458, 0.809657), (-0.501502, -0.808531, 0.307854), (0.808393, -0.311159, 0.499681)-39.8657, 351.0795, 25.094
5generate(0.498115, 0.809841, 0.309901), (-0.810764, 0.308253, 0.497636), (0.307478, -0.499136, 0.810136)159.638, 79.0233
6generate(-0.501326, 0.808419, 0.308433), (-0.809035, -0.311559, -0.49839), (-0.306813, -0.499389, 0.810232)25.284, 454.4221, 172.6155
7generate(0.500581, 0.808589, -0.309197), (-0.809395, 0.310462, -0.49849), (-0.30708, 0.499798, 0.809879)-14.9343, 340.8295, -9.8648
8generate(0.809504, -0.310023, -0.498587), (-0.306849, 0.500599, -0.809472), (0.500547, 0.808262, 0.310106)176.8129, 286.3095, -98.1293
9generate(-0.001355, -0.999998, -0.00139), (-0.000213, 0.001391, -0.999999), (0.999999, -0.001354, -0.000215)336.2619, 365.7619, 30.6066
10generate(-0.809884, -0.310089, 0.497928), (-0.30532, -0.501961, -0.809207), (0.500866, -0.807391, 0.311854)242.3479, 469.1439, 196.6324
11generate(0.3074, -0.499387, 0.810011), (-0.498218, -0.809695, -0.310118), (0.810731, -0.308232, -0.497703)48.8032, 463.6329, 206.414
12generate(0.000411, -0.000502, 1), (-1, 0.000688, 0.000411), (-0.000688, -1, -0.000502)-30.3791, 335.2771, 366.3716
13generate(0.306138, 0.501056, 0.809458), (-0.500315, 0.808071, -0.310977), (-0.809916, -0.309782, 0.498067)168.6835, 272.7784
14generate(0.808985, 0.309546, 0.499725), (0.308761, 0.499642, -0.809336), (-0.50021, 0.809036, 0.308627)192.5359, 55.3438
15generate(0.808494, -0.308576, 0.501117), (0.310266, -0.500058, -0.808503), (0.500072, 0.80915, -0.308553)-6.1852, 374.6981, 15.3558

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Components

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Capsid protein ... , 4 types, 4 molecules 111222333444

#1: Protein Capsid protein VP1 / Cosackievirus A24v viral capsid protein 1


Mass: 34378.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxsackievirus A24 / Strain: A24v / Production host: Homo sapiens (human) / References: UniProt: V9VEF3
#2: Protein Capsid protein VP2 / Cosackievirus A24v viral capsid protein 2


Mass: 29817.412 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxsackievirus A24 / Strain: A24v / Production host: Homo sapiens (human) / References: UniProt: V9VEF3
#3: Protein Capsid protein VP3 / Cosackievirus A24v viral capsid protein 3


Mass: 26637.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxsackievirus A24 / Strain: A24v / Production host: Homo sapiens (human) / References: UniProt: V9VEF3
#4: Protein Capsid protein VP4 / Cosackievirus A24v viral capsid protein 4


Mass: 7319.045 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxsackievirus A24 / Strain: A24v / Production host: Homo sapiens (human) / References: UniProt: V9VEF3

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Sugars , 1 types, 1 molecules

#7: Sugar ChemComp-0H0 / Carbohydrate component from a pentavalent N-acetylneuraminic acid conjugate / (1R,2R)-1-[(2R,3R,4S,6R)-6-[bis(oxidanyl)methyl]-3-(1-hydroxyethylamino)-4-oxidanyl-6-propoxy-oxan-2-yl]propane-1,2,3-triol / (2R,4S,5R,6R)-5-acetamido-2-butoxy-4-oxidanyl-6-[(1R,2R)-1,2,3-tris(oxidanyl)propyl]oxane-2-carboxylic acid


Type: saccharide / Mass: 365.376 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H27NO9

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Non-polymers , 3 types, 826 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 816 / 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: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 200 mM Magnesium chloride, 3.4 M 1,6-Hexanediol, 100 mM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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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 PILATUS 6M-F / Detector: PIXEL / Date: Apr 26, 2018
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.78→49.962 Å / Num. obs: 1921680 / % possible obs: 99.9 % / Redundancy: 7.7 % / Biso Wilson estimate: 22 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.263 / Rrim(I) all: 0.282 / Net I/σ(I): 6.6
Reflection shellResolution: 1.78→1.89 Å / Rmerge(I) obs: 1.331 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 308924 / CC1/2: 0.506 / Rrim(I) all: 1.428 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0232 2018/13/08refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Q4W

4q4w


Resolution: 1.78→49.96 Å / Cor.coef. Fo:Fc: 0.97 / SU B: 2.14 / SU ML: 0.06 / Cross valid method: NONE / ESU R: 0.018
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rwork0.1577 1920652 -
all0.158 --
obs-1921680 99.919 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 32.077 Å2
Baniso -1Baniso -2Baniso -3
1--0.059 Å20 Å2-0 Å2
2--0.19 Å20 Å2
3----0.131 Å2
Refinement stepCycle: LAST / Resolution: 1.78→49.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6529 0 34 816 7379
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0136852
X-RAY DIFFRACTIONr_bond_other_d0.0020.0176111
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.6589387
X-RAY DIFFRACTIONr_angle_other_deg1.2961.5714251
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.065876
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.66422.44332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.772151068
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0651535
X-RAY DIFFRACTIONr_chiral_restr0.0640.2938
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027720
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021451
X-RAY DIFFRACTIONr_nbd_refined0.1840.22288
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1620.211578
X-RAY DIFFRACTIONr_nbtor_refined0.1630.26664
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.26080
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.21432
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0430.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.5620.270
X-RAY DIFFRACTIONr_nbd_other0.540.2397
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1580.2110
X-RAY DIFFRACTIONr_mcbond_it2.2527.4513385
X-RAY DIFFRACTIONr_mcbond_other2.247.4483384
X-RAY DIFFRACTIONr_mcangle_it2.99810.7344234
X-RAY DIFFRACTIONr_mcangle_other3.00110.7374235
X-RAY DIFFRACTIONr_scbond_it4.1278.2213467
X-RAY DIFFRACTIONr_scbond_other4.1158.2113464
X-RAY DIFFRACTIONr_scangle_it5.80911.5755130
X-RAY DIFFRACTIONr_scangle_other5.81211.5725129
X-RAY DIFFRACTIONr_lrange_it7.18352.8947966
X-RAY DIFFRACTIONr_lrange_other6.8849.1487709
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Num. reflection Rfree: _ / Total num. of bins used: 20

Resolution (Å)Rfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)WRfactor Rwork
1.78-1.8260.3614017214154399.03140.364
1.826-1.8760.29713804313805199.99420.298
1.876-1.930.25813420213421399.99180.253
1.93-1.990.2313044813046299.98930.223
1.99-2.0550.21312638512639399.99370.203
2.055-2.1270.19712223812224899.99180.182
2.127-2.2070.17511811411811699.99830.158
2.207-2.2970.16311367311367599.99820.146
2.297-2.3990.1551090601090601000.137
2.399-2.5160.14610419210419399.9990.127
2.516-2.6510.142992909929199.9990.124
2.651-2.8120.134940209402199.99890.118
2.812-3.0050.128883288832999.99890.116
3.005-3.2450.12582292822921000.116
3.245-3.5530.1275854758541000.116
3.553-3.970.1268727687271000.119
3.97-4.5790.11160791607911000.115
4.579-5.5970.11851565515651000.123
5.597-7.8660.14940224402241000.153
7.866-49.9620.2230392304699.96960.208

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