PDB-7zv1: Crystal Structure of Aichivirus A 2A protein L64M, L109M mutant

ID or keywords:

Entry

Database: PDB / ID: 7zv1

Title

Crystal Structure of Aichivirus A 2A protein L64M, L109M mutant

Components

Protein 2A

Keywords

VIRAL PROTEIN / unknown function / 2A protein / NlpC/P60 protein

Function / homology

Function and homology information

host cell Golgi membrane / symbiont-mediated suppression of host mRNA export from nucleus /

picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane /

: / protein complex oligomerization / monoatomic ion channel activity /

RNA helicase activity /

RNA helicase ...
Similarity search - Function

Biological species

Aichi virus A846/88

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.74 Å

Authors

von Castelmur, E. / Perrakis, A.

Funding support

Netherlands, 1items

Citation

Journal: To Be Published
Title: Structural and functional repurposing of picornavirus H/NC-motif 2A proteins
Authors: von Castelmur, E. / Perrakis, A.

History

Deposition	May 13, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 31, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7zv1.cif.gz	173.2 KB	Display	PDBx/mmCIF format
PDB format	pdb7zv1.ent.gz	108.7 KB	Display	PDB format
PDBx/mmJSON format	7zv1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zv/7zv1 ftp://data.pdbj.org/pub/pdb/validation_reports/zv/7zv1	HTTPS FTP

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Related structure data

Related structure data	7zv6C C: citing same article (ref.)
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 (9) #200 - Aug 2016 Quasisymmetry in Icosahedral Viruses similarity (1)

Deposited unit

A: Protein 2A

B: Protein 2A

C: Protein 2A

43.4 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Protein 2A

defined by author
Evidence: light scattering
14.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Protein 2A

defined by author
14.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Protein 2A

defined by author
14.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	52.569, 77.445, 98.858
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	1	A	11 - 119
2	1	1	A	11 - 119
3	2	2	A	11 - 119
4	2	2	A	11 - 119
5	3	3	A	11 - 119
6	3	3	A	11 - 119

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6

#1: Protein	Protein 2A / P2A Mass: 14469.345 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: L64M, L109M mutant / Source: (gene. exp.) Aichi virus A846/88 / Strain: Human/A846/88/1989 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O91464
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.32 Å³/Da / Density % sol: 46.94 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1M MES pH6.75 30% PEG 30000 10mM TCEP

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97934 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 2, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97934 Å / Relative weight: 1
Reflection	Resolution: 1.74→41.67 Å / Num. obs: 41619 / % possible obs: 99 % / Redundancy: 4 % / CC_1/2: 0.999 / R_merge(I) obs: 0.056 / R_pim(I) all: 0.044 / Net I/σ(I): 14.8
Reflection shell	Resolution: 1.74→1.77 Å / R_merge(I) obs: 1.093 / Num. unique obs: 2258 / CC_1/2: 0.536 / R_pim(I) all: 0.84

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0349	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.74→41.67 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.946 / SU B: 4.831 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.1
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2181	2113	5.082 %
R_work	0.1977	39465	-
all	0.199	-	-
obs	-	41578	98.61 %

Solvent computation

Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 29.109 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.122 Å²	0 Å²	-0 Å²
2-	-	-0.753 Å²	0 Å²
3-	-	-	0.631 Å²

Refinement step

Cycle: LAST / Resolution: 1.74→41.67 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2476	0	0	106	2582

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	2571
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2324
X-RAY DIFFRACTION	r_angle_refined_deg	1.329	1.633	3520
X-RAY DIFFRACTION	r_angle_other_deg	0.441	1.572	5435
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.085	5	329
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	14.903	13.6	25
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.649	10.112	403
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.556	10	97
X-RAY DIFFRACTION	r_chiral_restr	0.068	0.2	397
X-RAY DIFFRACTION	r_chiral_restr_other	0.009	0.2	1
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	2923
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	493
X-RAY DIFFRACTION	r_nbd_refined	0.201	0.2	380
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.186	0.2	2015
X-RAY DIFFRACTION	r_nbtor_refined	0.175	0.2	1257
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	1309
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.118	0.2	118
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.183	0.2	14
X-RAY DIFFRACTION	r_nbd_other	0.219	0.2	61
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.177	0.2	15
X-RAY DIFFRACTION	r_mcbond_it	1.934	2.29	1292
X-RAY DIFFRACTION	r_mcbond_other	1.934	2.29	1292
X-RAY DIFFRACTION	r_mcangle_it	2.988	3.411	1611
X-RAY DIFFRACTION	r_mcangle_other	2.987	3.414	1612
X-RAY DIFFRACTION	r_scbond_it	2.37	2.493	1279
X-RAY DIFFRACTION	r_scbond_other	2.37	2.495	1280
X-RAY DIFFRACTION	r_scangle_it	3.557	3.664	1903
X-RAY DIFFRACTION	r_scangle_other	3.556	3.666	1904
X-RAY DIFFRACTION	r_lrange_it	5.64	35.367	2786
X-RAY DIFFRACTION	r_lrange_other	5.615	35.301	2770
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.098	0.05	3382
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.11	0.05	2958
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.124	0.05	2998

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.09772	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.09772	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.11047	0.05008
2	4	A	X-RAY DIFFRACTION	Local ncs	0.11047	0.05008
3	5	A	X-RAY DIFFRACTION	Local ncs	0.12427	0.05008
3	6	A	X-RAY DIFFRACTION	Local ncs	0.12427	0.05008

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.74-1.785	0.307	153	0.306	2883	X-RAY DIFFRACTION	99.77
1.785-1.834	0.333	145	0.278	2878	X-RAY DIFFRACTION	99.9009
1.834-1.887	0.254	160	0.253	2729	X-RAY DIFFRACTION	99.6894
1.887-1.945	0.242	130	0.232	2705	X-RAY DIFFRACTION	99.6835
1.945-2.009	0.241	137	0.217	2574	X-RAY DIFFRACTION	99.6691
2.009-2.079	0.196	146	0.202	2510	X-RAY DIFFRACTION	99.5502
2.079-2.157	0.23	124	0.197	2433	X-RAY DIFFRACTION	99.5716
2.157-2.245	0.214	117	0.191	2355	X-RAY DIFFRACTION	99.5971
2.245-2.345	0.213	125	0.184	2229	X-RAY DIFFRACTION	98.9491
2.345-2.459	0.219	109	0.176	2151	X-RAY DIFFRACTION	99.4281
2.459-2.591	0.182	99	0.175	2053	X-RAY DIFFRACTION	98.8516
2.591-2.748	0.239	107	0.189	1922	X-RAY DIFFRACTION	98.4474
2.748-2.936	0.21	105	0.204	1822	X-RAY DIFFRACTION	98.5174
2.936-3.17	0.206	80	0.214	1691	X-RAY DIFFRACTION	98.062
3.17-3.471	0.225	102	0.199	1536	X-RAY DIFFRACTION	96.8658
3.471-3.877	0.218	71	0.192	1414	X-RAY DIFFRACTION	96.8689
3.877-4.471	0.177	69	0.156	1240	X-RAY DIFFRACTION	95.9677
4.471-5.46	0.186	54	0.166	1067	X-RAY DIFFRACTION	95.3231
5.46-7.656	0.214	50	0.201	829	X-RAY DIFFRACTION	94.6179
7.656-41.67	0.278	30	0.247	445	X-RAY DIFFRACTION	83.7743

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.3087	-0.0339	0.2196	2.2952	0.9407	0.9009	0.0593	0.0072	-0.0247	0.0812	-0.0071	-0.1471	-0.0839	0.0222	-0.0522	0.0951	-0.0127	-0.0134	0.0055	-0.0057	0.0668	10.0609	6.6732	103.8906
2	1.5528	0.8682	-0.4542	1.0085	-0.185	0.2947	0.0405	-0.0658	0.008	0.0608	-0.0979	-0.0042	-0.0036	-0.0066	0.0574	0.0378	-0.0032	-0.0102	0.0292	-0.0016	0.0687	-7.625	-16.1135	105.573
3	0.7493	-0.9171	0.6318	1.3655	-1.0207	2.0057	0.0674	0.0076	0.0507	-0.1056	-0.0157	0.0446	0.0425	-0.0007	-0.0518	0.0786	0.0127	-0.0361	0.0097	0.0024	0.0755	46.6352	9.089	84.8159

Refinement TLS group

Selection: ALL

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