PDB-7dxp: Influenza H5N1 nucleoprotein in complex with nucleotides

ID or keywords:

Entry

Database: PDB / ID: 7dxp

Title

Influenza H5N1 nucleoprotein in complex with nucleotides

Components

Nucleoprotein
RNA (5'-R(P*(OMU)P*(OMU)P*(OMU)P*(OMU))-3')

Keywords

VIRAL PROTEIN/RNA / nucleocapsid / RNA-binding / influenza nucleoprotein / VIRAL PROTEIN-RNA complex

Function / homology

DNA

Function and homology information

Biological species

Influenza A virus

unidentified influenza virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Tang, Y.S. / Xu, S. / Chen, Y.W. / Wang, J.H. / Shaw, P.C.

Funding support

Hong Kong, 1items

Citation

Journal: Nucleic Acids Res. / Year: 2021
Title: Crystal structures of influenza nucleoprotein complexed with nucleic acid provide insights into the mechanism of RNA interaction.
Authors: Tang, Y.S. / Xu, S. / Chen, Y.W. / Wang, J.H. / Shaw, P.C.

History

Deposition	Jan 19, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 14, 2021	Provider: repository / Type: Initial release
Revision 1.1	Apr 28, 2021	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Mar 27, 2024	Group: Data collection / Database references / Derived calculations Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7dxp.cif.gz	186.5 KB	Display	PDBx/mmCIF format
PDB format	pdb7dxp.ent.gz	140.1 KB	Display	PDB format
PDBx/mmJSON format	7dxp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7dxp_validation.pdf.gz	470.2 KB	Display	wwPDB validaton report
Full document	7dxp_full_validation.pdf.gz	492.4 KB	Display
Data in XML	7dxp_validation.xml.gz	33.3 KB	Display
Data in CIF	7dxp_validation.cif.gz	46.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dx/7dxp ftp://data.pdbj.org/pub/pdb/validation_reports/dx/7dxp	HTTPS FTP

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Related structure data

Related structure data	7dkgC C: citing same article (ref.)
Similar structure data	7dkg-d 4j4l-d 6tsi-d 3gyr-7 3gyr-8 4mgk-d 3gyr-6 3gyr-5 5jm0-d 6h1l-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Nucleoprotein

B: Nucleoprotein

C: RNA (5'-R(P*(OMU)P*(OMU)P*(OMU)P*(OMU))-3')

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: Microscale thermophoresis

Unit cell

Length a, b, c (Å)	54.010, 60.630, 82.710
Angle α, β, γ (deg.)	106.700, 109.010, 96.620
Int Tables number	1
Space group name H-M	P1

#1: Protein	Nucleoprotein Mass: 57243.684 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/Hong Kong/483/1997(H5N1)) Strain: A/Hong Kong/483/97(H5N1) / Production host: Escherichia coli (E. coli)
#2: DNA chain	RNA (5'-R(P(OMU)P(OMU)P(OMU)P(OMU))-3') Mass: 2836.778 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified influenza virus
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Sequence details	Missing residues contain expression tags, disordered residues and a deletion from 402-428.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.94 Å³/Da / Density % sol: 36.54 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES, pH 6.0, 0.1 M NaCl and 11% PEG2000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9789 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 18, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9789 Å / Relative weight: 1
Reflection	Resolution: 2.3→25.52 Å / Num. obs: 37106 / % possible obs: 90.4 % / Redundancy: 1.9 % / R_merge(I) obs: 0.102 / Net I/σ(I): 7.1
Reflection shell	Resolution: 2.3→2.42 Å / Redundancy: 1.9 % / R_merge(I) obs: 0.253 / Num. unique obs: 5475 / % possible all: 91.6

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
iMOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.3→24.501 Å / Cor.coef. F_o:F_c: 0.937 / Cor.coef. F_o:F_c free: 0.897 / WR_factor R_free: 0.254 / WR_factor R_work: 0.199 / SU B: 7.704 / SU ML: 0.185 / Average fsc free: 0.8967 / Average fsc work: 0.9135 / Cross valid method: NONE / ESU R: 0.42 / ESU R Free: 0.263
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2484	1866	5.032 %
R_work	0.193	35220	-
all	0.196	-	-
obs	-	37086	90.33 %

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: 34.447 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.848 Å²	0.252 Å²	-0.659 Å²
2-	-	1.025 Å²	-0.067 Å²
3-	-	-	-0.864 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→24.501 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6461	66	8	155	6690

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	6680
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	6268
X-RAY DIFFRACTION	r_angle_refined_deg	1.709	1.661	8976
X-RAY DIFFRACTION	r_angle_other_deg	1.327	1.588	14433
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.059	5	815
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.146	19.543	416
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.897	15	1208
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.464	15	90
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	865
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	7496
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1578
X-RAY DIFFRACTION	r_nbd_refined	0.21	0.2	1447
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.187	0.2	6064
X-RAY DIFFRACTION	r_nbtor_refined	0.162	0.2	3234
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	3370
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.186	0.2	241
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.056	0.2	4
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.242	0.2	23
X-RAY DIFFRACTION	r_nbd_other	0.273	0.2	67
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.163	0.2	15
X-RAY DIFFRACTION	r_mcbond_it	3.406	3.423	3272
X-RAY DIFFRACTION	r_mcbond_other	3.404	3.422	3271
X-RAY DIFFRACTION	r_mcangle_it	5.141	5.11	4077
X-RAY DIFFRACTION	r_mcangle_other	5.141	5.111	4078
X-RAY DIFFRACTION	r_scbond_it	3.846	3.927	3408
X-RAY DIFFRACTION	r_scbond_other	3.845	3.927	3409
X-RAY DIFFRACTION	r_scangle_it	5.902	5.705	4897
X-RAY DIFFRACTION	r_scangle_other	5.901	5.705	4898
X-RAY DIFFRACTION	r_lrange_it	8.392	39.509	7624
X-RAY DIFFRACTION	r_lrange_other	8.392	39.512	7625
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.091	0.05	12562

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
2.3-2.359	0.281	125	0.239	2627	0.241	3006	0.825	0.848	91.5502	0.218
2.359-2.423	0.298	128	0.228	2540	0.232	2916	0.839	0.864	91.4952	0.208
2.423-2.493	0.284	123	0.223	2511	0.225	2858	0.852	0.882	92.1624	0.199
2.493-2.569	0.28	139	0.208	2434	0.212	2805	0.871	0.896	91.7291	0.184
2.569-2.652	0.254	131	0.208	2312	0.21	2675	0.891	0.898	91.3271	0.188
2.652-2.744	0.245	116	0.201	2249	0.203	2598	0.901	0.915	91.0316	0.185
2.744-2.846	0.257	115	0.186	2192	0.189	2538	0.915	0.927	90.8983	0.167
2.846-2.961	0.252	121	0.179	2067	0.183	2412	0.902	0.926	90.7131	0.164
2.961-3.09	0.264	101	0.194	1968	0.198	2280	0.895	0.919	90.7456	0.183
3.09-3.238	0.242	109	0.174	1920	0.178	2245	0.921	0.941	90.3786	0.168
3.238-3.41	0.232	107	0.188	1826	0.191	2137	0.917	0.92	90.4539	0.186
3.41-3.613	0.245	100	0.196	1693	0.199	2005	0.913	0.928	89.4264	0.196
3.613-3.856	0.257	73	0.18	1575	0.183	1876	0.928	0.939	87.8465	0.186
3.856-4.157	0.221	59	0.172	1451	0.174	1760	0.937	0.951	85.7955	0.183
4.157-4.54	0.201	62	0.165	1264	0.166	1612	0.945	0.956	82.2581	0.184
4.54-5.055	0.223	60	0.173	1157	0.176	1470	0.937	0.95	82.7891	0.2
5.055-5.796	0.279	67	0.208	1184	0.212	1289	0.936	0.939	97.052	0.238
5.796-7.001	0.247	63	0.203	1016	0.206	1114	0.922	0.947	96.8582	0.237
7.001-9.52	0.23	44	0.166	784	0.169	877	0.938	0.958	94.4128	0.216
9.52-24.501	0.236	23	0.286	450	0.283	546	0.916	0.924	86.63	0.393

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