PDB-7zv6: Crystal Structure of Aichivirus A 2A protein

ID or keywords:

Entry

Database: PDB / ID: 7zv6

Title

Crystal Structure of Aichivirus A 2A protein

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 / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / RNA helicase / symbiont entry into host cell ...
Similarity search - Function

Biological species

Aichi virus A846/88

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.83 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 24, 2023	Provider: repository / Type: Initial release
Revision 1.1	Feb 7, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7zv6.cif.gz	182.5 KB	Display	PDBx/mmCIF format
PDB format	pdb7zv6.ent.gz	112.4 KB	Display	PDB format
PDBx/mmJSON format	7zv6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7zv6_validation.pdf.gz	448.6 KB	Display	wwPDB validaton report
Full document	7zv6_full_validation.pdf.gz	449.7 KB	Display
Data in XML	7zv6_validation.xml.gz	13.2 KB	Display
Data in CIF	7zv6_validation.cif.gz	17.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zv/7zv6 ftp://data.pdbj.org/pub/pdb/validation_reports/zv/7zv6	HTTPS FTP

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Related structure data

Related structure data	7zv1SC S: Starting model for refinement 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

B: Protein 2A

A: Protein 2A

C: Protein 2A

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

1

B: Protein 2A

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

2

A: Protein 2A

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

3

C: Protein 2A

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

Unit cell

Length a, b, c (Å)	157.456, 52.776, 61.470
Angle α, β, γ (deg.)	90.000, 108.632, 90.000
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

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

NCS domain segments:

End auth comp-ID: ILE / End label comp-ID: ILE / Auth asym-ID: B / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	VAL	VAL	9 - 119	12 - 122
2	1	1	VAL	VAL	9 - 119	12 - 122
3	2	2	ASP	ASP	10 - 119	13 - 122
4	2	2	ASP	ASP	10 - 119	13 - 122
5	3	3	ASP	ASP	10 - 119	13 - 122
6	3	3	ASP	ASP	10 - 119	13 - 122

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: 14644.486 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source 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 Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.75 Å³/Da / Density % sol: 55.34 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1M Hepes-NaOH pH7.5 20% PEG1500 0.1M CaCl2

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 2, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8726 Å / Relative weight: 1
Reflection	Resolution: 2.83→49.76 Å / Num. obs: 11153 / % possible obs: 95.4 % / Redundancy: 3.6 % / R_merge(I) obs: 0.158 / R_pim(I) all: 0.116 / Net I/σ(I): 6.6
Reflection shell	Resolution: 2.83→2.98 Å / R_merge(I) obs: 0.674 / Num. unique obs: 1247 / R_pim(I) all: 0.583

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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:

MOLECULAR REPLACEMENT
Starting model: 7ZV1

7zv1

Resolution: 2.83→49.76 Å / Cor.coef. F_o:F_c: 0.896 / Cor.coef. F_o:F_c free: 0.864 / SU B: 38.748 / SU ML: 0.334 / Cross valid method: THROUGHOUT / ESU R: 6.808 / ESU R Free: 0.365
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2507	543	4.87 %
R_work	0.24	10608	-
all	0.241	-	-
obs	-	11151	95.397 %

Solvent computation

Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 42.262 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.583 Å²	0 Å²	0.807 Å²
2-	-	-0.497 Å²	-0 Å²
3-	-	-	-2.143 Å²

Refinement step

Cycle: LAST / Resolution: 2.83→49.76 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2618	0	0	27	2645

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.002	0.012	2685
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2435
X-RAY DIFFRACTION	r_angle_refined_deg	0.716	1.629	3677
X-RAY DIFFRACTION	r_angle_other_deg	0.249	1.57	5677
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.904	5	340
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	10.451	13.75	24
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.791	10.111	404
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	11.055	10	100
X-RAY DIFFRACTION	r_chiral_restr	0.034	0.2	421
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	3054
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	510
X-RAY DIFFRACTION	r_nbd_refined	0.17	0.2	410
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.174	0.2	2205
X-RAY DIFFRACTION	r_nbtor_refined	0.161	0.2	1354
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	1363
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.098	0.2	57
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.111	0.2	12
X-RAY DIFFRACTION	r_nbd_other	0.134	0.2	76
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.119	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	1.503	3.109	1369
X-RAY DIFFRACTION	r_mcbond_other	1.503	3.109	1369
X-RAY DIFFRACTION	r_mcangle_it	2.617	4.653	1706
X-RAY DIFFRACTION	r_mcangle_other	2.617	4.654	1707
X-RAY DIFFRACTION	r_scbond_it	1.351	3.136	1316
X-RAY DIFFRACTION	r_scbond_other	1.351	3.136	1317
X-RAY DIFFRACTION	r_scangle_it	2.272	4.718	1971
X-RAY DIFFRACTION	r_scangle_other	2.271	4.718	1972
X-RAY DIFFRACTION	r_lrange_it	6.084	58.393	10650
X-RAY DIFFRACTION	r_lrange_other	6.084	58.398	10648
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.049	0.05	3453
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.067	0.05	3372
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.074	0.05	3375

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	B	X-RAY DIFFRACTION	Local ncs	0.04878	0.05011
1	2	B	X-RAY DIFFRACTION	Local ncs	0.04878	0.05011
2	3	B	X-RAY DIFFRACTION	Local ncs	0.06724	0.05011
2	4	B	X-RAY DIFFRACTION	Local ncs	0.06724	0.05011
3	5	B	X-RAY DIFFRACTION	Local ncs	0.07361	0.0501
3	6	B	X-RAY DIFFRACTION	Local ncs	0.07361	0.0501

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 (%)
2.83-2.899	0.348	14	0.379	564	X-RAY DIFFRACTION	67.5234
2.899-2.978	0.214	32	0.344	632	X-RAY DIFFRACTION	80.4848
2.978-3.064	0.356	29	0.346	707	X-RAY DIFFRACTION	90.7522
3.064-3.158	0.291	29	0.324	738	X-RAY DIFFRACTION	98.9677
3.158-3.261	0.319	43	0.266	735	X-RAY DIFFRACTION	99.8716
3.261-3.375	0.182	35	0.261	693	X-RAY DIFFRACTION	99.8628
3.375-3.502	0.316	49	0.26	676	X-RAY DIFFRACTION	100
3.502-3.644	0.287	36	0.256	645	X-RAY DIFFRACTION	100
3.644-3.805	0.287	38	0.254	613	X-RAY DIFFRACTION	99.6937
3.805-3.99	0.252	30	0.229	597	X-RAY DIFFRACTION	99.8408
3.99-4.204	0.203	40	0.202	565	X-RAY DIFFRACTION	100
4.204-4.457	0.229	25	0.19	554	X-RAY DIFFRACTION	99.8276
4.457-4.762	0.205	22	0.168	510	X-RAY DIFFRACTION	100
4.762-5.14	0.192	26	0.182	480	X-RAY DIFFRACTION	99.8028
5.14-5.625	0.212	27	0.224	437	X-RAY DIFFRACTION	99.7849
5.625-6.279	0.283	10	0.23	414	X-RAY DIFFRACTION	100
6.279-7.231	0.324	19	0.216	354	X-RAY DIFFRACTION	99.7326
7.231-8.81	0.142	19	0.196	310	X-RAY DIFFRACTION	99.0964
8.81-12.268	0.235	13	0.174	233	X-RAY DIFFRACTION	99.5951
12.268-49.76	0.501	7	0.296	151	X-RAY DIFFRACTION	100

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	1.559	-1.2021	-0.2612	1.1204	0.4972	1.1267	-0.0662	0.0496	-0.0098	-0.0027	0.0185	0.0265	0.0712	-0.0009	0.0477	0.2699	-0.0256	0.1013	0.0282	0.0078	0.0501	14.7646	2.4732	63.2763
2	0.7211	0.6716	0.3675	1.0865	1.3037	2.2764	-0.0139	-0.0162	0.0162	-0.0121	-0.0205	0.0502	-0.1243	-0.0599	0.0344	0.2936	0.0191	0.1021	0.0262	0.0111	0.04	9.6029	-22.0936	80.1133
3	1.3684	-0.792	0.0622	0.7314	0.5926	4.0044	-0.0315	-0.2152	0.0763	0.0028	0.0184	-0.0786	0.219	0.3862	0.0131	0.09	0.0554	-0.0171	0.2503	0.036	0.0246	36.3171	-26.0824	80.9556

Refinement TLS group

Selection: ALL

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