PDB-7tni: Structure of EC12 Y1392W variant of BT-R1 from Manduca sexta, a C...

ID or keywords:

Entry

Database: PDB / ID: 7tni

Title

Structure of EC12 Y1392W variant of BT-R1 from Manduca sexta, a Cry1A toxin binding domain

Components

Cadherin

Keywords

CELL ADHESION / ectodomain / EC12 / Cry1A / toxin-binding

Function / homology

Function and homology information

homophilic cell adhesion via plasma membrane adhesion molecules / membrane => GO:0016020 / calcium ion binding / plasma membrane
Similarity search - Function

Biological species

Manduca sexta (tobacco hornworm)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Fisher, A.J. / Wilcox, X.E.

Funding support

United States, 1items

Citation

Journal: Biochemistry / Year: 2022
Title: Functional and Structural Analysis of the Toxin-Binding Site of the Cadherin G-Protein-Coupled Receptor, BT-R 1 , for Cry1A Toxins of Bacillus thuringiensis .
Authors: Liu, L. / Wilcox, X.E. / Fisher, A.J. / Boyd, S.D. / Zhi, J. / Winkler, D.D. / Bulla Jr., L.A.

History

Deposition	Jan 21, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 4, 2022	Provider: repository / Type: Initial release
Revision 1.1	May 18, 2022	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7tni.cif.gz	184.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7tni.ent.gz	139.9 KB	Display	PDB format
PDBx/mmJSON format	7tni.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7tni_validation.pdf.gz	1.8 MB	Display	wwPDB validaton report
Full document	7tni_full_validation.pdf.gz	1.8 MB	Display
Data in XML	7tni_validation.xml.gz	20.4 KB	Display
Data in CIF	7tni_validation.cif.gz	29 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tn/7tni ftp://data.pdbj.org/pub/pdb/validation_reports/tn/7tni	HTTPS FTP

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Related structure data

Related structure data	2ee0S S: Starting model for refinement
Similar structure data	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	#99 - Mar 2008 Cadherin similarity (8)

Deposited unit

A: Cadherin

B: Cadherin

C: Cadherin

D: Cadherin

hetero molecules

67.6 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Cadherin

hetero molecules

defined by author
Evidence: gel filtration
16.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Cadherin

hetero molecules

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

3

C: Cadherin

hetero molecules

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

4

D: Cadherin

hetero molecules

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

Unit cell

Length a, b, c (Å)	59.133, 44.579, 94.797
Angle α, β, γ (deg.)	90.000, 107.156, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	2	A
4	2	C
5	3	A
6	3	D
7	4	B
8	4	C
9	5	B
10	5	D
11	6	C
12	6	D

NCS domain segments:

Beg auth comp-ID: ASP / Beg label comp-ID: ASP

Dom-ID	Component-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	GLN	GLN	A	A	1349 - 1458	44 - 153
2	1	1	GLN	GLN	B	B	1349 - 1458	44 - 153
3	2	2	SER	SER	A	A	1349 - 1457	44 - 152
4	2	2	SER	SER	C	C	1349 - 1457	44 - 152
5	3	3	GLN	GLN	A	A	1349 - 1458	44 - 153
6	3	3	GLN	GLN	D	D	1349 - 1458	44 - 153
7	4	4	SER	SER	B	B	1349 - 1457	44 - 152
8	4	4	SER	SER	C	C	1349 - 1457	44 - 152
9	5	5	GLN	GLN	B	B	1349 - 1458	44 - 153
10	5	5	GLN	GLN	D	D	1349 - 1458	44 - 153
11	6	6	SER	SER	C	C	1349 - 1457	44 - 152
12	6	6	SER	SER	D	D	1349 - 1457	44 - 152

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

#1: Protein	Cadherin Mass: 16877.727 Da / Num. of mol.: 4 / Fragment: Protein receptor BT-R1 residues 1349-1460 / Mutation: Y1392W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Manduca sexta (tobacco hornworm) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q8MZK3
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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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: 41.34 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M Tris-HCl pH 7.0, 2.8M Magnesium Sulfate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97911 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 1, 2020
Radiation	Monochromator: Cryo-Cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97911 Å / Relative weight: 1
Reflection	Resolution: 1.9→56.5 Å / Num. obs: 37385 / % possible obs: 99.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.5 % / B_iso Wilson estimate: 36.2 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.07 / R_pim(I) all: 0.032 / R_rim(I) all: 0.078 / Χ²: 0.98 / Net I/σ(I): 9.9
Reflection shell	Resolution: 1.9→1.94 Å / Redundancy: 5.6 % / R_merge(I) obs: 0.837 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2417 / CC_1/2: 0.804 / R_pim(I) all: 0.382 / R_rim(I) all: 0.922 / Χ²: 0.93 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2ee0

2ee0

Resolution: 1.9→56.5 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.954 / SU B: 9.689 / SU ML: 0.137 / Cross valid method: FREE R-VALUE / ESU R: 0.171 / ESU R Free: 0.149
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2399	1926	5.155 %	Random selection
R_work	0.2105	35436	-	-
all	0.212	-	-	-
obs	-	37362	99.309 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 44.391 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.962 Å²	-0 Å²	-0.171 Å²
2-	-	-0.051 Å²	0 Å²
3-	-	-	-2.356 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→56.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3348	0	4	227	3579

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.013	3486
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	3300
X-RAY DIFFRACTION	r_angle_refined_deg	1.765	1.649	4777
X-RAY DIFFRACTION	r_angle_other_deg	1.437	1.572	7558
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.383	5	457
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.513	21.351	185
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.258	15	551
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	23.572	15	30
X-RAY DIFFRACTION	r_chiral_restr	0.077	0.2	503
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	3999
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	817
X-RAY DIFFRACTION	r_nbd_refined	0.209	0.2	553
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.199	0.2	2912
X-RAY DIFFRACTION	r_nbtor_refined	0.161	0.2	1706
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.087	0.2	1673
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.193	0.2	235
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.182	0.2	2
X-RAY DIFFRACTION	r_metal_ion_refined	0.164	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.285	0.2	18
X-RAY DIFFRACTION	r_nbd_other	0.252	0.2	42
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.274	0.2	13
X-RAY DIFFRACTION	r_mcbond_it	2.259	2.793	1780
X-RAY DIFFRACTION	r_mcbond_other	2.249	2.791	1779
X-RAY DIFFRACTION	r_mcangle_it	3.33	4.164	2223
X-RAY DIFFRACTION	r_mcangle_other	3.33	4.166	2224
X-RAY DIFFRACTION	r_scbond_it	2.993	3.143	1706
X-RAY DIFFRACTION	r_scbond_other	2.992	3.144	1707
X-RAY DIFFRACTION	r_scangle_it	4.533	4.592	2544
X-RAY DIFFRACTION	r_scangle_other	4.532	4.593	2545
X-RAY DIFFRACTION	r_lrange_it	7.538	34.126	3726
X-RAY DIFFRACTION	r_lrange_other	7.491	33.633	3672
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.116	0.05	3271
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.101	0.05	3250
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.097	0.05	3280
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.103	0.05	3218
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.111	0.05	3220
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.071	0.05	3255

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.11598	0.05009
1	2	B	X-RAY DIFFRACTION	Local ncs	0.11598	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.10052	0.05009
2	4	C	X-RAY DIFFRACTION	Local ncs	0.10052	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.09682	0.05009
3	6	D	X-RAY DIFFRACTION	Local ncs	0.09682	0.05009
4	7	B	X-RAY DIFFRACTION	Local ncs	0.10295	0.05008
4	8	C	X-RAY DIFFRACTION	Local ncs	0.10295	0.05008
5	9	B	X-RAY DIFFRACTION	Local ncs	0.11071	0.05008
5	10	D	X-RAY DIFFRACTION	Local ncs	0.11071	0.05008
6	11	C	X-RAY DIFFRACTION	Local ncs	0.07096	0.05009
6	12	D	X-RAY DIFFRACTION	Local ncs	0.07096	0.05009

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 (%)
1.9-1.949	0.308	140	0.338	2634	X-RAY DIFFRACTION	99.856
1.949-2.003	0.257	142	0.296	2517	X-RAY DIFFRACTION	99.5507
2.003-2.061	0.366	135	0.296	2472	X-RAY DIFFRACTION	99.5798
2.061-2.124	0.334	122	0.269	2397	X-RAY DIFFRACTION	99.1732
2.124-2.194	0.291	130	0.257	2287	X-RAY DIFFRACTION	98.332
2.194-2.271	0.268	112	0.242	2257	X-RAY DIFFRACTION	99.7894
2.271-2.356	0.299	116	0.234	2176	X-RAY DIFFRACTION	99.3068
2.356-2.453	0.327	125	0.248	2088	X-RAY DIFFRACTION	99.7296
2.453-2.561	0.368	106	0.252	2039	X-RAY DIFFRACTION	99.3976
2.561-2.686	0.249	105	0.226	1916	X-RAY DIFFRACTION	99.7532
2.686-2.832	0.275	104	0.218	1825	X-RAY DIFFRACTION	99.5356
2.832-3.003	0.206	93	0.209	1725	X-RAY DIFFRACTION	99.2358
3.003-3.21	0.234	88	0.216	1624	X-RAY DIFFRACTION	98.2778
3.21-3.467	0.228	96	0.213	1509	X-RAY DIFFRACTION	99.4424
3.467-3.797	0.219	87	0.201	1391	X-RAY DIFFRACTION	99.328
3.797-4.245	0.187	66	0.159	1274	X-RAY DIFFRACTION	99.4065
4.245-4.9	0.177	47	0.148	1146	X-RAY DIFFRACTION	98.4323
4.9-5.996	0.226	37	0.178	965	X-RAY DIFFRACTION	98.4283
5.996-8.462	0.183	52	0.196	752	X-RAY DIFFRACTION	99.1369
8.462-56.5	0.228	23	0.225	442	X-RAY DIFFRACTION	99.359

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	4.8232	-0.7482	-5.8987	1.8504	1.9258	7.8215	-0.1899	0.6032	-0.0609	-0.0903	0.0399	0.2	0.1896	-0.6367	0.15	0.1365	-0.0018	-0.011	0.2996	0.0274	0.1411	-3.5597	-2.0227	11.4777
2	0.9228	-0.0872	-1.311	0.2693	-0.2003	4.02	-0.1012	0.137	-0.1082	0.2069	0.1018	0.0196	0.0989	0.1704	-0.0005	0.1941	0.097	0.0197	0.2106	-0.0583	0.0887	12.0928	0.4967	8.2956
3	0.5503	0.444	-1.171	0.7036	-0.1493	4.9099	0.0045	-0.0921	-0.04	0.1377	0.0711	-0.0498	-0.0876	0.7271	-0.0757	0.1761	0.0295	0.0084	0.2793	-0.0488	0.0691	19.3271	2.1023	8.1637
4	1.3623	0.4237	-1.6609	0.2928	-0.5822	5.449	-0.0669	0.2861	-0.1915	0.1042	0.1334	-0.0952	0.3077	-0.1404	-0.0665	0.1918	0.0403	0.0234	0.1432	-0.0476	0.1376	10.1341	-3.2638	6.907
5	5.1508	2.4026	-1.9125	5.649	-4.177	3.1089	-0.1386	0.0324	0.1382	-0.5036	0.1281	-0.009	0.4459	-0.0424	0.0105	0.4137	0.212	0.0393	0.2769	0.0368	0.0103	18.8877	-2.8002	33.0892
6	0.3221	-0.1532	0.7701	0.2876	-1.2456	5.4917	0.2093	-0.2239	0.084	-0.124	0.102	0.0864	0.506	-0.3986	-0.3113	0.2421	-0.1167	0.048	0.2057	-0.0339	0.1483	3.3234	-0.3493	36.2356
7	1.4453	-0.0091	-0.2156	0.2054	-0.9699	5.1789	0.2768	-0.2708	0.0976	-0.1274	0.2237	0.0597	0.2723	-1.0486	-0.5005	0.3199	-0.1732	0.0384	0.3602	0.1091	0.1528	-3.8436	1.0768	36.4412
8	1.2285	-0.2018	-0.9821	0.1225	-0.577	7.0206	0.3064	-0.3129	0.089	-0.1758	0.1067	0.0381	0.8819	-0.0261	-0.4131	0.2904	-0.0989	-0.0174	0.1263	0.0355	0.0848	5.2275	-4.0966	37.3318
9	7.7457	-1.2075	0.9012	0.4753	-1.0005	2.705	-0.0412	0.3478	0.2038	0.023	-0.0923	-0.0581	-0.0723	0.2263	0.1335	0.088	-0.0358	-0.0083	0.188	0.0316	0.1149	10.0979	23.3974	7.5927
10	2.9444	0.0915	0.8844	0.1384	-0.3695	1.8009	-0.0535	0.2102	-0.0421	0.0955	0.0875	-0.0109	-0.0844	-0.1169	-0.034	0.2234	0.0522	0.003	0.1155	-0.0067	0.1191	-4.3776	20.7206	14.6044
11	4.8097	-0.0026	0.5548	0.236	0.2733	0.4177	0.2047	-0.2225	0.0319	0.1467	-0.0747	-0.1041	0.1574	-0.1926	-0.13	0.17	-0.0012	0.0066	0.2125	0.0322	0.1402	-10.1484	19.0367	18.792
12	4.7439	0.5403	1.7874	0.1255	-0.0773	2.4359	-0.1341	0.3659	0.1348	0.0863	0.0777	0.0087	-0.2846	-0.0936	0.0564	0.2529	0.019	-0.0033	0.0955	0.0396	0.1511	-4.2267	24.4398	12.5688
13	6.7296	2.7642	4.0204	3.8381	3.4674	3.6254	0.0852	-0.6592	0.3741	0.0145	-0.3261	0.2268	0.0537	-0.3752	0.2409	0.018	0.0162	0.0218	0.3257	0.0501	0.0898	5.5651	22.368	38.6094
14	2.8854	-0.5494	0.6302	0.5989	0.0186	0.8745	0.0205	-0.2092	0.0228	-0.1994	0.1297	0.0527	0.0609	0.0519	-0.1502	0.1193	-0.0141	-0.0036	0.133	0.0201	0.131	19.9448	20.1844	31.5559
15	4.1891	0.007	1.1688	0.3215	-0.1497	0.4151	0.0117	0.0713	0.0709	-0.2098	0.0376	0.0774	0.0998	0.0554	-0.0493	0.1587	-0.0095	0.0016	0.2229	-0.0142	0.1658	25.6847	18.7159	27.2318
16	5.6146	-1.086	1.8009	0.3047	-0.352	1.5543	0.0736	-0.4474	0.1817	-0.1121	0.1097	-0.0001	0.0329	0.019	-0.1833	0.113	-0.0096	-0.005	0.145	-0.0073	0.1656	19.1933	23.9555	33.8302

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	1349 - 1357
2	X-RAY DIFFRACTION	2	ALL	A	1358 - 1404
3	X-RAY DIFFRACTION	3	ALL	A	1405 - 1430
4	X-RAY DIFFRACTION	4	ALL	A	1431 - 1458
5	X-RAY DIFFRACTION	5	ALL	B	1349 - 1357
6	X-RAY DIFFRACTION	6	ALL	B	1358 - 1404
7	X-RAY DIFFRACTION	7	ALL	B	1405 - 1430
8	X-RAY DIFFRACTION	8	ALL	B	1431 - 1458
9	X-RAY DIFFRACTION	9	ALL	C	1349 - 1357
10	X-RAY DIFFRACTION	10	ALL	C	1358 - 1404
11	X-RAY DIFFRACTION	11	ALL	C	1405 - 1430
12	X-RAY DIFFRACTION	12	ALL	C	1431 - 1459
13	X-RAY DIFFRACTION	13	ALL	D	1349 - 1357
14	X-RAY DIFFRACTION	14	ALL	D	1358 - 1404
15	X-RAY DIFFRACTION	15	ALL	D	1405 - 1430
16	X-RAY DIFFRACTION	16	ALL	D	1431 - 1458

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