PDB-8a2g: Crystal structure of Sebokelevirus 2A2 protein

ID or keywords:

Entry

Database: PDB / ID: 8a2g

Title

Crystal structure of Sebokelevirus 2A2 protein

Components

2A2 protein

Keywords

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

Function / homology

Function and homology information

RNA-protein covalent cross-linking / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane /

viral capsid /

: / protein complex oligomerization / monoatomic ion channel activity /

RNA helicase activity / symbiont entry into host cell / viral RNA genome replication ...
Similarity search - Function

Biological species

Sebokele virus 1

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.56 Å

Authors

Zhu, L. / Von Castelmur, E. / Whang, X. / Ren, J. / Fry, E. / Perrakis, A. / Stuart, D.I.

Funding support

Netherlands, 1items

Citation

Journal: to be published
Title: Structural plasticity of 2A proteins in the Parechovirus family
Authors: Von Castelmur, E. / Zhu, L. / Perrakis, A.

History

Deposition	Jun 3, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 14, 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	8a2g.cif.gz	167.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8a2g.ent.gz	102.1 KB	Display	PDB format
PDBx/mmJSON format	8a2g.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/a2/8a2g ftp://data.pdbj.org/pub/pdb/validation_reports/a2/8a2g	HTTPS FTP

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Related structure data

Related structure data	8a2fSC 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 (10)

Deposited unit

A: 2A2 protein

B: 2A2 protein

hetero molecules

32.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: homology, the related Parechovirus A and Parechovirus B proteins are dimeric in solution, as shown by light scattering

Unit cell

Length a, b, c (Å)	64.350, 69.730, 57.270
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ALA / End label comp-ID: ALA / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: -4 - 138 / Label seq-ID: 1 - 143

Dom-ID	Component-ID
1	1
2	2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

#1: Protein	2A2 protein Mass: 15898.903 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sebokele virus 1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: S0DHJ0
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.02 Å³/Da / Density % sol: 39.12 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20% PEG3350, 0.2M sodium fluoride (according to info sent to us) or 30% PEG4000, 0.005 M magnesium acetate, 0.050 M sodium cacodylate pH 6.5 (thesis info)

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97957 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97957 Å / Relative weight: 1
Reflection	Resolution: 1.56→57.3 Å / Num. obs: 37407 / % possible obs: 100 % / Redundancy: 12.9 % / R_merge(I) obs: 0.055 / Net I/σ(I): 26.3
Reflection shell	Resolution: 1.56→1.6 Å / Redundancy: 11.8 % / R_merge(I) obs: 0.726 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 2713 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0349	refinement
xia2		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 8A2F

8a2f

Resolution: 1.56→57.27 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.961 / SU B: 3.16 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.086
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2016	1807	4.836 %
R_work	0.1703	35558	-
all	0.172	-	-
obs	-	37365	99.957 %

Solvent computation

Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 23.277 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.366 Å²	-0 Å²	0 Å²
2-	-	0.628 Å²	-0 Å²
3-	-	-	-0.993 Å²

Refinement step

Cycle: LAST / Resolution: 1.56→57.27 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2220	0	17	255	2492

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	2364
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2158
X-RAY DIFFRACTION	r_angle_refined_deg	1.486	1.621	3229
X-RAY DIFFRACTION	r_angle_other_deg	0.524	1.572	5033
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.761	5	317
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	23.658	13.75	16
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.54	10.077	392
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.169	10	97
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	374
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	2719
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	469
X-RAY DIFFRACTION	r_nbd_refined	0.219	0.2	478
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.182	0.2	2072
X-RAY DIFFRACTION	r_nbtor_refined	0.184	0.2	1188
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	1315
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.144	0.2	198
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.014	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.242	0.2	25
X-RAY DIFFRACTION	r_nbd_other	0.221	0.2	75
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.217	0.2	24
X-RAY DIFFRACTION	r_mcbond_it	3.018	1.935	1188
X-RAY DIFFRACTION	r_mcbond_other	3.017	1.935	1188
X-RAY DIFFRACTION	r_mcangle_it	4.249	2.901	1491
X-RAY DIFFRACTION	r_mcangle_other	4.248	2.9	1492
X-RAY DIFFRACTION	r_scbond_it	4.589	2.283	1176
X-RAY DIFFRACTION	r_scbond_other	4.589	2.285	1177
X-RAY DIFFRACTION	r_scangle_it	6.135	3.262	1724
X-RAY DIFFRACTION	r_scangle_other	6.134	3.263	1725
X-RAY DIFFRACTION	r_lrange_it	7.943	35.624	2819
X-RAY DIFFRACTION	r_lrange_other	7.944	35.632	2820
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.133	0.05	4387

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	0.13281	0.05007
1	2	A	X-RAY DIFFRACTION	Local ncs	0.13281	0.05007

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.56-1.601	0.272	134	0.223	2574	0.226	2708	0.959	0.968	100	0.193
1.601-1.644	0.234	128	0.206	2519	0.208	2648	0.966	0.973	99.9622	0.175
1.644-1.692	0.245	114	0.199	2489	0.201	2603	0.964	0.974	100	0.169
1.692-1.744	0.212	110	0.188	2378	0.189	2488	0.973	0.977	100	0.16
1.744-1.801	0.219	107	0.184	2343	0.185	2451	0.968	0.978	99.9592	0.156
1.801-1.864	0.265	117	0.19	2222	0.194	2339	0.956	0.976	100	0.164
1.864-1.935	0.225	123	0.183	2171	0.185	2298	0.969	0.978	99.8259	0.162
1.935-2.013	0.207	118	0.175	2084	0.177	2204	0.973	0.981	99.9093	0.16
2.013-2.103	0.203	114	0.178	1988	0.179	2103	0.974	0.98	99.9524	0.165
2.103-2.205	0.216	105	0.176	1924	0.178	2029	0.971	0.981	100	0.164
2.205-2.324	0.199	107	0.154	1815	0.156	1922	0.974	0.985	100	0.147
2.324-2.465	0.21	77	0.161	1739	0.163	1816	0.971	0.984	100	0.157
2.465-2.635	0.193	84	0.154	1644	0.156	1729	0.977	0.985	99.9422	0.155
2.635-2.846	0.203	70	0.167	1550	0.169	1621	0.974	0.982	99.9383	0.173
2.846-3.117	0.223	79	0.178	1404	0.18	1484	0.968	0.98	99.9326	0.186
3.117-3.483	0.166	42	0.169	1328	0.169	1370	0.983	0.984	100	0.184
3.483-4.019	0.182	58	0.155	1142	0.157	1201	0.979	0.985	99.9167	0.173
4.019-4.917	0.149	57	0.141	982	0.141	1039	0.985	0.989	100	0.17
4.917-6.928	0.251	38	0.181	788	0.184	826	0.976	0.983	100	0.214
6.928-57.27	0.186	25	0.194	474	0.193	502	0.974	0.971	99.4024	0.245

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	0.7882	-0.0613	-0.0962	1.4894	-0.216	0.7214	0.0027	0.0035	-0.0981	-0.0886	0.0197	0.0485	0.0103	0.0876	-0.0223	0.0118	-0.0001	-0.0108	0.0144	-0.0013	0.0364	21.5959	13.6833	-2.0484
2	0.2271	-0.1986	0.0009	0.2888	-0.1131	1.8248	-0.0085	0.0515	0.0368	-0.0015	-0.0422	-0.0003	0.0456	-0.0056	0.0507	0.0125	-0.0012	0.0011	0.0118	0.0092	0.0196	19.4638	21.3749	-25.4814

Refinement TLS group

Selection: ALL

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