PDB-3ie4: b-glucan binding domain of Drosophila GNBP3 defines a novel famil...

ID or keywords:

Entry

Database: PDB / ID: 3ie4

Title

b-glucan binding domain of Drosophila GNBP3 defines a novel family of pattern recognition receptor

Components

Gram-Negative Binding Protein 3

Keywords

IMMUNE SYSTEM / immunoglobulin fold

Function / homology

Function and homology information

positive regulation of melanization defense response / detection of molecule of fungal origin / (1->3)-beta-D-glucan binding / positive regulation of Toll signaling pathway / innate immune response-activating signaling pathway / antifungal humoral response /

pattern recognition receptor activity /

regulation of innate immune response / pattern recognition receptor signaling pathway / hydrolase activity, hydrolyzing O-glycosyl compounds ...
Similarity search - Function

Biological species

Drosophila melanogaster (fruit fly)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.45 Å

Authors

Mishima, Y. / Coste, F. / Kellenberger, C. / Roussel, A.

Citation

Journal: To be Published
Title: The N-terminal domain of drosophila gram-negative binding protein 3 (GNBP3) defines a novel family of fungal pattern recognition receptors
Authors: Mishima, Y. / Quintin, J. / Aimanianda, V. / Kellenberger, C. / Coste, F. / Clavaud, C. / Hetru, C. / Hoffmann, J.A. / Latge, J.P. / Ferrandon, D. / Roussel, A.

History

Deposition	Jul 22, 2009	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Aug 18, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Mar 20, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site 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_label_seq_id / _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	3ie4.cif.gz	61.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3ie4.ent.gz	46.4 KB	Display	PDB format
PDBx/mmJSON format	3ie4.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/ie/3ie4 ftp://data.pdbj.org/pub/pdb/validation_reports/ie/3ie4	HTTPS FTP

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Related structure data

Similar structure data	1hkf-d 1noa-d 2oj1-1 3fqy-d 3jtb-1 5mgl-d 5mgm-d 4hmm-1 5yt7-3 3fq1-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) 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	#124 - Apr 2010 Concanavalin A and Circular Permutation similarity (3)

Deposited unit

A: Gram-Negative Binding Protein 3

B: Gram-Negative Binding Protein 3

hetero molecules

24.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Gram-Negative Binding Protein 3

hetero molecules

defined by author&software
12.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Gram-Negative Binding Protein 3

hetero molecules

defined by author&software
12.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	135.530, 30.680, 51.650
Angle α, β, γ (deg.)	90.00, 107.57, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Gram-Negative Binding Protein 3 Mass: 12189.536 Da / Num. of mol.: 2 / Fragment: N-terminal domain (UNP residues 26-132) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Genus: GNBP3, CG5008 / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q9NHA8
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.1 Å³/Da / Density % sol: 41.42 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.2M zinc acetate dehydrate, 18% PEG 8000, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0332 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 25, 2008
Radiation	Monochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0332 Å / Relative weight: 1
Reflection	Resolution: 1.45→46.52 Å / Num. all: 36216 / Num. obs: 36216 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / B_iso Wilson estimate: 14.135 Å² / R_merge(I) obs: 0.067 / Net I/σ(I): 12.2
Reflection shell	Resolution: 1.45→1.52 Å / Redundancy: 3.5 % / R_merge(I) obs: 0.296 / Mean I/σ(I) obs: 4.1 / % possible all: 95.6

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Processing

Software

Name	Version	Classification
DNA		data collection
PHENIX		model building
REFMAC	5.2.0019	refinement
XDS		data reduction
SCALA		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.45→29.85 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.948 / SU B: 1.836 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19811	1807	5 %	RANDOM
R_work	0.16525	-	-	-
all	0.1871	34308	-	-
obs	0.16686	34308	99.13 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 11.226 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0 Å²	0 Å²	0.02 Å²
2-	-	0 Å²	0 Å²
3-	-	-	0.02 Å²

Refinement step

Cycle: LAST / Resolution: 1.45→29.85 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1612	0	14	192	1818

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	1670
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	1131
X-RAY DIFFRACTION	r_angle_refined_deg	1.433	1.943	2255
X-RAY DIFFRACTION	r_angle_other_deg	0.795	3	2729
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.756	5	200
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.466	23.924	79
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.212	15	255
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.138	15	7
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	228
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	1870
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	376
X-RAY DIFFRACTION	r_nbd_refined	0.193	0.2	252
X-RAY DIFFRACTION	r_nbd_other	0.21	0.2	1103
X-RAY DIFFRACTION	r_nbtor_refined	0.193	0.2	819
X-RAY DIFFRACTION	r_nbtor_other	0.088	0.2	874
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.18	0.2	141
X-RAY DIFFRACTION	r_metal_ion_refined	0.03	0.2	5
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.125	0.2	14
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.196	0.2	47
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.18	0.2	24
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.08	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	0.862	1.5	1041
X-RAY DIFFRACTION	r_mcbond_other	0.238	1.5	418
X-RAY DIFFRACTION	r_mcangle_it	1.231	2	1586
X-RAY DIFFRACTION	r_scbond_it	1.881	3	791
X-RAY DIFFRACTION	r_scangle_it	2.599	4.5	669

LS refinement shell

Resolution: 1.45→1.488 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.251	139	-
R_work	0.196	2477	-
obs	-	-	97.5 %

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	17.8685	7.5408	0.0381	5.4218	-0.1072	0.0069	0.0878	0.0262	0.2311	-0.1962	-0.1285	0.085	-0.0636	-0.1627	0.0407	0.0581	-0.0095	-0.003	0.0329	0.0001	-0.0171	22.2388	4.4718	11.6063
2	32.6913	18.131	-7.4227	13.0671	-5.5506	4.6763	-0.3995	0.9617	-0.1069	-0.4166	0.5135	0.031	0.1224	-0.5878	-0.114	-0.0689	-0.0172	-0.0493	0.1388	-0.0603	0.0089	4.4704	-4.4479	12.6252
3	23.2693	3.8048	-5.2857	2.4029	-2.7731	3.7982	-0.2596	0.0444	-0.6873	-0.3243	0.167	0.1007	0.3608	-0.2798	0.0926	-0.0351	-0.0421	-0.026	0.1084	-0.0324	0.0419	6.4815	-6.0819	16.6841
4	2.7123	-0.7866	-0.1073	0.7568	0.4405	1.2112	0.024	0.1049	0.0014	-0.031	-0.06	-0.034	-0.0794	-0.0869	0.036	0.049	0.0079	0.0032	-0.0059	-0.0079	0.0157	26.756	-3.6199	11.6298
5	12.6822	-5.8563	-5.5894	2.7092	2.4973	3.8983	0.0014	0.1702	-0.092	0.0538	-0.0443	-0.0371	0.1153	-0.2535	0.0429	0.0168	-0.0119	0.0182	0.0194	-0.0178	0.0237	16.1748	0.6035	22.1516
6	21.1956	7.3221	12.3382	3.0302	5.7573	11.9997	0.0039	-0.5798	0.467	0.0176	-0.3014	0.1331	-0.3373	-0.7275	0.2976	-0.0131	0.0517	-0.0344	0.0328	-0.0268	0.0443	9.8236	9.6135	26.9084
7	2.1194	-0.9497	-1.9289	4.5386	0.606	2.7123	-0.0689	0.0763	-0.1389	0.1006	-0.003	0.294	0.2182	-0.1781	0.0719	0.0491	-0.0152	-0.0006	0.0341	-0.0024	0.0005	13.9908	2.2845	27.5069
8	2.7735	-4.8292	-5.7018	8.5519	10.7126	16.015	-0.3444	-0.145	-0.2598	0.7912	0.1143	0.3621	1.1803	-0.1055	0.2301	0.1178	-0.0207	0.0343	0.0125	-0.0144	0.0254	21.7555	-9.1483	19.3913
9	4.1283	-2.1107	-0.242	3.5226	0.8795	2.2845	0.0233	-0.0145	-0.2534	0.0623	-0.0399	0.2799	0.1294	-0.3177	0.0166	0.0201	-0.0095	0.0014	0.0354	-0.0313	0.0201	18.0798	-7.6802	13.9131
10	14.9607	-10.8575	3.9885	19.0818	-6.9148	6.4221	-0.2511	-0.4747	-0.6358	0.5271	0.1407	0.7703	-0.1159	-0.5809	0.1104	-0.0751	-0.0634	0.0079	0.1314	-0.0571	0.0149	3.1558	-4.9698	20.3708
11	10.2999	2.2293	2.5671	4.3212	1.2485	0.7649	-0.0333	0.1217	0.3833	-0.3606	-0.1906	0.2923	-0.1284	-0.1851	0.2239	-0.0098	0.0426	-0.0333	0.1445	-0.0234	-0.0125	6.0918	5.8681	18.5572
12	10.6084	-0.1313	-6.94	1.2714	-1.8511	7.4952	-0.097	0.0518	-0.0174	0.2329	-0.0134	-0.1111	0.0329	0.0859	0.1105	0.0406	0.0061	0.0023	-0.0135	-0.0298	0.0153	22.4284	3.394	21.2685
13	3.9192	-2.4333	2.9174	7.6197	1.3418	4.7815	-0.0731	-0.0213	0.1845	0.0653	0.0237	-0.4078	-0.1136	0.3176	0.0494	0.0425	-0.0154	-0.0037	-0.028	-0.0033	0.0387	33.0669	1.4718	17.5776
14	16.4423	-2.9462	-1.0275	2.6308	0.3357	0.2566	-0.0286	0.3746	0.4178	-0.1102	0.0088	-0.0966	-0.0721	-0.1168	0.0198	0.0445	0.0169	-0.0021	0.0074	0.0262	0.0076	20.7767	8.5772	18.4201
15	6.2088	9.7179	3.7928	15.5246	5.1435	4.3185	-0.2066	0.662	0.0541	-0.61	0.3845	0.3464	-0.2296	0.1202	-0.1779	-0.0597	0.061	-0.1281	0.1971	-0.0685	0.0043	3.1503	0.9928	11.5628
16	14.7999	6.4359	-2.9652	4.3503	-1.753	0.7326	0.1552	-0.2094	0.1819	-0.039	-0.0314	0.1071	0.0038	-0.1952	-0.1238	0.0365	-0.05	-0.0098	0.0868	0.0053	-0.0011	27.1026	3.7278	-12.4787
17	18.1833	3.0943	0.9411	4.1163	-2.9434	3.9757	0.0059	0.0577	-0.5293	-0.0725	0.1488	0.0837	0.19	-0.4931	-0.1547	-0.0865	-0.0533	-0.025	0.1206	0.014	0.0389	10.107	-5.9461	-7.2539
18	20.7452	-1.5705	-10.4321	1.5367	1.5727	6.0754	-0.1623	0.133	-0.3178	-0.1855	0.0982	0.1547	0.1011	-0.1636	0.064	-0.0091	-0.0347	-0.0265	0.0393	0.0026	0.0085	24.8384	-3.8133	-11.4351
19	3.0114	-0.1161	1.0233	4.4491	3.5773	3.2908	-0.1293	0.0052	0.0911	-0.255	-0.0598	0.1813	-0.0108	-0.0044	0.189	0.06	-0.0045	0.0003	-0.0395	-0.0022	0.0227	36.5054	-3.4569	-11.1699
20	7.0265	-2.4939	-2.281	0.9903	1.2017	3.008	-0.0406	0.0977	0.0093	-0.1036	0.0647	-0.0104	0.009	-0.3395	-0.0242	0.0119	-0.0016	0.018	0.0411	-0.0063	0.025	22.1597	1.5797	-0.967
21	42.3282	8.5278	12.4929	9.6162	5.9598	12.9851	-0.2102	-1.5797	1.7093	0.0188	0.1169	-0.3532	-0.7455	-0.4692	0.0934	-0.0082	0.0621	-0.0135	0.0667	-0.1515	0.1476	17.1976	10.2685	3.785
22	9.4613	1.9106	-1.6146	1.7861	0.2984	3.0025	-0.2262	-0.6023	0.137	-0.2408	0.057	0.539	0.008	0.0322	0.1692	0.0289	0.0158	-0.0186	0.0102	-0.0067	0.0035	21.9907	3.24	4.1788
23	6.0598	-8.6298	-7.343	12.7655	11.5233	23.8856	-0.3119	-0.2067	-0.5512	0.6057	0.0381	0.3264	1.0897	-0.1887	0.2738	0.0726	-0.0329	0.0256	-0.0287	-0.0147	0.028	29.2147	-7.8057	-2.9094
24	5.638	0.3313	-0.8766	1.16	-0.0275	0.9409	-0.1502	0.0997	-0.3605	-0.1361	0.1188	0.1064	0.3724	-0.1809	0.0314	0.0318	-0.0397	-0.0044	0.0242	-0.0145	0.0187	24.3587	-7.8554	-8.8138
25	23.8316	-15.2883	10.3925	28.174	-15.2918	9.395	-0.1196	-0.5059	-0.6784	0.1161	0.1861	0.5894	-0.0792	-0.6827	-0.0665	-0.1096	-0.069	0.011	0.1439	-0.0086	-0.0348	9.3043	-3.9105	-2.7153
26	24.2425	0.8619	-1.2356	2.3888	1.0174	1.1053	-0.0151	0.1159	0.6053	-0.2621	-0.0578	0.1021	-0.1428	-0.3743	0.0729	-0.027	0.0417	-0.0133	0.0925	0.0282	0.0061	14.5318	6.5757	-3.6845
27	9.3943	0.0925	-7.6263	1.1589	-0.2201	6.2092	-0.0723	-0.1006	-0.037	0.1658	0.107	-0.0552	0.0552	0.1326	-0.0347	0.0259	-0.0115	0.0161	-0.0078	-0.034	0.0305	29.7001	3.7056	-2.9619
28	5.2153	-1.8613	-2.971	5.4011	0.2974	3.8838	0.0324	0.0009	0.1171	0.1555	-0.0123	-0.0958	-0.0391	0.0678	-0.0201	0.0404	-0.0113	-0.0041	-0.0306	-0.01	0.0073	37.7716	3.6744	-7.1207
29	37.5716	-1.1948	5.0064	3.3841	0.6897	2.2027	-0.2388	1.1837	2.3247	-0.164	-0.0353	-0.1037	-0.2443	0.0349	0.2741	-0.0169	0.0114	-0.0025	0.0326	0.1213	0.0637	20.1747	8.9125	-6.6298
30	8.8146	11.6515	2.2105	16.0839	5.4874	10.2	-0.2634	0.5624	-0.1573	-0.5866	0.0214	0.4751	-0.1278	-0.0342	0.242	-0.0593	0.0436	-0.1427	0.2384	-0.0207	0.0866	8.378	-1.0901	-11.7466

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 7
2	X-RAY DIFFRACTION	2	A	8 - 12
3	X-RAY DIFFRACTION	3	A	13 - 18
4	X-RAY DIFFRACTION	4	A	19 - 27
5	X-RAY DIFFRACTION	5	A	28 - 35
6	X-RAY DIFFRACTION	6	A	36 - 41
7	X-RAY DIFFRACTION	7	A	42 - 48
8	X-RAY DIFFRACTION	8	A	49 - 55
9	X-RAY DIFFRACTION	9	A	56 - 62
10	X-RAY DIFFRACTION	10	A	63 - 69
11	X-RAY DIFFRACTION	11	A	70 - 76
12	X-RAY DIFFRACTION	12	A	77 - 80
13	X-RAY DIFFRACTION	13	A	81 - 86
14	X-RAY DIFFRACTION	14	A	87 - 93
15	X-RAY DIFFRACTION	15	A	94 - 101
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