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- PDB-7qb5: Coxsackievirus A24v (CVA24v) in complex with a dimeric C2-C9-link... -

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Basic information

Entry
Database: PDB / ID: 7qb5
TitleCoxsackievirus A24v (CVA24v) in complex with a dimeric C2-C9-linked sialic acid inhibitor
Components(Capsid protein ...) x 4
KeywordsVIRUS / Coxsackievirus A24v / CVA24v / sialic acid based inhibitor
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
HEXANE-1,6-DIOL / N-acetyl-alpha-neuraminic acid / Genome polyprotein
Similarity search - Component
Biological speciesCoxsackievirus A24
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.728 Å
AuthorsZocher, G. / Stehle, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
Baden-Wuerttemberg-StiftungGlycobiology Germany
CitationJournal: Rsc Adv / Year: 2022
Title: Exploring divalent conjugates of 5- N -acetyl-neuraminic acid as inhibitors of coxsackievirus A24 variant (CVA24v) transduction.
Authors: Johansson, E. / Caraballo, R. / Zocher, G. / Mistry, N. / Arnberg, N. / Stehle, T. / Elofsson, M.
History
DepositionNov 18, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2022Group: Database references / Derived calculations / Refinement description
Category: pdbx_struct_assembly / pdbx_struct_oper_list ...pdbx_struct_assembly / pdbx_struct_oper_list / struct_ncs_oper / struct_ref
Item: _pdbx_struct_assembly.oligomeric_details / _struct_ncs_oper.vector[1] ..._pdbx_struct_assembly.oligomeric_details / _struct_ncs_oper.vector[1] / _struct_ncs_oper.vector[3] / _struct_ref.pdbx_seq_one_letter_code
Revision 1.2Jan 31, 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
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)98,88214
Polymers98,1534
Non-polymers73010
Water14,610811
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)305.763, 365.707, 366.921
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(0.499142, -0.808993, 0.310465), (0.810588, 0.309284, -0.497284), (0.306277, 0.499874, 0.810136)167.5183, 93.1396
3generate(-0.308408, -0.499481, 0.80957), (0.501045, -0.808726, -0.308086), (0.808603, 0.310614, 0.49968)142.7967, 310.4966, -88.5697
4generate(-0.30819, 0.499398, 0.809704), (-0.501493, -0.808553, 0.30781), (0.808408, -0.311197, 0.499633)-39.9929, 351.2609, 25.2158
5generate(0.498411, 0.809649, 0.309929), (-0.810625, 0.308489, 0.497716), (0.307366, -0.499303, 0.810076)159.576, 79.1782
6generate(-0.501156, 0.808547, 0.308374), (-0.809046, -0.311336, -0.498513), (-0.307063, -0.499321, 0.810179)25.2576, 454.8253, 172.7823
7generate(0.500465, 0.808722, -0.309035), (-0.809393, 0.310371, -0.49855), (-0.307273, 0.499638, 0.809905)-14.9054, 341.2038, -9.7883
8generate(0.809574, -0.309745, -0.498646), (-0.306977, 0.500659, -0.809386), (0.500355, 0.808331, 0.310236)176.9708, 286.6406, -98.0739
9generate(-0.002312, -0.999992, -0.003193), (5.9E-5, 0.003193, -0.999995), (0.999997, -0.002312, 5.2E-5)337.2306, 365.7385, 30.9045
10generate(-0.810045, -0.309717, 0.497898), (-0.305759, -0.501436, -0.809366), (0.500339, -0.80786, 0.311487)242.4434, 469.6404, 197.1601
11generate(0.30738, -0.499631, 0.809868), (-0.498488, -0.809496, -0.310204), (0.810572, -0.308359, -0.497883)48.7977, 464.0442, 206.8469
12generate(-0.000114, -0.00039, 1), (-1, 0.000576, -0.000114), (-0.000576, -1, -0.00039)-30.429, 335.6889, 366.6289
13generate(0.306156, 0.501048, 0.809456), (-0.50048, 0.808013, -0.310861), (-0.809807, -0.309944, 0.498143)168.8916, 272.9315
14generate(0.809509, 0.308741, 0.499374), (0.308555, 0.499905, -0.809252), (-0.499489, 0.809181, 0.309414)192.7678, 55.0126
15generate(0.809011, -0.310031, 0.499382), (0.308385, -0.499396, -0.809631), (0.5004, 0.809002, -0.308408)-5.6572, 375.695, 15.4443

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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 / Cell line (production host): corneal cells / 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 / Cell line: corneal cells / Cell line (production host): corneal cells / 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 / Cell line (production host): corneal cells / 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 / Variant: variant / Cell line (production host): corneal cells / Production host: Homo sapiens (human) / References: UniProt: V9VEF3

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Sugars , 1 types, 1 molecules

#5: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H19NO9 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 820 molecules

#6: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2
#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#8: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 811 / 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: DECTRIS PILATUS 6M
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.728→50 Å / Num. obs: 6338512 / % possible obs: 91.4 % / Redundancy: 6.6 % / CC1/2: 0.992 / Rrim(I) all: 0.158 / Net I/σ(I): 6.5
Reflection shellResolution: 1.73→1.83 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 973400 / CC1/2: 0.604 / Rrim(I) all: 0.79 / % possible all: 93.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Q4W

4q4w


Resolution: 1.728→49.922 Å / Cor.coef. Fo:Fc: 0.962 / SU B: 1.937 / SU ML: 0.057 / Cross valid method: NONE / ESU R: 0.019
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rwork0.1656 1918801 -
all0.166 --
obs-1918801 90.916 %
Rfree--0 %
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: 24.874 Å2
Baniso -1Baniso -2Baniso -3
1--0.012 Å20 Å2-0 Å2
2--0.199 Å20 Å2
3----0.187 Å2
Refinement stepCycle: LAST / Resolution: 1.728→49.922 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6521 0 37 811 7369
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0136873
X-RAY DIFFRACTIONr_bond_other_d0.0020.0176136
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.6599423
X-RAY DIFFRACTIONr_angle_other_deg1.2691.56814310
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0995884
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.54622.417331
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.378151069
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7081535
X-RAY DIFFRACTIONr_chiral_restr0.0650.2945
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027748
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021458
X-RAY DIFFRACTIONr_nbd_refined0.1790.22254
X-RAY DIFFRACTIONr_symmetry_nbd_other0.160.211412
X-RAY DIFFRACTIONr_nbtor_refined0.160.26626
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.26030
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.21356
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.6180.296
X-RAY DIFFRACTIONr_nbd_other0.5760.2501
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2090.2123
X-RAY DIFFRACTIONr_mcbond_it1.7585.7393393
X-RAY DIFFRACTIONr_mcbond_other1.7515.7373392
X-RAY DIFFRACTIONr_mcangle_it2.4088.2914246
X-RAY DIFFRACTIONr_mcangle_other2.4128.2934247
X-RAY DIFFRACTIONr_scbond_it3.1656.3263480
X-RAY DIFFRACTIONr_scbond_other3.1656.3283481
X-RAY DIFFRACTIONr_scangle_it4.4788.9275150
X-RAY DIFFRACTIONr_scangle_other4.4788.9295151
X-RAY DIFFRACTIONr_lrange_it7.60942.1517923
X-RAY DIFFRACTIONr_lrange_other7.18238.8627674
LS refinement shell
Resolution (Å)Num. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.728-1.77200.297137745X-RAY DIFFRACTION88.787
1.772-1.82100.272141599X-RAY DIFFRACTION93.5672
1.821-1.87400.251137731X-RAY DIFFRACTION93.5851
1.874-1.93100.23132316X-RAY DIFFRACTION92.5455
1.931-1.99400.21129428X-RAY DIFFRACTION93.3366
1.994-2.06400.195124359X-RAY DIFFRACTION92.7879
2.064-2.14200.183119715X-RAY DIFFRACTION92.4669
2.142-2.22900.17115249X-RAY DIFFRACTION92.4677
2.229-2.32800.162109456X-RAY DIFFRACTION91.5774
2.328-2.44200.158105043X-RAY DIFFRACTION91.8826
2.442-2.57300.15599274X-RAY DIFFRACTION91.2327
2.573-2.72900.14793120X-RAY DIFFRACTION90.4192
2.729-2.91700.14186959X-RAY DIFFRACTION89.8179
2.917-3.1500.13281254X-RAY DIFFRACTION90.08
3.15-3.44900.12774170X-RAY DIFFRACTION89.197
3.449-3.85400.12666407X-RAY DIFFRACTION88.1244
3.854-4.44600.11758210X-RAY DIFFRACTION87.4576
4.446-5.43400.11848855X-RAY DIFFRACTION86.4277
5.434-7.6400.15337016X-RAY DIFFRACTION84.049
7.64-49.92200.18620900X-RAY DIFFRACTION82.953

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