PDB-5or7: Atomic structure of the murine norovirus protruding domain and sC...

ID or keywords:

Entry

Database: PDB / ID: 5or7

Title

Atomic structure of the murine norovirus protruding domain and sCD300lf receptor complex

Components

CMRF35-like molecule 1
Capsid protein

Keywords

VIRAL PROTEIN / CR10 / sCD300lf / complex

Function / homology

Function and homology information

negative regulation of MyD88-dependent toll-like receptor signaling pathway / interleukin-13-mediated signaling pathway / negative regulation of apoptotic cell clearance / interleukin-4 receptor binding / positive regulation of interleukin-4-mediated signaling pathway / negative regulation of mast cell activation / ceramide binding / positive regulation of apoptotic cell clearance / TRIF-dependent toll-like receptor signaling pathway / phosphatidylserine binding ...
Similarity search - Function

Biological species

Murine norovirus GV/CR10/2005/USA

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.046 Å

Authors

Kilic, T. / Hansman, G.S.

Citation

Journal: J. Virol. / Year: 2018
Title: Atomic Structure of the Murine Norovirus Protruding Domain and Soluble CD300lf Receptor Complex.
Authors: Kilic, T. / Koromyslova, A. / Malak, V. / Hansman, G.S.

History

Deposition	Aug 15, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 21, 2018	Provider: repository / Type: Initial release
Revision 1.1	Apr 4, 2018	Group: Data collection / Database references / Category: citation Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	May 23, 2018	Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3	Jan 17, 2024	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 / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Revision 1.4	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5or7.cif.gz	301.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5or7.ent.gz	237.3 KB	Display	PDB format
PDBx/mmJSON format	5or7.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/or/5or7 ftp://data.pdbj.org/pub/pdb/validation_reports/or/5or7	HTTPS FTP

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Related structure data

Related structure data	3lq6S 5fflS S: Starting model for refinement
Similar structure data	2e7j-d 5wt4-1 2e7i-1 3pbp-4 2e7i-2 1f06-d 3tkn-3 5loa-d 5z83-d 3dap-d 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	#156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (4)

Deposited unit

A: Capsid protein

B: Capsid protein

C: CMRF35-like molecule 1

hetero molecules

154 kDa, 3 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)	75.110, 77.460, 140.950
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Capsid protein Mass: 58821.707 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Murine norovirus GV/CR10/2005/USA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A7YK37
#2: Protein	CMRF35-like molecule 1 / CLM-1 / CD300 antigen-like family member F / Leukocyte mono-Ig-like receptor 3 / Myeloid-associated ...CLM-1 / CD300 antigen-like family member F / Leukocyte mono-Ig-like receptor 3 / Myeloid-associated immunoglobulin-like receptor 5 / MAIR-V Mass: 36024.770 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd300lf, Clm1, Lmir3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6SJQ7
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 459 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 25% (w/v) PEG3000, 0.1 M sodium acetate (pH 4.6)

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07252 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 8, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.07252 Å / Relative weight: 1
Reflection	Resolution: 2.046→46.98 Å / Num. obs: 52389 / % possible obs: 99.5 % / Redundancy: 5.5 % / R_merge(I) obs: 0.1085 / Net I/σ(I): 11.45
Reflection shell	Resolution: 2.046→2.12 Å / Redundancy: 5.1 % / R_merge(I) obs: 0.7051 / Mean I/σ(I) obs: 2.31 / Num. unique all: 5044 / % possible all: 97.5

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
XDS	VERSION Nov 1, 2016	data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3LQ6, 5FFL

3lq6

5ffl

Resolution: 2.046→42.825 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.55

	R_factor	Num. reflection	% reflection
R_free	0.2168	2619	5 %
R_work	0.1804	-	-
obs	0.1822	52383	99.52 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.046→42.825 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5367	0	6	459	5832

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	5513
X-RAY DIFFRACTION	f_angle_d	0.6	7542
X-RAY DIFFRACTION	f_dihedral_angle_d	12.84	3245
X-RAY DIFFRACTION	f_chiral_restr	0.043	850
X-RAY DIFFRACTION	f_plane_restr	0.004	981

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 (%)
2.0464-2.0836	0.2919	130	0.2384	2473	X-RAY DIFFRACTION	95
2.0836-2.1237	0.2458	136	0.2204	2583	X-RAY DIFFRACTION	100
2.1237-2.167	0.2262	138	0.2059	2607	X-RAY DIFFRACTION	100
2.167-2.2141	0.243	137	0.2021	2619	X-RAY DIFFRACTION	100
2.2141-2.2656	0.2575	136	0.1927	2573	X-RAY DIFFRACTION	100
2.2656-2.3223	0.2189	136	0.2005	2594	X-RAY DIFFRACTION	100
2.3223-2.3851	0.2343	137	0.1934	2595	X-RAY DIFFRACTION	100
2.3851-2.4553	0.2631	137	0.2046	2609	X-RAY DIFFRACTION	100
2.4553-2.5345	0.2281	137	0.1985	2594	X-RAY DIFFRACTION	100
2.5345-2.6251	0.2679	137	0.1972	2600	X-RAY DIFFRACTION	100
2.6251-2.7301	0.2086	138	0.1949	2624	X-RAY DIFFRACTION	100
2.7301-2.8544	0.2362	138	0.1918	2627	X-RAY DIFFRACTION	100
2.8544-3.0048	0.2454	139	0.1973	2638	X-RAY DIFFRACTION	100
3.0048-3.193	0.2524	137	0.1905	2605	X-RAY DIFFRACTION	100
3.193-3.4395	0.2104	139	0.1837	2649	X-RAY DIFFRACTION	100
3.4395-3.7854	0.1834	139	0.1666	2636	X-RAY DIFFRACTION	100
3.7854-4.3327	0.1763	140	0.1427	2662	X-RAY DIFFRACTION	100
4.3327-5.457	0.1591	141	0.1438	2682	X-RAY DIFFRACTION	99
5.457-42.8343	0.245	147	0.1819	2794	X-RAY DIFFRACTION	99

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	2.8069	0.1563	-0.3745	3.7983	-0.2828	1.8197	0.0125	-0.2508	0.1434	0.2319	-0.039	0.0283	-0.1845	-0.0521	0.0359	0.2294	0.0034	0.0247	0.2337	-0.038	0.1882	6.9021	157.9134	37.6198
2	1.3053	-0.0918	-0.6314	0.6642	0.4695	1.5508	-0.0285	-0.125	-0.0581	0.0821	-0.0056	0.0224	0.1493	0.0806	0.0361	0.2306	0.0016	-0.0071	0.1678	0.009	0.2066	20.834	145.0834	28.4162
3	2.2656	2.7985	-0.8163	3.6794	-0.2905	2.4539	-0.0745	0.2315	0.0274	-0.1974	0.0339	-0.1377	-0.0776	0.1373	0.0518	0.2359	-0.0105	-0.0005	0.2096	-0.0011	0.1987	24.3009	151.4296	15.9769
4	1.7523	0.4845	-1.2132	0.4637	-0.1417	4.8027	0.0264	0.1207	-0.1838	-0.1771	-0.0811	0.0922	0.5392	-0.0221	0.0466	0.2364	0.0059	-0.0156	0.1915	-0.0326	0.262	16.5161	138.6712	20.2463
5	1.93	-0.2116	-1.209	0.9494	-0.0193	1.9398	-0.0153	0.0863	0.018	-0.0898	-0.0042	0.0535	0.1135	-0.1549	0.0268	0.2096	-0.0064	-0.039	0.1826	-0.0165	0.2174	16.5366	145.5562	21.6097
6	1.7449	0.3382	-0.5072	1.714	-0.4635	2.4348	0.1636	-0.2296	0.2163	0.2829	-0.0438	0.1964	-0.3595	-0.2821	-0.051	0.2623	0.013	0.0504	0.237	-0.0705	0.2662	2.0509	158.9247	43.1664
7	1.5803	-0.1392	0.5649	1.2519	0.0939	1.7036	-0.0036	0.0125	0.0352	0.003	-0.02	0.0332	0.0384	0.0362	-0.0002	0.1926	-0.0196	-0.0058	0.1668	-0.0121	0.1888	31.9604	163.214	39.3085
8	2.107	-0.4565	0.9774	1.4834	0.0459	3.5612	0.0079	0.0958	0.2134	-0.1275	-0.1441	0.1632	-0.1496	-0.1991	0.1074	0.2043	0.0217	-0.0148	0.1908	-0.0019	0.2611	19.8492	172.678	30.0063
9	2.9895	-0.3821	1.0387	3.3765	1.3573	3.1518	-0.1484	0.2949	0.3813	-0.2589	0.0558	0.048	-0.1955	0.0982	0.037	0.2212	0.0357	-0.0319	0.2453	0.0408	0.3147	16.0201	177.7005	21.9137
10	2.6544	-0.2694	1.1721	2.9563	1.5741	3.2332	-0.0715	0.3452	0.0376	-0.3833	0.0436	0.0953	-0.2148	0.0252	0.0259	0.2768	-0.0226	-0.0379	0.2669	0.0328	0.256	20.9279	171.9377	18.3952
11	2.5454	0.0715	1.2183	3.4545	1.1492	1.7568	-0.1182	0.2299	0.2545	-0.0465	0.0094	-0.1487	-0.1868	-0.014	0.0416	0.2087	-0.0309	0.0031	0.1825	0.0061	0.2111	32.0277	179.6784	28.126
12	1.6299	0.2565	0.2352	1.2454	0.5457	2.2167	-0.051	0.1736	-0.0111	-0.1397	0.0444	0.029	0.013	0.0041	0.0298	0.1941	-0.0023	-0.026	0.1609	-0.0039	0.1842	33.7448	164.2322	36.4988
13	2.3634	-0.022	-0.579	1.9193	0.4648	2.7555	-0.1044	-0.1615	-0.1188	0.1974	0.1096	-0.0342	0.2304	0.0258	0.0272	0.1722	-0.0179	-0.0117	0.1854	0.011	0.1686	35.1538	161.0307	52.8621
14	1.2913	-0.1688	-0.1555	3.108	2.0525	4.0702	0.0954	-0.0202	-0.0586	-0.0169	0.0247	-0.0892	-0.0139	0.1575	-0.1187	0.1856	0.003	-0.0218	0.1572	0.0218	0.1946	40.2712	163.1322	48.7873
15	5.3589	-1.5959	1.5855	1.0206	-0.7514	1.0624	-0.03	0.0846	0.044	0.1511	0.0063	-0.0669	0.0302	0.0215	-0.0125	0.2391	-0.0128	-0.0295	0.2521	-0.0292	0.2055	7.44	136.1729	-4.1043
16	1.7387	-1.9432	-0.7623	6.8683	3.0077	4.1694	-0.0103	-0.1521	0.0801	0.3766	0.0365	-0.1524	0.0698	0.1131	-0.0268	0.1637	-0.023	-0.035	0.2084	-0.0378	0.1996	9.0069	135.1417	7.5885
17	6.0637	-1.5364	-0.823	2.0932	0.2981	1.581	-0.1096	0.0011	-0.4869	0.2109	0.0533	0.107	0.2966	-0.0527	0.0515	0.2546	-0.0295	-0.0427	0.2213	-0.0189	0.2642	3.9174	127.6229	1.6286
18	3.4556	-1.0575	0.489	1.5745	-0.0283	2.3003	0.0203	0.0577	-0.046	0.094	0.0139	0.0812	0.0114	-0.0101	-0.0276	0.2151	-0.0022	0.0146	0.1793	-0.0236	0.1761	2.5525	140.2447	1.6193

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 228 through 269 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 270 through 332 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 333 through 360 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 361 through 378 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 379 through 419 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 420 through 530 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 228 through 268 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 269 through 298 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 299 through 320 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 321 through 399 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 400 through 419 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 420 through 464 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 465 through 492 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 493 through 530 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 1 through 28 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 29 through 44 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 45 through 77 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 78 through 111 )

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