PDB-5xsq: Crystal Structure of the Marburg Virus Nucleoprotein Core Domain ...

ID or keywords:

Entry

Database: PDB / ID: 5xsq

Title

Crystal Structure of the Marburg Virus Nucleoprotein Core Domain Chaperoned by a VP35 Peptide

Components

Nucleoprotein
Peptide from Polymerase cofactor VP35

Keywords

VIRAL PROTEIN / Marburg virus / Nucleoprotein / VP35 / NPBP / filovirus

Function / homology

Function and homology information

viral RNA genome packaging / helical viral capsid / viral budding via host ESCRT complex / virion component / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / RNA binding
Similarity search - Function

Biological species

Lake Victoria marburgvirus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Zhu, T. / Song, H. / Shi, Y. / Qi, J. / Gao, G.F.

Citation

Journal: J. Virol. / Year: 2017
Title: Crystal Structure of the Marburg Virus Nucleoprotein Core Domain Chaperoned by a VP35 Peptide Reveals a Conserved Drug Target for Filovirus
Authors: Zhu, T. / Song, H. / Peng, R. / Shi, Y. / Qi, J. / Gao, G.F.

History

Deposition	Jun 15, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jun 28, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jul 5, 2017	Group: Data collection / Category: reflns_shell / Item: _reflns_shell.Rmerge_I_obs
Revision 1.2	Sep 13, 2017	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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year / _citation_author.name
Revision 1.3	Feb 7, 2018	Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4	Nov 22, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5xsq.cif.gz	397 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5xsq_validation.pdf.gz	472.7 KB	Display	wwPDB validaton report
Full document	5xsq_full_validation.pdf.gz	488.7 KB	Display
Data in XML	5xsq_validation.xml.gz	35.7 KB	Display
Data in CIF	5xsq_validation.cif.gz	48.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xs/5xsq ftp://data.pdbj.org/pub/pdb/validation_reports/xs/5xsq	HTTPS FTP

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Related structure data

Related structure data	4ypiS S: Starting model for refinement
Similar structure data	5f5o-1 6s9o-4 2gs9-d 5h65-d 2wee-d 3fbu-2 5hi6-d 5v76-d 6s9o-5 3q0i-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

4ypiS

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#178 - Oct 2014 Ebola Virus Proteins similarity (8)

Deposited unit

A: Nucleoprotein

B: Peptide from Polymerase cofactor VP35

C: Nucleoprotein

D: Peptide from Polymerase cofactor VP35

E: Nucleoprotein

F: Peptide from Polymerase cofactor VP35

118 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Nucleoprotein

B: Peptide from Polymerase cofactor VP35

defined by author&software
Evidence: gel filtration
39.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Nucleoprotein

D: Peptide from Polymerase cofactor VP35

defined by author&software
39.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Nucleoprotein

F: Peptide from Polymerase cofactor VP35

defined by author&software
39.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	101.320, 101.320, 96.330
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	145
Space group name H-M	P3₂

#1: Protein	Nucleoprotein / Nucleocapsid protein Mass: 36365.484 Da / Num. of mol.: 3 / Fragment: UNP residues 18-344 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lake Victoria marburgvirus (strain Ozolin-75) Strain: Ozolin-75 / Gene: NP / Plasmid: pet21a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6UY69
#2: Protein/peptide	Peptide from Polymerase cofactor VP35 Mass: 3120.512 Da / Num. of mol.: 3 / Source method: obtained synthetically Source: (synth.) Lake Victoria marburgvirus (strain Ozolin-75) References: UniProt: Q6UY68

#1: Protein

Nucleoprotein / Nucleocapsid protein

Mass: 36365.484 Da / Num. of mol.: 3 / Fragment: UNP residues 18-344
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Lake Victoria marburgvirus (strain Ozolin-75)
Strain: Ozolin-75 / Gene: NP / Plasmid: pet21a / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6UY69

#2: Protein/peptide

Peptide from Polymerase cofactor VP35

Mass: 3120.512 Da / Num. of mol.: 3 / Source method: obtained synthetically
Source: (synth.)

Lake Victoria marburgvirus (strain Ozolin-75)
References: UniProt: Q6UY68

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.41 Å³/Da / Density % sol: 48.96 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2M sodium citrate tribasic monohydrate, pH 8.3, 20% (w/v) PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97922 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 2, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97922 Å / Relative weight: 1
Reflection	Resolution: 2.6→50 Å / Num. obs: 35200 / % possible obs: 100 % / Redundancy: 6.3 % / CC_1/2: 0.99 / R_merge(I) obs: 0.141 / R_pim(I) all: 0.061 / Net I/σ(I): 14.937
Reflection shell	Resolution: 2.6→2.69 Å / Redundancy: 6.3 % / R_merge(I) obs: 2.307 / Mean I/σ(I) obs: 1.209 / CC_1/2: 0.457 / R_pim(I) all: 0.993 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4YPI

4ypi

Resolution: 2.6→34.907 Å / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 33.86

	R_factor	Num. reflection	% reflection
R_free	0.2442	1547	5.1 %
R_work	0.214	-	-
obs	0.2156	30340	86.95 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.6→34.907 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7871	0	0	0	7871

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	8016
X-RAY DIFFRACTION	f_angle_d	0.99	10862
X-RAY DIFFRACTION	f_dihedral_angle_d	16.493	2901
X-RAY DIFFRACTION	f_chiral_restr	0.046	1276
X-RAY DIFFRACTION	f_plane_restr	0.005	1386

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 (%)
2.5817-2.665	0.292	39	0.2959	840	X-RAY DIFFRACTION	27
2.665-2.7602	0.312	80	0.2768	1376	X-RAY DIFFRACTION	44
2.7602-2.8706	0.2964	124	0.2673	2593	X-RAY DIFFRACTION	82
2.8706-3.0012	0.2911	137	0.2615	3022	X-RAY DIFFRACTION	96
3.0012-3.1593	0.2765	159	0.2438	3009	X-RAY DIFFRACTION	95
3.1593-3.357	0.2864	176	0.2381	2971	X-RAY DIFFRACTION	94
3.357-3.6158	0.2553	163	0.2121	3015	X-RAY DIFFRACTION	95
3.6158-3.9791	0.204	161	0.1958	2985	X-RAY DIFFRACTION	95
3.9791-4.5534	0.2216	151	0.1757	3014	X-RAY DIFFRACTION	95
4.5534-5.731	0.2467	160	0.2059	2981	X-RAY DIFFRACTION	95
5.731-31.3606	0.23	176	0.1993	2976	X-RAY DIFFRACTION	94

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	0.2209	0.0163	0.0828	0.3555	-0.0101	0.1218	-0.0053	-0.0464	0.0879	-0.1661	-0.1887	0.1324	-0.041	-0.0942	-0.1528	0.0818	0.0581	-0.0328	0.1555	-0.0179	0.22	62.4487	95.8359	21.3208
2	0.0147	-0.0283	-0.0106	0.1156	0.0434	0.0405	0.1328	0.0821	-0.1431	-0.1018	0.051	0.0305	0.3638	0.1197	0.1127	0.5197	0.1149	-0.0111	0.1779	-0.024	0.2704	59.4942	74.6187	-8.4337
3	0.0023	0.0013	0.0012	0.0012	0.001	0.0026	0.0103	0.0008	-0.0356	0.0185	-0.0359	-0.0278	-0.0218	0.0338	0	0.194	0.1273	0.0363	0.4072	-0.0134	0.298	68.8004	82.8447	-8.3728
4	0.0021	-0.0011	-0.0002	0.0024	-0.0011	0.0028	0.0096	-0.0163	0.013	-0.0262	-0.0175	-0.0078	-0.0049	0.0287	0	0.5548	0.0516	0.1167	0.55	0.0285	0.374	60.8545	86.8627	-15.7673
5	0.2315	0.1237	0.0695	0.0991	0.0983	0.1613	-0.1085	-0.0268	0.3002	0.1232	0.0113	0.1138	-0.1494	-0.0961	-0.115	0.2831	0.1751	-0.0135	0.2386	-0.0164	0.2757	83.3233	117.7898	24.0915
6	0.0822	-0.0195	-0.0575	0.0352	0.0352	0.055	-0.0481	-0.0801	-0.0033	-0.0535	-0.0233	0.0022	-0.0722	-0.0111	-0.1489	0.4285	0.06	-0.1085	0.2491	0.1013	0.3668	86.1216	120.2715	9.7577
7	0.188	0.0746	0.099	0.1116	0.0953	0.1561	-0.0076	-0.1042	-0.0881	0.0619	-0.0117	-0.1152	0.1527	0.049	0.0575	0.1847	0.0909	-0.0013	0.1644	0.0365	0.1123	93.1556	101.8957	25.0944
8	0.084	0.0171	0.0125	0.1819	-0.1466	0.1375	0.0358	-0.0342	-0.1052	0.0738	0.0861	-0.0558	0.3106	0.1842	0.1017	0.384	0.2096	-0.0792	0.2911	-0.0286	0.1906	108.3119	102.8189	51.7751
9	0.0061	0.004	-0.0007	0.0163	0.0183	0.0269	-0.0202	-0.0148	-0.0343	0.0218	-0.0329	-0.0176	0.0625	-0.0125	-0.0084	0.4798	0.1794	-0.0786	0.237	0.0137	0.4691	96.5504	98.8618	51.7637
10	0.0042	0.0009	-0.002	0.0033	-0.0017	0.0027	-0.0742	0.0146	0.0004	0.0273	0.0069	-0.0205	0.0512	-0.0594	0	0.4948	0.0285	0.0418	0.2762	-0.0366	0.4582	96.9391	107.6625	59.2982
11	0.0217	0.0263	0.0355	0.0372	0.034	0.0785	-0.1206	-0.0004	0.1605	0.0963	-0.0797	-0.1248	-0.2497	0.0689	-0.2058	0.3169	0.0441	-0.2436	0.1041	0.1411	0.3763	100.2714	75.8334	34.3104
12	0.047	0.0227	0.0156	0.1028	0.1191	0.1684	-0.1525	-0.0154	0.0092	0.0863	0.0113	0.1518	0.1267	-0.42	-0.0337	0.1998	-0.0039	0.0351	0.3141	-0.0302	0.2778	88.3392	59.4606	51.3642
13	0.018	-0.0166	0.0061	0.0153	-0.0109	0.0425	-0.0086	-0.0185	-0.0419	-0.0729	0.0504	0.0048	0.0834	-0.0639	0.0317	0.281	-0.1128	0.1653	0.2669	-0.1103	0.5178	82.8624	39.7672	68.2771
14	0.0086	-0.0054	0.0031	0.0086	-0.0074	0.0064	0.0192	0.0224	0.0149	-0.0083	0.0289	0.0558	0.0265	-0.0358	0.0006	0.6171	0.2154	0.0927	0.5209	-0.122	0.45	82.8899	60.2555	66.5783
15	0.0006	-0.0001	-0.0031	0.0312	-0.0015	0.0224	0.0018	-0.0252	0.0042	0.0017	-0.0323	-0.025	-0.0281	-0.0004	0.0088	0.413	0.0856	-0.265	0.3783	-0.0464	0.4911	91.6878	60.948	74.0205

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 205 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 206 through 320 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 5 through 16 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 17 through 27 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 5 through 76 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 77 through 111 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 112 through 205 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 206 through 320 )
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 5 through 16 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 17 through 27 )
11	X-RAY DIFFRACTION	11	chain 'E' and (resid 5 through 111 )
12	X-RAY DIFFRACTION	12	chain 'E' and (resid 112 through 279 )
13	X-RAY DIFFRACTION	13	chain 'E' and (resid 280 through 320 )
14	X-RAY DIFFRACTION	14	chain 'F' and (resid 5 through 16 )
15	X-RAY DIFFRACTION	15	chain 'F' and (resid 17 through 27 )

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