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- PDB-6tsd: Crystal structure of human coxsackievirus A24v in complex with pe... -

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Basic information

Entry
Database: PDB / ID: 6tsd
TitleCrystal structure of human coxsackievirus A24v in complex with pentavalent inhibitor ME0752
Components(Capsid protein ...) x 4
KeywordsVIRUS / human Coxsackievirus A24v / starfish-like inhibitor / pentavelent
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: 1.81 Å
AuthorsZocher, G. / Stehle, T.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)FOR2327 Germany
German Federal Ministry for Education and ResearchBW-Stiftung - Glykobiologie Germany
Knut and Alice Wallenberg Foundation2013.0019 Germany
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Pentavalent Sialic Acid Conjugates Block Coxsackievirus A24 Variant and Human Adenovirus Type 37-Viruses That Cause Highly Contagious Eye Infections.
Authors: Johansson, E. / Caraballo, R. / Mistry, N. / Zocher, G. / Qian, W. / Andersson, C.D. / Hurdiss, D.L. / Chandra, N. / Thompson, R. / Frangsmyr, L. / Stehle, T. / Arnberg, N. / Elofsson, M.
History
DepositionDec 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2022Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: atom_type / database_2 ...atom_type / database_2 / entity / entity_name_com / entity_src_gen / pdbx_struct_oper_list / struct_ncs_oper / struct_ref / struct_ref_seq
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_src_gen.gene_src_strain / _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] / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
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)99,43023
Polymers98,1534
Non-polymers1,27819
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)5,965,8241380
Polymers5,889,154240
Non-polymers76,6691140
Water4,324240
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
Unit cell
Length a, b, c (Å)305.475, 365.351, 366.484
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(0.498412, -0.809326, 0.310767), (0.811369, 0.30919, -0.496066), (0.305393, 0.499392, 0.810767)167.5181, 92.3701
3generate(-0.308951, -0.499177, 0.80955), (0.501452, -0.808764, -0.307321), (0.808143, 0.311003, 0.500182)142.827, 309.7515, -88.6626
4generate(-0.308742, 0.499152, 0.809645), (-0.502087, -0.808498, 0.306984), (0.807829, -0.311733, 0.500235)-39.6254, 351.3227, 25.1639
5generate(0.497715, 0.80991, 0.310365), (-0.811357, 0.308283, 0.496651), (0.306562, -0.499007, 0.810563)160.0658, 79.0529
6generate(-0.501438, 0.808483, 0.308084), (-0.808762, -0.311511, -0.498864), (-0.307352, -0.499316, 0.810073)25.469, 454.549, 172.7284
7generate(0.500938, 0.808568, -0.308673), (-0.809042, 0.31079, -0.498859), (-0.307429, 0.499627, 0.809852)-15.092, 340.9213, -9.6715
8generate(0.809953, -0.309741, -0.498033), (-0.306093, 0.501101, -0.809448), (0.500284, 0.808058, 0.311059)176.4422, 286.1443, -98.1978
9generate(-0.000454, -1, -0.000488), (-0.000786, 0.000488, -1), (1, -0.000453, -0.000786)335.6632, 366.1323, 30.5555
10generate(-0.810307, -0.309919, 0.497346), (-0.304877, -0.501843, -0.809446), (0.500453, -0.807529, 0.31216)242.5342, 469.1013, 196.5665
11generate(0.306085, -0.499743, 0.810289), (-0.498257, -0.809352, -0.31095), (0.811204, -0.308556, -0.496731)49.0711, 463.756, 206.0425
12generate(-0.001333, -0.000797, 0.999999), (-0.999999, 0.000931, -0.001332), (-0.00093, -0.999999, -0.000798)-29.8822, 335.7758, 366.4031
13generate(0.304468, 0.501394, 0.809878), (-0.500332, 0.807688, -0.311941), (-0.810535, -0.310232, 0.496779)169.1383, 273.3489
14generate(0.808579, 0.310341, 0.499889), (0.308542, 0.499771, -0.80934), (-0.501001, 0.808652, 0.308351)192.57, 55.7894
15generate(0.808401, -0.31056, 0.50004), (0.308868, -0.499354, -0.809473), (0.501087, 0.808825, -0.307757)-5.4659, 375.0669, 15.0381

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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

#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: isolated from a genetically manipulated source
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 , 6 types, 834 molecules

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


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#10: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#11: 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: May 14, 2016
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.81→50 Å / Num. obs: 14074225 / % possible obs: 99.9 % / Redundancy: 7.71 % / CC1/2: 0.993 / Net I/σ(I): 8.18
Reflection shellResolution: 1.81→1.92 Å / Num. unique obs: 2244009 / CC1/2: 0.679 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0232 2018/13/08refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Q4w

4q4w


Resolution: 1.81→49.955 Å / Cor.coef. Fo:Fc: 0.97 / SU B: 1.889 / SU ML: 0.054 / Cross valid method: NONE / ESU R: 0.018
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rwork0.1502 1824194 -
all0.15 --
obs-1824194 99.892 %
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: 29.473 Å2
Baniso -1Baniso -2Baniso -3
1-0.084 Å2-0 Å20 Å2
2---0.174 Å2-0 Å2
3---0.091 Å2
Refinement stepCycle: LAST / Resolution: 1.81→49.955 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6519 0 67 816 7402
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0136857
X-RAY DIFFRACTIONr_bond_other_d0.0030.0176145
X-RAY DIFFRACTIONr_angle_refined_deg1.3811.6589380
X-RAY DIFFRACTIONr_angle_other_deg1.2821.56814326
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1285874
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.34722.378328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.624151062
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9441535
X-RAY DIFFRACTIONr_chiral_restr0.0650.2939
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027681
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021449
X-RAY DIFFRACTIONr_nbd_refined0.180.22324
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1610.211568
X-RAY DIFFRACTIONr_nbtor_refined0.1620.26598
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.26194
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.21346
X-RAY DIFFRACTIONr_metal_ion_refined0.0290.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.7570.2197
X-RAY DIFFRACTIONr_nbd_other0.6920.2923
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1710.2114
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.760.22
X-RAY DIFFRACTIONr_mcbond_it1.9626.7853383
X-RAY DIFFRACTIONr_mcbond_other1.966.7833382
X-RAY DIFFRACTIONr_mcangle_it2.5889.7864231
X-RAY DIFFRACTIONr_mcangle_other2.599.7884232
X-RAY DIFFRACTIONr_scbond_it3.9957.5533474
X-RAY DIFFRACTIONr_scbond_other4.0117.5593475
X-RAY DIFFRACTIONr_scangle_it5.43610.5975127
X-RAY DIFFRACTIONr_scangle_other5.43510.6055128
X-RAY DIFFRACTIONr_lrange_it7.02950.3587939
X-RAY DIFFRACTIONr_lrange_other6.83546.6657695
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
1.81-1.8570.32513264813443798.66930.321
1.857-1.9080.25913106413107299.99390.248
1.908-1.9630.22412762912763999.99220.209
1.963-2.0240.19812381912382699.99430.184
2.024-2.090.18512006812006999.99920.17
2.09-2.1630.17111618511618899.99740.155
2.163-2.2450.15611216911217399.99640.139
2.245-2.3360.14810791810792199.99720.129
2.336-2.440.14310367110367599.99610.123
2.44-2.5590.14990289903299.9960.12
2.559-2.6970.135943349433799.99680.117
2.697-2.860.131893128931699.99550.115
2.86-3.0560.12583893838931000.111
3.056-3.30.123782147821599.99870.112
3.3-3.6140.1272062720621000.112
3.614-4.0370.118652756527799.99690.113
4.037-4.6570.11577455774699.99830.108
4.657-5.6910.118490224902399.9980.115
5.691-7.9970.15382153821999.98950.144
7.997-49.9550.197219272194699.91340.198

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