PDB-7ev8: Structure of Human Parainfluenza Virus 3 Unassembled Nucleoprotei...

ID or keywords:

Entry

Database: PDB / ID: 7ev8

Title

Structure of Human Parainfluenza Virus 3 Unassembled Nucleoprotein in Complex with its viral chaperone

Components

Nucleoprotein
Phosphoprotein

Keywords

VIRAL PROTEIN / Complex / Inhibitor / HPIV3 / Nucleoprotein

Function / homology

Function and homology information

helical viral capsid / viral genome replication / viral nucleocapsid / host cell cytoplasm / RNA-dependent RNA polymerase activity / DNA-templated transcription / structural molecule activity / RNA binding
Similarity search - Function

Biological species

Human parainfluenza 3 virus

Human respirovirus 3

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.234 Å

Authors

Dong, X.F. / Chen, Z.

Funding support

China, 1items

Citation

Journal: J.Virol. / Year: 2022
Title: Structural Basis of Human Parainfluenza Virus 3 Unassembled Nucleoprotein in Complex with Its Viral Chaperone.
Authors: Dong, X. / Wang, X. / Xie, M. / Wu, W. / Chen, Z.

History

Deposition	May 20, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 10, 2021	Provider: repository / Type: Initial release
Revision 1.1	Apr 27, 2022	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Nov 29, 2023	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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PDBx/mmCIF format	7ev8.cif.gz	87.2 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7ev8_validation.pdf.gz	431.1 KB	Display	wwPDB validaton report
Full document	7ev8_full_validation.pdf.gz	433 KB	Display
Data in XML	7ev8_validation.xml.gz	14.2 KB	Display
Data in CIF	7ev8_validation.cif.gz	19.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ev/7ev8 ftp://data.pdbj.org/pub/pdb/validation_reports/ev/7ev8	HTTPS FTP

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Related structure data

Related structure data	6h5qS S: Starting model for refinement
Similar structure data	6fl0-2 5e8c-d 4cnj-4 7nzj-2 4o1s-d 7nzj-1 4fda-1 2rf6-1 24253 1wcv-1 Search similar-shape structures by Omokage search (details) 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	#231 - Mar 2019 Measles Virus Proteins similarity (3) #62 - Feb 2005 Major Histocompatibility Complex similarity (2)

Deposited unit

A: Nucleoprotein

B: Phosphoprotein

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	117.090, 117.090, 143.177
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	97
Space group name H-M	I422

#1: Protein	Nucleoprotein / Nucleocapsid protein / NP / Protein N Mass: 38831.461 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human parainfluenza 3 virus (strain Wash/47885/57) Strain: Wash/47885/57 / Gene: N, NP / Production host: Escherichia coli (E. coli) / References: UniProt: P06159
#2: Protein/peptide	Phosphoprotein Mass: 4879.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human respirovirus 3 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A346TKJ9
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.81 Å³/Da / Density % sol: 56.18 %
Crystal grow	Temperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: PEG 6000, Cacodylate, Nickel chloride

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Data collection

Diffraction

Mean temperature: 80 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL17U1 / Wavelength: 0.979 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 22, 2020

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 3.23→50 Å / Num. obs: 8248 / % possible obs: 99.8 % / Redundancy: 6.8 % / R_merge(I) obs: 0.098 / R_pim(I) all: 0.04 / R_rim(I) all: 0.106 / Χ²: 0.903 / Net I/σ(I): 9.1 / Num. measured all: 56267

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
3.23-3.29	5.3	0.901	395	0.686	0.422	1	0.944	99.5
3.29-3.35	5.5	0.754	404	0.77	0.341	0.831	1.021	100
3.35-3.41	5.8	0.613	402	0.789	0.272	0.673	0.964	99.8
3.41-3.48	6.2	0.535	398	0.844	0.229	0.584	0.991	99.7
3.48-3.55	6.4	0.492	409	0.884	0.208	0.536	1.027	99.8
3.55-3.64	7.1	0.397	404	0.929	0.16	0.43	0.993	100
3.64-3.73	7.7	0.277	394	0.947	0.105	0.297	1.02	100
3.73-3.83	7.5	0.254	416	0.968	0.099	0.273	0.952	100
3.83-3.94	7.3	0.2	403	0.971	0.079	0.215	1.013	100
3.94-4.07	7.1	0.16	411	0.984	0.064	0.173	0.959	100
4.07-4.21	7.3	0.138	418	0.986	0.054	0.148	0.999	100
4.21-4.38	7.5	0.114	402	0.991	0.044	0.122	0.971	100
4.38-4.58	7.4	0.089	412	0.993	0.035	0.095	0.919	100
4.58-4.82	6.8	0.077	402	0.997	0.031	0.083	0.845	100
4.82-5.13	7.3	0.079	421	0.994	0.031	0.085	0.86	99.8
5.13-5.52	7.2	0.076	420	0.997	0.03	0.082	0.804	100
5.52-6.08	6.9	0.075	420	0.994	0.03	0.081	0.754	100
6.08-6.95	7.1	0.059	421	0.996	0.024	0.064	0.713	100
6.95-8.75	6.8	0.038	429	0.999	0.015	0.042	0.694	99.3
8.75-50	6.1	0.032	467	0.999	0.013	0.035	0.689	98.1

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
HKL-2000		data scaling
PDB_EXTRACT	3.27	data extraction
HKL-2000		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6H5Q

6h5q

Resolution: 3.234→49.178 Å / Cor.coef. F_o:F_c: 0.899 / Cor.coef. F_o:F_c free: 0.842 / WR_factor R_free: 0.243 / WR_factor R_work: 0.205 / SU B: 14.998 / SU ML: 0.27 / Average fsc free: 0.9682 / Average fsc work: 0.9757 / Cross valid method: THROUGHOUT / ESU R Free: 0.1
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2378	385	4.803 %	RANDOM
R_work	0.2192	7630	-	-
all	0.22	-	-	-
obs	-	8015	96.823 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 45.392 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.885 Å²	0 Å²	0 Å²
2-	-	3.885 Å²	0 Å²
3-	-	-	-7.77 Å²

Refinement step

Cycle: LAST / Resolution: 3.234→49.178 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2654	0	0	54	2708

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	2698
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	2517
X-RAY DIFFRACTION	r_ext_dist_refined_d	0.002	0.01	4949
X-RAY DIFFRACTION	r_angle_refined_deg	1.411	1.637	3659
X-RAY DIFFRACTION	r_angle_other_deg	1.47	1.57	5802
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.026	5	348
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.802	22.308	117
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.88	15	449
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.184	15	15
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	385
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	3010
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	560
X-RAY DIFFRACTION	r_nbd_refined	0.214	0.2	652
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.196	0.2	2324
X-RAY DIFFRACTION	r_nbtor_refined	0.174	0.2	1380
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.086	0.2	1200
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.151	0.2	60
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.315	0.2	4
X-RAY DIFFRACTION	r_nbd_other	0.167	0.2	20
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.103	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	3.612	5.071	1401
X-RAY DIFFRACTION	r_mcbond_other	3.579	5.068	1400
X-RAY DIFFRACTION	r_mcangle_it	6.02	7.595	1746
X-RAY DIFFRACTION	r_mcangle_other	6.02	7.599	1747
X-RAY DIFFRACTION	r_scbond_it	3.377	5.09	1297
X-RAY DIFFRACTION	r_scbond_other	3.376	5.094	1298
X-RAY DIFFRACTION	r_scangle_it	5.531	7.555	1913
X-RAY DIFFRACTION	r_scangle_other	5.532	7.555	1913
X-RAY DIFFRACTION	r_lrange_it	10.467	100.795	6363
X-RAY DIFFRACTION	r_lrange_other	10.438	100.692	6357

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 (%)
3.234-3.318	0.265	13	0.281	399	X-RAY DIFFRACTION	68.0992
3.318-3.408	0.294	28	0.264	499	X-RAY DIFFRACTION	92.1329
3.408-3.506	0.256	32	0.256	517	X-RAY DIFFRACTION	98.2111
3.506-3.614	0.212	25	0.236	526	X-RAY DIFFRACTION	99.6383
3.614-3.732	0.175	23	0.211	504	X-RAY DIFFRACTION	100
3.732-3.862	0.195	33	0.214	482	X-RAY DIFFRACTION	100
3.862-4.007	0.189	20	0.203	474	X-RAY DIFFRACTION	100
4.007-4.169	0.271	22	0.191	474	X-RAY DIFFRACTION	100
4.169-4.353	0.222	27	0.183	440	X-RAY DIFFRACTION	100
4.353-4.564	0.179	22	0.183	424	X-RAY DIFFRACTION	100
4.564-4.808	0.201	30	0.174	394	X-RAY DIFFRACTION	100
4.808-5.097	0.201	15	0.199	384	X-RAY DIFFRACTION	99.75
5.097-5.445	0.324	15	0.22	371	X-RAY DIFFRACTION	100
5.445-5.875	0.178	15	0.239	345	X-RAY DIFFRACTION	100
5.875-6.427	0.375	19	0.252	315	X-RAY DIFFRACTION	100
6.427-7.171	0.255	11	0.242	294	X-RAY DIFFRACTION	100
7.171-8.251	0.173	13	0.19	262	X-RAY DIFFRACTION	98.9209
8.251-10.037	0.177	9	0.181	224	X-RAY DIFFRACTION	100
10.037-13.912	0.285	7	0.204	187	X-RAY DIFFRACTION	99.4872
13.912-49.178	1.264	6	0.515	115	X-RAY DIFFRACTION	93.7984

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