PDB-8v9w: X-ray crystal structure of JGFN4 complexed with fentanyl

ID or keywords:

Entry

Database: PDB / ID: 8v9w

Title

X-ray crystal structure of JGFN4 complexed with fentanyl

Components

JGFN4

Keywords

ANTITOXIN

Function / homology

Chem-7V7

Function and homology information

Biological species

Camelidae (mammal)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.68 Å

Authors

Moller, N. / Shi, K. / Aihara, H.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Cancer Institute (NIH/NCI)	P01-CA214279	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	R37-AI064064	United States

Citation

Journal: J.Biol.Chem. / Year: 2024
Title: Identification and biophysical characterization of a novel domain-swapped camelid antibody specific for fentanyl.
Authors: Gallant, J.P. / Hicks, D. / Shi, K. / Moeller, N.H. / Hoppe, B. / Lake, E.W. / Baehr, C. / Pravetoni, M. / Aihara, H. / LeBeau, A.M.

History

Deposition	Dec 10, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 7, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8v9w.cif.gz	198 KB	Display	PDBx/mmCIF format
PDB format	pdb8v9w.ent.gz	159.2 KB	Display	PDB format
PDBx/mmJSON format	8v9w.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8v9w_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	8v9w_full_validation.pdf.gz	1.5 MB	Display
Data in XML	8v9w_validation.xml.gz	24.5 KB	Display
Data in CIF	8v9w_validation.cif.gz	34.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v9/8v9w ftp://data.pdbj.org/pub/pdb/validation_reports/v9/8v9w	HTTPS FTP

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Related structure data

Related structure data	8v9xC 8v9yC 8v9zC 8va0C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#217 - Jan 2018 Opioid Receptors similarity (1) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: JGFN4

B: JGFN4

C: JGFN4

D: JGFN4

hetero molecules

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

1

A: JGFN4

C: JGFN4

hetero molecules

defined by author&software
26.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: JGFN4

D: JGFN4

hetero molecules

defined by author&software
26.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	85.431, 97.138, 57.578
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Antibody	JGFN4 Mass: 12935.386 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Camelidae (mammal) / Production host: Escherichia coli (E. coli)
#2: Chemical	ChemComp-7V7 / N-phenyl-N-[1-(2-phenylethyl)piperidin-4-yl]propanamide Mass: 336.471 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₂H₂₈N₂O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 411 / 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: 2.31 Å³/Da / Density % sol: 46.72 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop Details: RD22EH09, D4.1 20 v/v 2-propanol, 20 w/v polyethylene glycol 4000, 0.1 M sodium citrate - citric acid pH5.6

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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: 0.97918 Å
Detector	Type: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Apr 22, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 1.68→49.53 Å / Num. obs: 63322 / % possible obs: 97.6 % / Redundancy: 3.6 % / CC_1/2: 0.998 / R_merge(I) obs: 0.067 / R_pim(I) all: 0.04 / R_rim(I) all: 0.078 / Net I/σ(I): 8.2
Reflection shell	Resolution: 1.68→1.71 Å / Redundancy: 3.2 % / R_merge(I) obs: 1.947 / Num. unique obs: 2674 / CC_1/2: 0.371 / R_pim(I) all: 1.218 / R_rim(I) all: 2.311

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.68→49.53 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 30.16 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2403	2639	4.89 %
R_work	0.1981	-	-
obs	0.2001	53932	97.44 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.68→49.53 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3352	0	104	411	3867

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_dihedral_angle_d	14.581	1290
X-RAY DIFFRACTION	f_chiral_restr	0.091	536
X-RAY DIFFRACTION	f_plane_restr	0.013	621

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 (%)
1.68-1.71	0.4079	136	0.3599	2674	X-RAY DIFFRACTION	98
1.71-1.74	0.3995	125	0.331	2675	X-RAY DIFFRACTION	98
1.74-1.78	0.3162	161	0.3073	2668	X-RAY DIFFRACTION	99
1.78-1.82	0.3044	146	0.2937	2682	X-RAY DIFFRACTION	98
1.82-1.86	0.3009	158	0.2631	2677	X-RAY DIFFRACTION	98
1.86-1.91	0.2987	135	0.2624	2711	X-RAY DIFFRACTION	99
1.91-1.96	0.3055	125	0.244	2680	X-RAY DIFFRACTION	98
1.96-2.02	0.2871	146	0.2219	2600	X-RAY DIFFRACTION	94
2.02-2.08	0.2707	147	0.2111	2698	X-RAY DIFFRACTION	99
2.08-2.16	0.2533	145	0.207	2706	X-RAY DIFFRACTION	99
2.16-2.24	0.2563	122	0.2062	2735	X-RAY DIFFRACTION	99
2.24-2.34	0.2692	133	0.2063	2723	X-RAY DIFFRACTION	99
2.34-2.47	0.2799	111	0.2093	2778	X-RAY DIFFRACTION	99
2.47-2.62	0.2465	137	0.2027	2736	X-RAY DIFFRACTION	98
2.62-2.82	0.2366	149	0.2004	2661	X-RAY DIFFRACTION	97
2.82-3.11	0.2501	143	0.1932	2664	X-RAY DIFFRACTION	96
3.11-3.56	0.2166	129	0.1706	2765	X-RAY DIFFRACTION	97
3.56-4.48	0.1911	135	0.154	2743	X-RAY DIFFRACTION	96
4.48-49.53	0.2008	156	0.1805	2717	X-RAY DIFFRACTION	92

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	4.4525	5.2529	-1.9805	6.1934	-2.09	2.4644	-0.4499	-0.3071	0.8311	-0.2153	0.4117	1.6039	-0.1778	-0.7855	-0.0858	0.2854	0.0226	-0.0125	0.3659	0.0552	0.4747	10.0966	12.3485	-29.567
2	9.6579	-0.0303	0.9886	5.715	-2.0213	2.4121	0.2915	-0.4772	0.0338	1.0177	-0.5477	-0.3731	-0.5544	0.3285	0.2082	0.2806	-0.0411	-0.0482	0.2212	-0.0388	0.2123	23.6169	21.1086	-28.9587
3	4.7362	-0.3021	-2.6726	6.6742	-2.0919	7.0406	-0.0218	0.2073	-0.1497	0.0341	0.2036	0.4895	0.3836	-0.6009	-0.1482	0.1805	-0.0252	-0.0277	0.2272	-0.0186	0.2033	16.2669	6.1777	-28.199
4	1.7834	1.8277	-1.9512	3.9407	-4.3388	4.6015	-0.2114	-0.0451	-0.1779	-0.6265	-0.3916	-0.5087	1.1666	1.2793	0.4631	0.342	0.0102	0.0075	0.2709	-0.014	0.2011	25.1256	7.9864	-36.0151
5	8.2688	3.1202	-1.8073	5.3782	-4.455	6.7852	-0.1634	0.1771	-0.0942	0.6491	-0.3244	-1.398	0.1947	0.4247	0.6038	0.3028	0.0021	-0.0801	0.2776	0.0526	0.3704	30.087	6.3766	-26.0485
6	3.501	0.8753	-5.2207	8.6016	-2.0002	7.8879	-0.1363	-0.3489	-0.0173	0.9538	-0.1971	-0.0475	-0.2845	-0.0344	0.2522	0.3588	0.0018	-0.0616	0.2975	-0.0041	0.1494	20.9812	11.7686	-19.9211
7	4.1159	2.0302	-5.5869	8.8631	-2.7705	7.9351	0.0287	0.1607	0.3718	0.6544	0.0182	-0.0125	-0.5386	-0.1671	0.0141	0.343	-0.0187	-0.0381	0.3003	0.0273	0.2085	21.1567	14.6582	-23.5581
8	9.8597	2.4585	6.9623	6.5109	0.6532	5.0364	-0.3821	0.4328	-0.2072	0.0343	-0.0525	-1.177	0.0659	0.789	0.5632	0.2192	0.002	-0.0175	0.3496	0.0617	0.4376	33.2912	19.0371	-34.4194
9	2.7004	-0.3321	0.1726	3.4429	-1.0066	0.4401	0.0447	-0.0709	-0.3532	0.0356	0.1278	0.2826	0.0054	0.0245	-0.1641	0.2306	-0.0057	-0.017	0.2845	-0.0373	0.0996	24.1826	-5.8726	-25.8096
10	0.353	-0.4672	-0.0662	1.1256	-0.9103	2.3379	-0.3037	0.0706	-1.0052	0.0312	0.3818	-2.7042	-0.2114	0.8612	-0.0094	0.2333	-0.0076	0.0542	0.3715	-0.0696	0.6063	32.7014	-14.0396	-0.7747
11	0.3862	-0.4547	0.7513	7.004	3.3031	3.0441	0.1632	0.0057	-0.1951	0.6216	-0.0984	-0.3938	0.2827	0.0643	-0.072	0.2158	0.0145	-0.0004	0.2322	0.0292	0.2027	23.7231	-16.8987	1.9187
12	4.3001	4.759	5.6446	7.6475	7.0046	8.2768	-0.2973	0.3574	0.1379	-0.5822	0.0528	0.3508	-0.4749	0.117	0.2509	0.1855	0.0063	0.0051	0.2915	-0.0308	0.1862	19.4927	-11.4596	-8.4103
13	6.2206	-0.0979	-4.0897	6.0408	0.1934	6.3684	0.031	-0.0759	-0.0353	0.1032	-0.4618	0.2663	-0.0923	-1.1013	0.5786	0.1638	0.0418	0.0178	0.146	-0.0066	0.1383	19.2703	-5.9506	3.6804
14	5.7375	5.5415	0.7924	6.2005	1.5646	6.4691	-0.3714	0.4861	0.4623	0.1804	0.428	2.022	-0.5863	-0.5428	0.0329	0.1888	0.0205	0.0231	0.3496	0.0386	0.5051	9.6393	-9.6662	0.6212
15	2.2961	3.0419	3.3791	7.9783	2.6567	8.9231	-0.035	-0.586	-0.0598	0.6923	-0.1415	-0.0683	0.3109	-0.1451	0.1169	0.2527	0.0328	0.0095	0.2791	-0.0008	0.2016	21.8236	-14.9026	7.2368
16	6.1963	2.3352	-4.3249	6.8049	-0.5826	3.2839	0.2528	0.1559	0.2052	-0.2258	-0.1867	1.5649	-0.4708	-1.0894	-0.2167	0.1429	0.0149	-0.011	0.4824	-0.0812	0.4427	9.8481	-20.8085	-5.7769
17	1.1145	0.3212	0.0538	1.6409	0.932	0.6687	0.0304	0.0331	0.1964	0.0509	0.0032	-0.0421	0.008	-0.1841	-0.0593	0.1509	0.0083	0.0212	0.236	0.0066	0.1661	18.5234	4.1647	2.9029
18	9.3727	-5.5139	-2.6276	3.3301	1.4579	2.4244	0.4518	0.4218	-0.2448	-0.8012	-0.4007	0.6431	0.0443	-0.3859	-0.1781	0.2939	0.0093	-0.0399	0.2774	0.0282	0.3174	17.6373	-17.6616	-28.3371
19	6.3192	2.0144	1.1952	2.821	-0.29	1.8402	-0.041	0.0914	-0.6763	-0.1016	0.1114	-0.6406	-0.0713	0.4638	-0.1498	0.207	0.0412	0.0013	0.3642	-0.0629	0.3393	33.1154	-19.2818	-28.2937
20	4.9296	-1.2987	3.8241	4.0477	-1.2842	6.8285	-0.0083	-0.3048	-0.4272	-0.3339	0.1677	0.4392	-0.2061	-0.3708	-0.1226	0.183	-0.005	0.0081	0.3054	-0.0097	0.2187	21.0069	-9.3694	-28.5237
21	2.2817	-2.8447	0.9707	5.3867	-4.9793	7.1405	-0.4028	-0.5433	0.2673	0.4758	0.2664	-0.1606	-0.7889	-0.018	0.0664	0.2493	0.0294	0.0054	0.3307	-0.0655	0.2094	28.3997	-6.5224	-21.5728
22	9.3325	-3.3179	3.82	3.543	-1.7033	5.3935	0.0706	0.1676	0.6001	-0.0938	-0.3832	-0.7685	-0.6418	0.5513	0.5542	0.3743	-0.0774	0.0353	0.3261	0.0101	0.3506	32.8543	-3.3103	-31.0903
23	4.0368	3.4899	5.0102	6.9781	1.4394	9.1408	-0.2261	0.5027	0.0827	-0.7824	0.0312	-0.2503	-0.2754	0.7769	0.1109	0.2977	-0.0118	0.0478	0.303	-0.0427	0.2296	28.0389	-13.4455	-35.6825
24	5.5122	-4.2089	-0.4094	5.1364	-0.6331	3.1384	-0.0705	0.0377	0.037	-0.1067	0.0653	-0.3749	-0.3285	0.5758	0.0327	0.1694	-0.0617	0.0196	0.2684	-0.0241	0.2226	32.8799	-12.5727	-22.9175
25	3.3015	3.3618	-1.0077	7.6852	-3.9969	3.1104	-0.1871	0.1276	0.1997	-0.3474	0.1809	0.1538	-0.0029	-0.0631	-0.0382	0.203	0.0223	0.0074	0.2418	-0.0038	0.1671	19.7961	14.0551	-35.7373
26	2.1928	2.615	-0.8673	3.6853	0.0463	2.6762	0.1338	0.1698	0.5131	-0.4379	-0.006	-0.132	-0.1435	0.0024	-0.1181	0.2392	0.01	-0.0054	0.1835	0.0339	0.1648	18.3838	14.7267	-1.175
27	5.1321	-2.0842	-3.3764	4.804	3.2694	6.4324	-0.1329	-0.561	-0.0872	0.2743	0.0757	0.0196	0.5635	0.2844	0.0728	0.1383	0.021	-0.0214	0.2486	0.0388	0.1761	14.896	6.2405	5.9669
28	7.9112	-2.611	-2.4633	6.5886	2.2014	4.3721	0.2203	0.4132	-0.5201	-0.435	-0.4522	0.9597	0.244	-0.6838	0.2972	0.2755	-0.0321	-0.0611	0.1944	0.0281	0.2281	9.8516	1.5601	-2.2299
29	4.6369	4.2598	-3.9011	5.2549	-1.878	6.0473	-0.1169	-0.177	0.2284	-0.7026	0.0132	0.1002	-0.0883	0.1247	0.0587	0.3255	0.0462	-0.0414	0.2517	0.016	0.2034	14.7332	11.7049	-7.1614
30	4.4194	-0.5634	5.7096	5.3894	-0.0778	7.3768	-0.0219	-0.2776	-0.7427	0.0916	0.5377	0.6375	0.7258	-0.8814	-0.4841	0.1552	-0.0036	-0.0281	0.3884	0.0471	0.4333	2.1072	11.5942	6.4518
31	2.2705	0.2495	-0.2104	6.0687	2.8877	1.4652	0.0214	0.123	-0.0557	-0.1563	0.1161	-0.2279	-0.0111	0.0063	-0.1623	0.144	0.0491	-0.0499	0.2177	0.0543	0.04	21.0307	-6.7354	-2.6875

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 7 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 8 through 25 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 26 through 39 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 40 through 52 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 53 through 66 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 67 through 75 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 76 through 82 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 83 through 91 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 92 through 113 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 1 through 7 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 8 through 32 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 33 through 45 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 46 through 56 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 57 through 66 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 67 through 82 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 83 through 91 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 92 through 113 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 1 through 7 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 8 through 25 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 26 through 40 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 41 through 52 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 53 through 66 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 67 through 82 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 83 through 98 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 99 through 113 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 1 through 32 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 33 through 52 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 53 through 66 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 67 through 82 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 83 through 91 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 92 through 113 )

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Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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-Related structure data

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-Experimental details

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-Sample preparation

-Data collection

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+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

+
Open data

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Basic information

-
Structure visualization

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Downloads & links

-
Download

-
Validation report

-
Related structure data

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Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

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Sample preparation

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Data collection

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Processing

+
About Yorodumi

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News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi