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

ID or keywords:

Entry

Database: PDB / ID: 7qb5

Title

Coxsackievirus A24v (CVA24v) in complex with a dimeric C2-C9-linked sialic acid inhibitor

Components

(Capsid protein ...

Capsid) x 4

Keywords

VIRUS / Coxsackievirus A24v / CVA24v / sialic acid based inhibitor

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 ...
Similarity search - Function

Biological species

Coxsackievirus A24

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.728 Å

Authors

Zocher, G. / Stehle, T.

Funding support

Germany, 1items

Citation

Journal: 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

Deposition	Nov 18, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 18, 2022	Provider: repository / Type: Initial release
Revision 1.1	Nov 9, 2022	Group: 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 1.2	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7qb5.cif.gz	212.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7qb5.ent.gz		Display	PDB format
PDBx/mmJSON format	7qb5.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qb/7qb5 ftp://data.pdbj.org/pub/pdb/validation_reports/qb/7qb5	HTTPS FTP

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Related structure data

Related structure data	4q4wS S: Starting model for refinement
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#20 - Aug 2001 Poliovirus and Rhinovirus similarity (21) #113 - May 2009 Influenza Neuraminidase similarity (1) #200 - Aug 2016 Quasisymmetry in Icosahedral Viruses similarity (1)

Deposited unit

111: Capsid protein VP1

222: Capsid protein VP2

333: Capsid protein VP3

444: Capsid protein VP4

hetero molecules

98.9 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

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 number	23
Space group name H-M	I222

Noncrystallographic symmetry (NCS)

NCS oper:

ID	Code	Matrix	Vector
1	given	(1), (1), (1)
2	generate	(0.499142, -0.808993, 0.310465), (0.810588, 0.309284, -0.497284), (0.306277, 0.499874, 0.810136)	167.5183, 93.1396
3	generate	(-0.308408, -0.499481, 0.80957), (0.501045, -0.808726, -0.308086), (0.808603, 0.310614, 0.49968)	142.7967, 310.4966, -88.5697
4	generate	(-0.30819, 0.499398, 0.809704), (-0.501493, -0.808553, 0.30781), (0.808408, -0.311197, 0.499633)	-39.9929, 351.2609, 25.2158
5	generate	(0.498411, 0.809649, 0.309929), (-0.810625, 0.308489, 0.497716), (0.307366, -0.499303, 0.810076)	159.576, 79.1782
6	generate	(-0.501156, 0.808547, 0.308374), (-0.809046, -0.311336, -0.498513), (-0.307063, -0.499321, 0.810179)	25.2576, 454.8253, 172.7823
7	generate	(0.500465, 0.808722, -0.309035), (-0.809393, 0.310371, -0.49855), (-0.307273, 0.499638, 0.809905)	-14.9054, 341.2038, -9.7883
8	generate	(0.809574, -0.309745, -0.498646), (-0.306977, 0.500659, -0.809386), (0.500355, 0.808331, 0.310236)	176.9708, 286.6406, -98.0739
9	generate	(-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
10	generate	(-0.810045, -0.309717, 0.497898), (-0.305759, -0.501436, -0.809366), (0.500339, -0.80786, 0.311487)	242.4434, 469.6404, 197.1601
11	generate	(0.30738, -0.499631, 0.809868), (-0.498488, -0.809496, -0.310204), (0.810572, -0.308359, -0.497883)	48.7977, 464.0442, 206.8469
12	generate	(-0.000114, -0.00039, 1), (-1, 0.000576, -0.000114), (-0.000576, -1, -0.00039)	-30.429, 335.6889, 366.6289
13	generate	(0.306156, 0.501048, 0.809456), (-0.50048, 0.808013, -0.310861), (-0.809807, -0.309944, 0.498143)	168.8916, 272.9315
14	generate	(0.809509, 0.308741, 0.499374), (0.308555, 0.499905, -0.809252), (-0.499489, 0.809181, 0.309414)	192.7678, 55.0126
15	generate	(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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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 /

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

Identifier	Type	Program
DNeup5Aca	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-a-D-neuraminic acid	COMMON NAME	GMML 1.0
a-D-Neup5Ac	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
Neu5Ac	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

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Non-polymers , 4 types, 820 molecules

#6: Chemical	ChemComp-HEZ / HEXANE-1,6-DIOL / 1,6-Hexanediol 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 / Chloride Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#9: Water	ChemComp-HOH / water / 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 interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: DECTRIS PILATUS 6M
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Relative weight: 1
Reflection	Resolution: 1.728→50 Å / Num. obs: 6338512 / % possible obs: 91.4 % / Redundancy: 6.6 % / CC_1/2: 0.992 / R_rim(I) all: 0.158 / Net I/σ(I): 6.5
Reflection shell	Resolution: 1.73→1.83 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 973400 / CC_1/2: 0.604 / R_rim(I) all: 0.79 / % possible all: 93.3

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
XDS		data reduction
XDS		data scaling
REFMAC		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4Q4W

4q4w

Resolution: 1.728→49.922 Å / Cor.coef. F_o:F_c: 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

	R_factor	Num. reflection	% reflection
R_work	0.1656	1918801	-
all	0.166	-	-
obs	-	1918801	90.916 %
R_free	-	-	0 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK

Displacement parameters

B_iso mean: 24.874 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.012 Å²	0 Å²	-0 Å²
2-	-	0.199 Å²	0 Å²
3-	-	-	-0.187 Å²

Refinement step

Cycle: LAST / Resolution: 1.728→49.922 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6521	0	37	811	7369

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.013	6873
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	6136
X-RAY DIFFRACTION	r_angle_refined_deg	1.357	1.659	9423
X-RAY DIFFRACTION	r_angle_other_deg	1.269	1.568	14310
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	9.099	5	884
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.546	22.417	331
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.378	15	1069
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.708	15	35
X-RAY DIFFRACTION	r_chiral_restr	0.065	0.2	945
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	7748
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1458
X-RAY DIFFRACTION	r_nbd_refined	0.179	0.2	2254
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.16	0.2	11412
X-RAY DIFFRACTION	r_nbtor_refined	0.16	0.2	6626
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	6030
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.114	0.2	1356
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.618	0.2	96
X-RAY DIFFRACTION	r_nbd_other	0.576	0.2	501
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.209	0.2	123
X-RAY DIFFRACTION	r_mcbond_it	1.758	5.739	3393
X-RAY DIFFRACTION	r_mcbond_other	1.751	5.737	3392
X-RAY DIFFRACTION	r_mcangle_it	2.408	8.291	4246
X-RAY DIFFRACTION	r_mcangle_other	2.412	8.293	4247
X-RAY DIFFRACTION	r_scbond_it	3.165	6.326	3480
X-RAY DIFFRACTION	r_scbond_other	3.165	6.328	3481
X-RAY DIFFRACTION	r_scangle_it	4.478	8.927	5150
X-RAY DIFFRACTION	r_scangle_other	4.478	8.929	5151
X-RAY DIFFRACTION	r_lrange_it	7.609	42.151	7923
X-RAY DIFFRACTION	r_lrange_other	7.182	38.862	7674

LS refinement shell

Resolution (Å)	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.728-1.772	0.297	137745	X-RAY DIFFRACTION	88.787
1.772-1.821	0.272	141599	X-RAY DIFFRACTION	93.5672
1.821-1.874	0.251	137731	X-RAY DIFFRACTION	93.5851
1.874-1.931	0.23	132316	X-RAY DIFFRACTION	92.5455
1.931-1.994	0.21	129428	X-RAY DIFFRACTION	93.3366
1.994-2.064	0.195	124359	X-RAY DIFFRACTION	92.7879
2.064-2.142	0.183	119715	X-RAY DIFFRACTION	92.4669
2.142-2.229	0.17	115249	X-RAY DIFFRACTION	92.4677
2.229-2.328	0.162	109456	X-RAY DIFFRACTION	91.5774
2.328-2.442	0.158	105043	X-RAY DIFFRACTION	91.8826
2.442-2.573	0.155	99274	X-RAY DIFFRACTION	91.2327
2.573-2.729	0.147	93120	X-RAY DIFFRACTION	90.4192
2.729-2.917	0.141	86959	X-RAY DIFFRACTION	89.8179
2.917-3.15	0.132	81254	X-RAY DIFFRACTION	90.08
3.15-3.449	0.127	74170	X-RAY DIFFRACTION	89.197
3.449-3.854	0.126	66407	X-RAY DIFFRACTION	88.1244
3.854-4.446	0.117	58210	X-RAY DIFFRACTION	87.4576
4.446-5.434	0.118	48855	X-RAY DIFFRACTION	86.4277
5.434-7.64	0.153	37016	X-RAY DIFFRACTION	84.049
7.64-49.922	0.186	20900	X-RAY DIFFRACTION	82.953

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

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Sugars , 1 types, 1 molecules

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Non-polymers , 4 types, 820 molecules

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

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