PDB-3un9: Crystal structure of an immune receptor

ID or keywords:

Entry

Database: PDB / ID: 3un9

Title

Crystal structure of an immune receptor

Components

NLR family member X1

Keywords

IMMUNE SYSTEM / Leucine rich repeat (LRR) / antiviral signaling / MAVS / TRAF6 / IKK / UQCRC2

Function / homology

Function and homology information

negative regulation of RIG-I signaling pathway / negative regulation of interferon-beta production / negative regulation of type I interferon production / negative regulation of interleukin-6 production / negative regulation of canonical NF-kappaB signal transduction / negative regulation of innate immune response / viral process / Negative regulators of DDX58/IFIH1 signaling / DDX58/IFIH1-mediated induction of interferon-alpha/beta / negative regulation of inflammatory response ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.65 Å

Authors

Hong, M. / Yoon, S.I. / Wilson, I.A.

Citation

Journal: Immunity / Year: 2012
Title: Structure and Functional Characterization of the RNA-Binding Element of the NLRX1 Innate Immune Modulator.
Authors: Hong, M. / Yoon, S.I. / Wilson, I.A.

History

Deposition	Nov 15, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 28, 2012	Provider: repository / Type: Initial release
Revision 1.1	Apr 18, 2012	Group: Database references
Revision 1.2	Feb 28, 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 / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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	3un9.cif.gz	348.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3un9.ent.gz	287.5 KB	Display	PDB format
PDBx/mmJSON format	3un9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3un9_validation.pdf.gz	459.7 KB	Display	wwPDB validaton report
Full document	3un9_full_validation.pdf.gz	476.2 KB	Display
Data in XML	3un9_validation.xml.gz	31.2 KB	Display
Data in CIF	3un9_validation.cif.gz	42.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/un/3un9 ftp://data.pdbj.org/pub/pdb/validation_reports/un/3un9	HTTPS FTP

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Related structure data

Similar structure data	6877 6z89-1 5jk0-d 10418 5uhp-d 10419 4y4l-2 6l8t-d 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#143 - Nov 2011 Toll-like Receptors similarity (2) #105 - Sep 2008 Ribonuclease A similarity (2) #248 - Aug 2020 Phytosulfokine Receptor similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #245 - May 2020 Spliceosomes similarity (1) #68 - Aug 2005 Neurotrophins similarity (1)

Deposited unit

A: NLR family member X1

B: NLR family member X1

C: NLR family member X1

hetero molecules

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

1

A: NLR family member X1

B: NLR family member X1

C: NLR family member X1

hetero molecules

A: NLR family member X1

B: NLR family member X1

C: NLR family member X1

hetero molecules

defined by author&software
245 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	99.011, 123.469, 145.848
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
1	2	A
2	2	B
3	2	C
1	3	A
2	3	B
3	3	C
1	4	A
2	4	B

NCS domain segments:

Component-ID: 1 / Refine code: 3

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	PRO	PRO	SER	SER	A	A	671 - 696	47 - 72
2	1	PRO	PRO	SER	SER	B	B	671 - 696	47 - 72
3	1	PRO	PRO	SER	SER	C	C	671 - 696	47 - 72
1	2	SER	SER	LEU	LEU	A	A	697 - 886	73 - 262
2	2	SER	SER	LEU	LEU	B	B	697 - 886	73 - 262
3	2	SER	SER	LEU	LEU	C	C	697 - 886	73 - 262
1	3	GLY	GLY	SER	SER	A	A	893 - 899	269 - 275
2	3	GLY	GLY	SER	SER	B	B	893 - 899	269 - 275
3	3	GLY	GLY	SER	SER	C	C	893 - 899	269 - 275
1	4	VAL	VAL	LEU	LEU	A	A	906 - 970	282 - 346
2	4	VAL	VAL	LEU	LEU	B	B	906 - 970	282 - 346

NCS ensembles :

ID
1
2
3
4

#1: Protein	NLR family member X1 / Caterpiller protein 11.3 / CLR11.3 / Nucleotide-binding oligomerization domain protein 26 / ...Caterpiller protein 11.3 / CLR11.3 / Nucleotide-binding oligomerization domain protein 26 / Nucleotide-binding oligomerization domain protein 5 / Nucleotide-binding oligomerization domain protein 9 Mass: 40615.336 Da / Num. of mol.: 3 / Fragment: RNA-binding element (UNP residues 629-975) Source method: isolated from a genetically manipulated source Details: pAcGP67 / Source: (gene. exp.) Homo sapiens (human) / Gene: NLRX1, NOD26, NOD5, NOD9 / Plasmid: Plasmid / Cell line (production host): Hi-5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q86UT6
#2: Chemical	ChemComp-PT / PLATINUM (II) ION Mass: 195.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Pt
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 8 / 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: 1.83 Å³/Da / Density % sol: 32.75 %
Crystal grow	Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 18% PEG 1000 and 200 mM Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 296.0K

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Data collection

Diffraction

Mean temperature: 273 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL9-2 / Wavelength: 1.0719, 1.0716, 0.8550

Detector

Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 14, 2010

Radiation

Monochromator: mirror / Protocol: Platinum / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.0719	1
2	1.0716	1
3	0.855	1

Reflection

Resolution: 2.65→77.24 Å / Num. obs: 25742 / % possible obs: 97.9 % / Observed criterion σ(F): 10.17 / Observed criterion σ(I): 2.7

Reflection shell

Resolution: 2.65→2.719 Å / Redundancy: 4.7 % / R_merge(I) obs: 0.282 / Mean I/σ(I) obs: 6.9 / Num. unique all: 25742 / % possible all: 97.85

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Processing

Software

Name	Version	Classification
Blu-Ice		data collection
SOLVE		phasing
REFMAC	5.5.0109	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MAD / Resolution: 2.65→77.24 Å / Cor.coef. F_o:F_c: 0.937 / Cor.coef. F_o:F_c free: 0.909 / Cross valid method: THROUGHOUT / ESU R Free: 0.378 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26711	1311	5.1 %	RANDOM
R_work	0.22348	-	-	-
obs	0.22566	24448	97.85 %	-
all	-	25742	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 77.892 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.22 Å²	-0 Å²	0 Å²
2-	-	0.53 Å²	-0 Å²
3-	-	-	-0.75 Å²

Refinement step

Cycle: LAST / Resolution: 2.65→77.24 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6648	0	4	8	6660

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.021	6733
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.568	1.979	9147
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.025	5	862
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.492	23.672	305
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.362	15	1134
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.847	15	64
X-RAY DIFFRACTION	r_chiral_restr	0.1	0.2	1102
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	5036
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.819	1.5	4308
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.419	2	6847
X-RAY DIFFRACTION	r_scbond_it	2.111	3	2425
X-RAY DIFFRACTION	r_scangle_it	3.705	4.5	2297
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	104	TIGHT POSITIONAL	0.05	0.05
1	2	B	104	TIGHT POSITIONAL	0.05	0.05
1	3	C	104	TIGHT POSITIONAL	0.05	0.05
1	1	A	116	LOOSE POSITIONAL	0.15	5
1	2	B	116	LOOSE POSITIONAL	0.15	5
1	3	C	116	LOOSE POSITIONAL	0.27	5
1	1	A	104	TIGHT THERMAL	0.14	0.5
1	2	B	104	TIGHT THERMAL	0.12	0.5
1	3	C	104	TIGHT THERMAL	0.14	0.5
1	1	A	116	LOOSE THERMAL	0.15	10
1	2	B	116	LOOSE THERMAL	0.15	10
1	3	C	116	LOOSE THERMAL	0.16	10
2	1	A	757	TIGHT POSITIONAL	0.06	0.05
2	2	B	757	TIGHT POSITIONAL	0.05	0.05
2	3	C	757	TIGHT POSITIONAL	0.06	0.05
2	1	A	636	LOOSE POSITIONAL	0.09	5
2	2	B	636	LOOSE POSITIONAL	0.08	5
2	3	C	636	LOOSE POSITIONAL	0.13	5
2	1	A	757	TIGHT THERMAL	0.15	0.5
2	2	B	757	TIGHT THERMAL	0.13	0.5
2	3	C	757	TIGHT THERMAL	0.14	0.5
2	1	A	636	LOOSE THERMAL	0.51	10
2	2	B	636	LOOSE THERMAL	0.98	10
2	3	C	636	LOOSE THERMAL	0.51	10
3	1	A	28	TIGHT POSITIONAL	0.08	0.05
3	2	B	28	TIGHT POSITIONAL	0.05	0.05
3	3	C	28	TIGHT POSITIONAL	0.06	0.05
3	1	A	16	LOOSE POSITIONAL	0.3	5
3	2	B	16	LOOSE POSITIONAL	0.2	5
3	3	C	16	LOOSE POSITIONAL	0.13	5
3	1	A	28	TIGHT THERMAL	0.13	0.5
3	2	B	28	TIGHT THERMAL	0.1	0.5
3	3	C	28	TIGHT THERMAL	0.1	0.5
3	1	A	16	LOOSE THERMAL	6.79	10
3	2	B	16	LOOSE THERMAL	3.37	10
3	3	C	16	LOOSE THERMAL	3.42	10
4	1	A	260	TIGHT POSITIONAL	0.2	0.05
4	1	A	269	LOOSE POSITIONAL	0.6	5
4	1	A	260	TIGHT THERMAL	2.99	0.5
4	1	A	269	LOOSE THERMAL	3.92	10

LS refinement shell

Resolution: 2.65→2.719 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.297	84	-
R_work	0.252	1539	-
obs	-	-	84.49 %

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	12.8156	-8.9892	-4.2357	11.6543	10.9105	16.41	0.1287	-0.0178	-1.1981	0.0275	0.0735	0.0977	0.6435	0.5124	-0.2021	0.2052	-0.0883	-0.0062	0.2609	0.1335	0.3217	81.631	25.4	39.13
2	7.9846	12.4217	-5.4451	23.4037	-6.0023	5.5049	-0.2064	-0.6452	-0.2766	-0.4734	0.0032	-0.4625	0.346	0.9909	0.2032	0.3088	-0.081	0.0497	0.3854	-0.0154	0.0738	80.979	24.734	28.172
3	9.3084	-3.2726	7.3727	3.8918	-7.0215	13.0304	-0.286	0.1059	-0.2161	0.102	-0.0177	-0.2207	-0.277	0.146	0.3037	0.0924	-0.1546	0.0444	0.2828	-0.0546	0.1068	81.058	34.644	33.351
4	8.8291	5.8639	1.3833	5.6942	1.6749	2.8446	-0.1892	0.6708	-0.3872	-0.2575	0.3773	-0.4945	0.0107	0.364	-0.188	0.131	-0.0539	0.0335	0.1513	-0.0411	0.0672	61.069	2.392	17.163
5	7.0279	-4.0625	2.9995	6.2952	-3.2707	3.2306	-0.5228	-0.1235	0.448	1.0782	0.4926	0.6787	-1.1642	-0.3907	0.0301	0.6404	0.0077	0.0871	0.2579	0.0293	0.2892	61.675	56.782	20.905
6	5.5808	0.4251	-2.2151	1.901	-0.5731	7.3836	-0.087	-0.3494	0.1661	0.1264	-0.0201	-0.083	0.1024	-0.0818	0.1072	0.1347	-0.044	-0.0528	0.129	0.0261	0.0379	65.289	25.491	66.541
7	4.4395	-1.1156	-0.4868	10.9885	-0.4185	7.7305	0.1457	0.4437	0.5849	-0.4805	0.1045	0.4836	-0.2062	0.1372	-0.2502	0.1637	0.0328	0.0416	0.2932	0.0869	0.1681	58.907	1.476	37.893
8	7.7184	-1.6443	-1.0823	13.277	-2.8703	11.1512	0.7247	0.2823	0.2713	-0.2067	-0.3192	-0.1045	-0.0554	-0.6348	-0.4054	0.0853	-0.0355	-0.007	0.2869	0.0947	0.3684	56.575	39.06	11.253
9	6.2295	2.735	1.7027	10.4865	0.9849	0.4905	0.1502	0.5451	0.0504	-0.0765	-0.1047	-0.3849	0.0054	0.2807	-0.0455	0.6831	0.0808	0.0909	1.257	-0.1906	1.2743	61.963	46.591	61.092
10	41.5679	3.1814	-29.444	12.3503	-16.3841	37.462	0.8475	4.1792	-0.5962	-0.5598	-1.2647	0.1648	0.395	-0.8088	0.4172	1.3599	0.5272	-0.0429	1.9897	0.2909	1.7676	54.982	35.075	58.956

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	669 - 696
2	X-RAY DIFFRACTION	2	B	669 - 696
3	X-RAY DIFFRACTION	3	C	669 - 696
4	X-RAY DIFFRACTION	4	A	697 - 901
5	X-RAY DIFFRACTION	5	B	697 - 901
6	X-RAY DIFFRACTION	6	C	697 - 901
7	X-RAY DIFFRACTION	7	A	906 - 970
8	X-RAY DIFFRACTION	8	B	906 - 970
9	X-RAY DIFFRACTION	9	C	929 - 969
10	X-RAY DIFFRACTION	10	C	906 - 918

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