PDB-4h5m: Crystal Structure of Rift Valley Fever Virus Nucleocapsid Protein...

ID or keywords:

Entry

Database: PDB / ID: 4h5m

Title

Crystal Structure of Rift Valley Fever Virus Nucleocapsid Protein Hexamer

Components

Nucleocapsid protein

Keywords

VIRAL PROTEIN / nucleocapsid protein / N protein / ribonucleoprotein / viral nucleoprotein / RNA binding / virus / RNP

Function / homology

Function and homology information

host cell endoplasmic reticulum-Golgi intermediate compartment / viral nucleocapsid / host cell Golgi apparatus / ribonucleoprotein complex / host cell nucleus / RNA binding / identical protein binding
Similarity search - Function

Biological species

Rift Valley fever virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.1 Å

Authors

Raymond, D.D. / Smith, J.L.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Phleboviruses encapsidate their genomes by sequestering RNA bases.
Authors: Raymond, D.D. / Piper, M.E. / Gerrard, S.R. / Skiniotis, G. / Smith, J.L.

History

Deposition	Sep 18, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 7, 2012	Provider: repository / Type: Initial release
Revision 1.1	Nov 21, 2012	Group: Database references
Revision 1.2	Dec 5, 2012	Group: Database references
Revision 1.3	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4h5m.cif.gz	579.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4h5m.ent.gz	488 KB	Display	PDB format
PDBx/mmJSON format	4h5m.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/h5/4h5m ftp://data.pdbj.org/pub/pdb/validation_reports/h5/4h5m	HTTPS FTP

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Related structure data

Related structure data	4h5lC 4h5oC 4h5pC 4h5qC 4v9eC 3lyfS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4h5q-1 4v9e-5 4v9e-2 4v9e-6 4csg-2 5fva-4 4v9e-3 4v9e-4 4j4r-1 5fva-2 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

Deposited unit

A: Nucleocapsid protein

B: Nucleocapsid protein

C: Nucleocapsid protein

D: Nucleocapsid protein

E: Nucleocapsid protein

F: Nucleocapsid protein

hetero molecules

164 kDa, 6 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)	107.130, 107.130, 258.450
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	Nucleocapsid protein Mass: 27366.547 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rift Valley fever virus / Strain: ZH-501 / Gene: N / Plasmid: pSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Ai/prare2 / References: UniProt: D3K5I7
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.61 Å³/Da / Density % sol: 52.83 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 24% PEG3350, 350 mM ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-D / Wavelength: 1.0332 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 11, 2011
Details: K-B pair of biomorph mirrors for vertical and horizontal focusing

Radiation

Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.0332 Å / Relative weight: 1

Reflection

Resolution: 3.1→92.777 Å / Num. all: 32046 / Num. obs: 31959 / % possible obs: 91.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 6.2 % / B_iso Wilson estimate: 83.9 Å² / R_sym value: 0.098 / Net I/σ(I): 13.1

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
3.1-3.27	5	0.693	1.1	20670	4114	0.693	89.7
3.27-3.47	6.4	0.517	1.5	25651	3994	0.517	91
3.47-3.71	6.4	0.306	2.5	23904	3718	0.306	90.6
3.71-4	6.4	0.189	4.1	22247	3450	0.189	90.4
4-4.38	6.4	0.121	6.3	20408	3193	0.121	89.9
4.38-4.9	6.3	0.092	8.1	18482	2915	0.092	89.8
4.9-5.66	6.2	0.087	8.4	16664	2685	0.087	93.4
5.66-6.93	6.1	0.078	8.3	14589	2377	0.078	97.4
6.93-9.8	6.5	0.033	18.7	12490	1930	0.033	99.6
9.8-46.389	6.3	0.025	20.7	7175	1136	0.025	98.9

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Processing

Software

Name	Version	Classification
MOSFLM		data reduction
SCALA	3.3.16	data scaling
BUSTER-TNT	BUSTER 2.8.0	refinement
PDB_EXTRACT	3.11	data extraction
Blu-Ice	Epics	data collection
PHASER		phasing
BUSTER	2.1	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LYF

3lyf

Resolution: 3.1→46.39 Å / Cor.coef. F_o:F_c: 0.9092 / Cor.coef. F_o:F_c free: 0.8577 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2558	1617	5.06 %	RANDOM
R_work	0.2155	-	-	-
obs	0.2175	31959	-	-
all	-	32046	-	-

Displacement parameters

B_iso max: 300 Å² / B_iso mean: 122.4484 Å² / B_iso min: 3.41 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.1508 Å²	0 Å²	0 Å²
2-	-	4.1508 Å²	0 Å²
3-	-	-	-8.3015 Å²

Refine analyze

Luzzati coordinate error obs: 0.737 Å

Refinement step

Cycle: LAST / Resolution: 3.1→46.39 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11404	0	5	0	11409

Refine LS restraints

Refine-ID	Type	Number	Restraint function	Weight	Dev ideal
X-RAY DIFFRACTION	t_dihedral_angle_d	5515	SINUSOIDAL	2
X-RAY DIFFRACTION	t_trig_c_planes	281	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes	1696	HARMONIC	5
X-RAY DIFFRACTION	t_it	11629	HARMONIC	20
X-RAY DIFFRACTION	t_nbd
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_chiral_improper_torsion	1487	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact	13825	SEMIHARMONIC	4
X-RAY DIFFRACTION	t_bond_d	11629	HARMONIC	2	0.009
X-RAY DIFFRACTION	t_angle_deg	15694	HARMONIC	2	1.02
X-RAY DIFFRACTION	t_omega_torsion				2.22
X-RAY DIFFRACTION	t_other_torsion				3.14

LS refinement shell

Resolution: 3.1→3.2 Å / Total num. of bins used: 16

	R_factor	Num. reflection	% reflection
R_free	0.2872	143	4.98 %
R_work	0.2561	2728	-
all	0.2576	2871	-

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	1.079	-2.7207	3.0152	7.547	-4.9628	2.4158	0.1629	0.5668	0.3854	-0.0909	-0.4578	-0.8148	-0.2523	0.0527	0.2949	-0.3291	0.0469	0.0873	-0.4626	-0.0266	-0.3083	67.5173	25.1234	-25.544
2	0.171	0.2699	-0.4448	0.2547	0.0082	0	-0.1647	-0.0641	-0.0092	0.1572	-0.126	-0.2483	0.1718	-0.2252	0.2907	-0.1319	0.0886	-0.0381	-0.273	0.0553	-0.3243	45.123	38.873	-22.8233
3	1.5803	-1.0667	-0.0342	-1.0456	-0.2368	0	0.0137	0.0701	0.1243	0.1051	0.2043	-0.1883	0.175	0.0616	-0.218	0.4559	0.041	-0.1438	0.114	0.1454	-0.0365	51.9039	31.2415	-11.8804
4	2.2733	-1.0293	-0.1109	-1.9463	1.6148	1.202	-0.0853	-0.2906	-0.234	-0.643	0.3387	0.7919	0.2448	0.3839	-0.2535	-0.2232	-0.1256	0.0382	-0.3507	0.0997	-0.2716	57.827	-23.9673	-24.7014
5	0.3297	-0.1754	-0.9003	1.2435	0.1281	1.5667	0.1587	-0.0315	0.1842	-0.2104	-0.0627	-0.3057	0.013	-0.1113	-0.0961	-0.1935	0.0347	0.0131	-0.4511	0.035	-0.3887	65.7744	10.4712	-24.8982
6	-3.3497	1.7656	0.0014	3.933	2.6554	0.6028	-0.1339	0.1089	-0.6138	0.1936	0.2917	0.1516	-0.4831	-0.2163	-0.1578	0.1974	-0.0968	0.0425	0.1664	-0.1097	0.1852	56.4229	1.2343	-11.0118
7	1.1769	-1.3618	0.3208	1.1867	1.8054	1.8857	0.1927	0.1218	0.1386	0.1525	-0.0928	-0.1066	0.435	-0.4003	-0.0999	0.5154	-0.1019	-0.0329	0.2946	0.0189	0.1544	60.3368	-1.2279	-11.8721
8	1.7121	-3.4855	1.2118	12.5383	2.7835	12.2922	0.198	0.057	0.3825	-0.0912	-0.4421	-0.8475	-0.3535	-0.1117	0.2441	0.6847	-0.1672	-0.2457	0.1765	-0.0502	0.1796	57.8586	50.1415	-22.5209
9	2.7145	-1.8787	-1.5892	-1.6355	-7.5897	0	-0.6183	0.1208	0.0558	0.5529	0.958	0.0112	-0.4868	-0.2789	-0.3397	-0.1307	0.1496	0.0716	-0.2614	0.0006	-0.1731	33.8646	49.443	-25.803
10	0.9281	2.0656	2.2211	2.0758	0.7437	0.7095	-0.0623	-0.1205	-0.0949	-0.1392	-0.0128	0.0385	0.0178	-0.022	0.0752	-0.2214	-0.0519	0.1346	-0.3167	0.0915	-0.2584	8.3805	40.8958	-36.1947
11	15.541	3.3376	-5.1101	-1.3264	-2.7907	0	-0.1386	-0.2695	0.8494	0.3109	-0.2326	0.7007	0.1445	-0.748	0.3712	0.2752	-0.1416	0.2434	-0.2001	0.0161	-0.2772	6.4276	41.2195	-19.5146
12	-0.8105	0.4679	0.2594	0.8105	-2.0476	0	-0.1631	-0.2415	0.3574	0.0763	-0.1321	0.3161	0.4069	0.2337	0.2953	0.0218	0.0899	0.1826	-0.3836	0.0877	-0.6079	17.0801	37.6097	-14.1486
13	1.0826	-0.2263	-1.318	-0.6221	-4.8406	1.9687	0.2819	0.2143	-0.263	-0.0816	-0.6654	0.2917	0.2217	0.3291	0.3835	0.5545	0.0296	-0.0081	0.3787	-0.0741	0.2875	21.9678	42.635	-16.9359
14	-1.2463	-1.4191	-0.9485	8.7716	2.6194	7.9741	0.347	-0.5506	0.088	0.1806	-0.6099	-0.0803	-0.4341	0.1477	0.2629	0.8676	-0.1458	0.136	0.334	0.1741	-0.4843	21.6854	34.7005	-5.6104
15	7.3181	-1.4278	6.9352	-4.0881	-2.6706	0	-0.0297	0.3927	-0.0083	-0.1877	-0.3217	1.1587	0.673	-0.4396	0.3513	0.6283	-0.1635	0.1935	0.1283	0.0392	0.03	1.681	-31.7564	-22.8076
16	4.9482	0.8239	-4.6839	0.4068	-2.5049	0	-0.1727	-0.3751	-0.7343	-0.3328	-0.0531	-0.0933	-0.1016	-0.1355	0.2258	-0.3496	-0.0356	-0.0776	-0.2348	-0.1424	-0.3626	41.2833	-29.1882	-29.5068
17	-1.6939	0.9838	-1.8808	1.7006	2.1389	0	-0.0958	-0.0262	-0.1262	-0.4123	0.0502	-0.1367	-0.275	-0.0401	0.0456	-0.185	0.0053	0.0239	-0.4113	-0.0085	-0.5982	51.4667	-16.6164	-36.5605
18	0.2509	0.5072	-0.199	0.5021	-0.3553	2.188	-0.0569	-0.2407	-0.3408	-0.3591	-0.188	-0.0817	-0.2644	0.2209	0.2448	-0.1299	-0.1177	-0.0218	0.1124	-0.0188	-0.1457	44.1663	-21.2175	-14.4304
19	8.8709	-1.5142	1.9163	-2.6497	7.8277	0.8207	-0.127	0.6336	0.9896	-0.4634	0.1164	0.0571	-1.2257	0.2166	0.0106	0.2763	-0.0719	-0.1093	0.1829	0.1718	0.1491	32.6891	-7.9908	-17.2052
20	1.7309	0.6566	-1.0212	0.1812	0.1168	0	0.0942	-0.6689	-0.1866	-0.283	-0.1339	0.0992	-0.2801	-0.0283	0.0397	0.2539	-0.0747	-0.0356	0.5879	0.0513	0.1648	38.9997	-29.1008	-11.5533
21	7.6251	-7.479	1.9806	3.0327	2.8824	2.755	0.3659	-0.7322	-0.7435	1.0496	-0.0457	0.1955	0.5642	-0.048	-0.3202	0.4438	-0.2875	0.3142	0.2297	0.0637	0.6046	-10.6126	-2.3078	-23.191
22	0.3032	-0.2642	-0.3857	0.0057	1.5502	1.5867	-0.005	0.1166	0.2616	0.245	-0.0413	-0.1831	0.0683	0.0239	0.0464	-0.0216	0.0339	-0.1925	-0.3346	-0.033	-0.0392	11.362	-18.7763	-20.7242
23	1.3732	-0.7944	-0.5666	-1.3678	-4.3141	1.5293	0.0955	-0.1334	0.1617	-0.3579	0.0554	-0.0398	0.0865	-0.4069	-0.1509	0.5466	-0.1356	0.1976	0.2081	0.1629	0.2552	0.0558	40.2442	-25.6158
24	-2.2589	1.3042	2.1767	2.2589	1.2263	0.2012	0.4725	0.2546	0.224	-0.1044	-0.3485	-0.3748	-0.2459	0.231	-0.124	-0.4945	-0.0744	0.2825	-0.6906	0.1186	0.0593	-8.5026	5.9766	-34.216
25	3.619	-2.9314	7.4211	-0.7026	-1.2978	0	0.1373	-0.4525	-0.2226	0.4788	-0.2794	0.106	0.2675	-0.1404	0.1421	-0.2733	-0.2663	0.3748	-0.6209	-0.1346	0.3645	-6.992	7.9382	-21.1248
26	-0.6756	0.5397	3.7823	0.8484	-3.1232	0	-0.0378	0.1545	-0.1266	-0.033	-0.0922	-0.0452	-0.0397	0.1304	0.13	-0.3888	-0.1762	0.2108	-0.5175	0.2429	0.0274	4.2703	2.3002	-13.394
27	-3.2027	1.9745	3.353	3.3475	5.1823	0	0.1402	-0.3816	-0.3226	0.5773	-0.0136	-0.1549	0.8527	0.1394	-0.1266	-0.263	-0.2745	0.2344	-0.648	-0.2156	-0.3471	-2.529	15.2675	-12.5215
28	10.5649	4.3156	-2.677	12.1581	-1.533	16.5147	-0.0452	0.1392	0.4671	0.3855	0.3217	-0.4372	-0.6378	0.8882	-0.2765	0.4962	-0.3685	-0.4152	0.2197	0.1113	0.6079	5.2228	16.2494	-13.5028
29	5.2776	6.2384	6.0188	5.4443	0.1528	5.6652	0.0161	0.5222	-0.1874	-0.4016	-0.1448	-0.3541	0.236	0.7286	0.1287	0.3343	0.146	0.1925	0.8677	0.1771	0.2771	17.0103	13.8773	-21.9993
30	-0.4038	0.2331	-4.5546	0.4038	3.547	0.5059	0.2892	-0.2337	0.1476	0.0073	-0.1158	0.4461	-0.3977	-0.1663	-0.1735	-0.1491	-0.4908	0.1399	-0.2844	0.1815	-0.2697	-6.0263	21.9789	-17.2197
31	11.1999	2.9703	3.2313	1.4558	-1.0264	0	0.1506	-0.5	0.1933	0.5051	-0.1686	0.1403	-0.4551	-0.2721	0.0179	0.8625	-0.157	-0.2341	0.3418	0.1728	0.3684	1.8086	17.5435	-4.3534

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	{A\|5 - 46}	A	5 - 46
2	X-RAY DIFFRACTION	2	{A\|47 - 180}	A	47 - 180
3	X-RAY DIFFRACTION	3	{A\|181 - 245}	A	181 - 245
4	X-RAY DIFFRACTION	4	{B\|4 - 34}	B	4 - 34
5	X-RAY DIFFRACTION	5	{B\|35 - 158}	B	35 - 158
6	X-RAY DIFFRACTION	6	{B\|159 - 180}	B	159 - 180
7	X-RAY DIFFRACTION	7	{B\|181 - 245}	B	181 - 245
8	X-RAY DIFFRACTION	8	{C\|4 - 17}	C	4 - 17
9	X-RAY DIFFRACTION	9	{C\|18 - 34}	C	18 - 34
10	X-RAY DIFFRACTION	10	{C\|35 - 111}	C	35 - 111
11	X-RAY DIFFRACTION	11	{C\|112 - 124}	C	112 - 124
12	X-RAY DIFFRACTION	12	{C\|125 - 180}	C	125 - 180
13	X-RAY DIFFRACTION	13	{C\|181 - 231}	C	181 - 231
14	X-RAY DIFFRACTION	14	{C\|232 - 245}	C	232 - 245
15	X-RAY DIFFRACTION	15	{D\|4 - 17}	D	4 - 17
16	X-RAY DIFFRACTION	16	{D\|18 - 64}	D	18 - 64
17	X-RAY DIFFRACTION	17	{D\|65 - 103}	D	65 - 103
18	X-RAY DIFFRACTION	18	{D\|104 - 180}	D	104 - 180
19	X-RAY DIFFRACTION	19	{D\|181 - 196}	D	181 - 196
20	X-RAY DIFFRACTION	20	{D\|197 - 245}	D	197 - 245
21	X-RAY DIFFRACTION	21	{E\|7 - 36}	E	7 - 36
22	X-RAY DIFFRACTION	22	{E\|37 - 245}	E	37 - 245
23	X-RAY DIFFRACTION	23	{F\|7 - 34}	F	7 - 34
24	X-RAY DIFFRACTION	24	{F\|35 - 103}	F	35 - 103
25	X-RAY DIFFRACTION	25	{F\|104 - 124}	F	104 - 124
26	X-RAY DIFFRACTION	26	{F\|125 - 136}	F	125 - 136
27	X-RAY DIFFRACTION	27	{F\|137 - 158}	F	137 - 158
28	X-RAY DIFFRACTION	28	{F\|159 - 180}	F	159 - 180
29	X-RAY DIFFRACTION	29	{F\|181 - 193}	F	181 - 193
30	X-RAY DIFFRACTION	30	{F\|194 - 221}	F	194 - 221
31	X-RAY DIFFRACTION	31	{F\|222 - 245}	F	222 - 245

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