PDB-7zu4: Crystal Structure of Human Parechovirus 1 2A protein lacking the ...

ID or keywords:

Entry

Database: PDB / ID: 7zu4

Title

Crystal Structure of Human Parechovirus 1 2A protein lacking the C-terminal oligomerisation helix

Components

Protein 2A

Keywords

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

Function / homology

Function and homology information

host cell nucleolus / host cell Golgi membrane / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell ...
Similarity search - Function

Biological species

Human parechovirus 1

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

von Castelmur, E. / Perrakis, A.

Funding support

Netherlands,

Sweden, 2items

Citation

Journal: To Be Published
Title: Human Parechovirus 1 2A protein
Authors: von Castelmur, E. / Perrakis, A.

History

Deposition	May 11, 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	7zu4.cif.gz	143.8 KB	Display	PDBx/mmCIF format
PDB format	pdb7zu4.ent.gz	88.2 KB	Display	PDB format
PDBx/mmJSON format	7zu4.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/zu/7zu4 ftp://data.pdbj.org/pub/pdb/validation_reports/zu/7zu4	HTTPS FTP

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Related structure data

Related structure data	7ztwC 7zu3SC 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 (11) #200 - Aug 2016 Quasisymmetry in Icosahedral Viruses similarity (1)

Deposited unit

A: Protein 2A

B: Protein 2A

hetero molecules

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

1

A: Protein 2A

hetero molecules

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

2

B: Protein 2A

hetero molecules

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

Unit cell

Length a, b, c (Å)	76.425, 76.425, 121.724
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2

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: MET / Beg label comp-ID: MET / End auth comp-ID: ILE / End label comp-ID: ILE / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 12 - 128 / Label seq-ID: 15 - 131

Dom-ID	Component-ID
1	1
2	2

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

#1: Protein	Protein 2A / P2A Mass: 14886.942 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human parechovirus 1 / Strain: Harris / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q66578
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.98 Å³/Da / Density % sol: 58.79 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 15% PEG 8000 0.5 M lithium sulphate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97625 Å / Relative weight: 1
Reflection	Resolution: 2.1→49.39 Å / Num. obs: 21802 / % possible obs: 100 % / Redundancy: 8.6 % / CC_1/2: 0.999 / R_merge(I) obs: 0.09 / R_pim(I) all: 0.047 / Net I/σ(I): 15.9
Reflection shell	Resolution: 2.1→2.16 Å / R_merge(I) obs: 1.209 / Num. unique obs: 1740 / CC_1/2: 0.624 / R_pim(I) all: 0.618

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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: 7ZU3

7zu3

Resolution: 2.1→49.39 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.943 / SU B: 8.148 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.148
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2202	1082	4.976 %
R_work	0.1976	20661	-
all	0.199	-	-
obs	-	21743	99.982 %

Solvent computation

Ion probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 50.814 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.412 Å²	0 Å²	0 Å²
2-	-	0.412 Å²	0 Å²
3-	-	-	-0.825 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→49.39 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1920	0	73	57	2050

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.012	2020
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	1868
X-RAY DIFFRACTION	r_angle_refined_deg	0.9	1.634	2718
X-RAY DIFFRACTION	r_angle_other_deg	0.322	1.566	4341
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.978	5	240
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.213	10	5
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.163	10	366
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.668	10	85
X-RAY DIFFRACTION	r_chiral_restr	0.046	0.2	316
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	2162
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	394
X-RAY DIFFRACTION	r_nbd_refined	0.2	0.2	392
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.17	0.2	1660
X-RAY DIFFRACTION	r_nbtor_refined	0.176	0.2	978
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.072	0.2	1059
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.11	0.2	57
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.206	0.2	18
X-RAY DIFFRACTION	r_nbd_other	0.156	0.2	78
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.199	0.2	11
X-RAY DIFFRACTION	r_mcbond_it	5.035	3.148	960
X-RAY DIFFRACTION	r_mcbond_other	5.025	3.149	960
X-RAY DIFFRACTION	r_mcangle_it	6.893	4.693	1197
X-RAY DIFFRACTION	r_mcangle_other	6.891	4.701	1198
X-RAY DIFFRACTION	r_scbond_it	8.599	4.139	1060
X-RAY DIFFRACTION	r_scbond_other	8.599	4.144	1061
X-RAY DIFFRACTION	r_scangle_it	10.441	5.887	1520
X-RAY DIFFRACTION	r_scangle_other	10.437	5.89	1521
X-RAY DIFFRACTION	r_lrange_it	11.752	47.152	2219
X-RAY DIFFRACTION	r_lrange_other	11.751	47.174	2217
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.165	0.05	3222

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	0.16494	0.05007
1	2	A	X-RAY DIFFRACTION	Local ncs	0.16494	0.05007

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 (%)
2.1-2.154	0.272	82	0.284	1474	X-RAY DIFFRACTION	99.9358
2.154-2.213	0.259	89	0.257	1455	X-RAY DIFFRACTION	100
2.213-2.277	0.295	76	0.237	1417	X-RAY DIFFRACTION	100
2.277-2.347	0.25	63	0.213	1373	X-RAY DIFFRACTION	100
2.347-2.424	0.233	65	0.196	1337	X-RAY DIFFRACTION	100
2.424-2.509	0.223	68	0.194	1311	X-RAY DIFFRACTION	100
2.509-2.603	0.227	63	0.185	1250	X-RAY DIFFRACTION	100
2.603-2.709	0.238	66	0.171	1219	X-RAY DIFFRACTION	100
2.709-2.83	0.171	54	0.15	1170	X-RAY DIFFRACTION	100
2.83-2.967	0.194	48	0.161	1119	X-RAY DIFFRACTION	100
2.967-3.127	0.225	50	0.182	1072	X-RAY DIFFRACTION	100
3.127-3.316	0.223	65	0.191	1004	X-RAY DIFFRACTION	100
3.316-3.544	0.201	57	0.19	942	X-RAY DIFFRACTION	100
3.544-3.826	0.2	49	0.179	898	X-RAY DIFFRACTION	100
3.826-4.189	0.134	45	0.164	828	X-RAY DIFFRACTION	100
4.189-4.679	0.15	37	0.147	753	X-RAY DIFFRACTION	100
4.679-5.395	0.222	32	0.186	689	X-RAY DIFFRACTION	100
5.395-6.588	0.411	33	0.303	581	X-RAY DIFFRACTION	100
6.588-9.235	0.24	23	0.257	470	X-RAY DIFFRACTION	100
9.235-49.39	0.246	17	0.286	299	X-RAY DIFFRACTION	99.6845

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	1.6606	0.3521	0.3301	3.4157	-0.6931	2.8363	0.0884	0.0393	0.0584	-0.2287	-0.0365	0.5009	0.121	-0.5601	-0.0519	0.1115	-0.0165	-0.045	0.1402	-0.0055	0.0852	-33.251	-8.9618	-21.236
2	2.0481	0.4646	0.4969	3.6354	-0.158	2.9625	0.0575	-0.2415	0.1399	0.3186	-0.0711	0.5021	0.0531	-0.5246	0.0136	0.0873	-0.0229	0.0458	0.1063	-0.0213	0.0723	-30.2453	13.5334	-16.8433

Refinement TLS group

Selection: ALL

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