PDB-8va0: X-ray crystal structure of JGFN4 N76D complexed with fentanyl in ...

ID or keywords:

Entry

Database: PDB / ID: 8va0

Title

X-ray crystal structure of JGFN4 N76D complexed with fentanyl in dimer form

Components

JGFN4

Keywords

ANTITOXIN

Function / homology

Chem-7V7 / TRIETHYLENE GLYCOL

Function and homology information

Biological species

Camelidae (mammal)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Shi, K. / Moller, N. / 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
Revision 1.1	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8va0.cif.gz	126.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8va0.ent.gz	81.8 KB	Display	PDB format
PDBx/mmJSON format	8va0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/va/8va0 ftp://data.pdbj.org/pub/pdb/validation_reports/va/8va0	HTTPS FTP

-
Related structure data

Related structure data	8v9wC 8v9xC 8v9yC 8v9zC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
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

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	57.309, 83.845, 96.605
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁
Space group name Hall	C2c2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	(chain "A" and (resid 2 through 53 or resid 55...
d_2	ens_1	(chain "B" and (resid 2 through 53 or resid 55...

NCS domain segments:

Ens-ID: ens_1

Dom-ID	Component-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
d_1	1	VAL	VAL	ARG	ARG	A	A	2 - 53	3 - 54
d_1	2	GLY	GLY	ILE	ILE	A	A	55 - 77	56 - 78
d_1	3	LEU	LEU	TYR	TYR	A	A	80 - 94	81 - 95
d_1	4	ARG	ARG	SER	SER	A	A	96 - 113	97 - 114
d_2	1	VAL	VAL	ARG	ARG	B	B	2 - 53	3 - 54
d_2	2	GLY	GLY	ILE	ILE	B	B	55 - 77	56 - 78
d_2	3	LEU	LEU	TYR	TYR	B	B	80 - 94	81 - 95
d_2	4	ARG	ARG	SER	SER	B	B	96 - 113	97 - 114

#1: Antibody	JGFN4 Mass: 12936.370 Da / Num. of mol.: 2 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.: 2 / Source method: obtained synthetically / Formula: C₂₂H₂₈N₂O / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#3: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.24 Å³/Da / Density % sol: 45.16 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop Details: J348, C03_00 8.0 0.2 M, Sodium acetate trihy 20 % w/v, Polyethylene glycol

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 8, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 1.85→96.61 Å / Num. obs: 20160 / % possible obs: 99.6 % / Redundancy: 7.4 % / B_iso Wilson estimate: 31.59 Å² / CC_1/2: 1 / R_merge(I) obs: 0.054 / R_pim(I) all: 0.021 / R_rim(I) all: 0.058 / Net I/σ(I): 19 / Num. measured all: 148724
Reflection shell	Resolution: 1.85→1.89 Å / % possible obs: 100 % / Redundancy: 7.5 % / R_merge(I) obs: 0.903 / Num. measured all: 9355 / Num. unique obs: 1240 / CC_1/2: 0.875 / R_pim(I) all: 0.347 / R_rim(I) all: 0.969 / Net I/σ(I) obs: 2

-
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: 1.85→48.3 Å / SU ML: 0.2605 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.5264
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2401	1037	5.16 %
R_work	0.2026	19049	-
obs	0.2046	20086	99.21 %

Solvent computation

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

Displacement parameters

B_iso mean: 45.13 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→48.3 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1676	0	68	104	1848

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0059	1789
X-RAY DIFFRACTION	f_angle_d	0.831	2397
X-RAY DIFFRACTION	f_chiral_restr	0.052	266
X-RAY DIFFRACTION	f_plane_restr	0.0054	308
X-RAY DIFFRACTION	f_dihedral_angle_d	14.0529	648

Refine LS restraints NCS

Type: Torsion NCS / Rms dev position: 0.704409991423 Å

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 (%)
1.85-1.95	0.3974	144	0.3476	2687	X-RAY DIFFRACTION	99.3
1.95-2.07	0.3276	163	0.2645	2657	X-RAY DIFFRACTION	99.44
2.07-2.23	0.2575	126	0.2332	2717	X-RAY DIFFRACTION	99.13
2.23-2.45	0.3017	134	0.2267	2702	X-RAY DIFFRACTION	99.23
2.45-2.81	0.268	161	0.2305	2727	X-RAY DIFFRACTION	99.48
2.81-3.54	0.2293	139	0.2012	2723	X-RAY DIFFRACTION	98.72
3.54-48.3	0.202	170	0.1649	2836	X-RAY DIFFRACTION	99.24

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	9.44646332464	1.04173437783	1.3798495634	2.19292427207	1.71815779435	2.27338644083	-0.158187367558	-0.0707225613874	0.541383778752	-0.870120228727	0.0987466620495	0.547508522681	-1.79630819939	0.180183770204	-0.0261416194718	0.533499237209	-0.0048993869254	0.0217450051724	0.372242937809	0.0768565990295	0.339420815844	13.2290554405	32.3518369247	-13.3584187363
2	8.67753131988	-3.67735782036	3.13413729331	6.01601556453	-6.56658595602	9.53699833514	0.515982649371	0.191237279866	-0.716146215742	-0.16199919803	-0.459495311618	-0.0417431249893	1.53602762461	0.725592592511	-0.117485156619	0.461081675069	0.0752987795185	-0.0139504305897	0.341559919297	-0.0290236693763	0.282448531446	11.9096482577	12.7498769008	-26.4081763337
3	7.6304340995	5.35801338061	5.24013599603	5.86609245154	4.92414873076	4.36523841852	-0.00411877257954	0.254586292363	-0.0799989450652	0.781238603668	0.0522722172047	-0.40945230508	0.00685122334584	0.414679862784	-0.0604617735392	0.406711210845	-0.00803707269294	-0.00256863360727	0.448980326264	0.0381978191186	0.251722883214	17.1911239005	25.6149931175	-16.8670704441
4	4.47248840455	0.200472334172	0.116173470943	7.08359788579	-1.61054397099	5.28087925223	-0.0104616969115	-0.384086232785	0.0404247061095	0.122166091682	0.157890457226	0.0693078342825	-0.548907481933	-0.0119880971495	-0.115291160692	0.279305375172	-0.00318037213748	0.0139833985102	0.374209136069	-0.0255917049475	0.211848464779	14.6989089711	25.8663189403	-6.85211638679
5	3.71422438383	4.06891611826	5.6645316073	5.43871769849	6.15941025186	9.64428450012	0.641362362111	-1.78892527595	0.958081644038	0.286145546765	-0.707633577334	0.481642306891	0.629991337787	-1.75327975272	0.0308368126734	0.333874893545	0.0100175507051	0.0312387522087	0.705235937947	-0.0810929600589	0.367836362135	-0.583039276683	17.0828056593	-11.4243513325
6	5.56451261768	-4.77313670538	-0.214392261465	7.4341240823	-2.73780184959	6.25944388775	0.88585923663	0.212999453401	-1.09393761847	0.173418812469	-0.192023593709	-0.291915616263	0.756035233769	-0.00466009284125	-0.685369363789	0.324224432984	0.0326982025874	-0.0311252810646	0.381552784437	-0.0355300426541	0.204603186417	14.1829012554	17.6144963257	-6.63025297369
7	8.68885513593	4.32453035493	1.92609623612	5.9634802629	1.96924752214	8.34281604406	0.394889782062	-0.480827378122	-0.372676488942	0.0380289133968	-0.168970194189	-0.2636632533	1.06067129925	0.622706556437	-0.282063978341	0.319708897485	0.118381718426	-0.0354465482266	0.429718560656	-0.00935923037547	0.302318008913	19.2233971829	14.8055447797	-8.5880448287
8	2.91007810191	3.32277542291	2.86520588252	9.81444435922	2.99772030479	6.9116179375	0.0764439839752	0.0728262541137	0.0405370670481	-0.344517072543	-0.173997701794	-0.831898763637	-0.333128499099	1.20289400313	0.0210867962846	0.328380299288	0.038825574464	0.0342213196984	0.602179292735	0.0125463044497	0.345496907996	21.4781010967	23.7439242905	-14.7198316294
9	4.09593490771	-4.34814641639	2.10399280946	5.35310660728	-0.324361497789	8.9196797832	0.16917000681	-1.10482603704	-1.07625742718	-0.536145035227	0.260047257297	0.88038348495	2.25724766339	-0.148850806752	-0.350223443145	0.731914912259	-0.00180218401538	-0.0562549543637	0.456283393175	0.0696564246448	0.436448588554	9.00017567515	9.60725652623	-19.7426604492
10	0.30141752966	-0.590818762226	1.29387123782	0.813099598178	-0.980250697878	4.30151259939	-0.0788678137353	-0.0912696292716	-0.131265200694	0.0181551118186	0.0574435173548	0.0109451974774	-0.115156019122	-0.287050505434	0.0702626644062	0.210955435057	0.00695201910637	0.0212364360921	0.425437209189	0.011520955463	0.304888354903	17.0905925463	18.1893846213	5.03270470062
11	2.86989329968	-2.49635464246	1.63371201892	3.55752275652	-3.21169032948	3.24027723982	-0.585662981717	0.140250688755	0.429271042031	0.212370994366	0.518926105091	-0.709135714005	-0.685995429017	-0.710617866619	0.0794439046421	0.403535433942	0.044290406855	0.00270243028	0.437876100262	0.0389536745314	0.301778600978	14.4243147119	24.6644632046	16.5936188959
12	5.94112919509	-2.89450308056	-0.31454356981	9.64970416437	2.97327187895	3.5599355245	0.19173570883	-0.248548982365	-1.15805519751	0.846044346398	-0.740630922233	0.707435990628	0.585745058551	-0.61614706517	0.512097841105	0.368863259089	-0.10799606028	0.0825200951545	0.439482510282	0.0516725736302	0.414405662649	14.4660307623	9.45613747993	18.1845946581
13	8.81863410389	-4.73422772043	3.07204095506	8.28173973269	-1.36014487138	6.47267184776	-0.206892291984	-0.220852690402	0.278060687606	0.181922883297	0.208198740814	0.182816852085	-0.578752093988	-0.779154759654	0.0219290163541	0.259681825892	0.0281816041969	0.0264050361983	0.4563603234	-0.0279741156721	0.261163119831	14.2301752563	20.8172842939	8.13225742071
14	4.43080503989	-3.62368458257	5.30445318978	3.47443001288	-3.53352021925	7.45458660896	0.655075036915	1.1859468995	0.400205803825	-0.263172574752	-0.741894380329	-0.440414400939	0.279512010672	0.664048341471	0.0458578019142	0.316837366822	-0.0373177819012	0.0555188601217	0.486245396911	-0.00465867549537	0.378117655229	21.3698545404	13.9080878423	5.7789466535
15	6.41173162834	-6.81079838483	3.95379553253	8.25331021548	-5.40087937205	7.62843991856	0.738715702599	0.624170578564	-0.772048820677	-1.02438997265	-0.27053079495	0.143256197707	0.909004049002	0.114617414902	-0.466454974332	0.368418834748	-0.0726156934491	0.00118290028303	0.485135391804	-0.183204101331	0.582740688247	12.0031719203	9.29344809599	2.12526121056
16	6.92646077412	-3.80637993706	-0.516143584061	9.83057470552	3.25862536776	6.34367619341	0.114783093	0.32020979385	-0.427189179601	0.482947325749	-0.385423081234	0.594854242226	0.177161866184	-1.16640847733	0.246591652085	0.290314607006	-0.0341360416834	0.0489367847465	0.535216851617	0.0146354211647	0.321914860497	7.14493146196	13.8955907549	12.3057036214
17	3.58628880102	-2.93956377659	0.448690341262	5.34960573225	-2.70830891257	4.87822673547	0.224419231768	0.206903643154	-0.653891832875	0.383867187077	-0.534952011695	0.539137520357	0.0982913316804	0.0251068866969	0.286727763312	0.206141386882	-0.0392316524781	0.0254886309415	0.405678355105	-0.0615302831765	0.399911253448	19.841058851	10.0273792474	11.64174642
18	3.03188119226	-0.373008720484	1.81197566314	1.04249585521	-2.06832318347	4.38406017415	-0.0232703285675	-0.185689811874	-0.0287371963189	-0.173304144603	0.114170903145	-0.071045159281	0.00102487587296	-0.449547133619	0.0578184077866	0.255717183991	0.0108737076645	-0.0138513211508	0.45825740041	0.0204654025605	0.285766245797	7.51280256091	21.9139032556	-15.4800255866

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 1 through 7 )	A	A	1 - 7	1 - 7
2	2	chain 'A' and (resid 8 through 17 )	A	A	8 - 17	8 - 17
3	3	chain 'A' and (resid 18 through 26 )	A	A	18 - 26	18 - 26
4	4	chain 'A' and (resid 27 through 39 )	A	A	27 - 39	27 - 39
5	5	chain 'A' and (resid 40 through 45 )	A	A	40 - 45	40 - 45
6	6	chain 'A' and (resid 46 through 52 )	A	A	46 - 52	46 - 52
7	7	chain 'A' and (resid 53 through 72 )	A	A	53 - 72	53 - 72
8	8	chain 'A' and (resid 73 through 82 )	A	A	73 - 82	73 - 82
9	9	chain 'A' and (resid 83 through 91 )	A	A	83 - 91	83 - 91
10	10	chain 'A' and (resid 92 through 113 )	A	A	92 - 113	92 - 113
11	11	chain 'B' and (resid 1 through 7 )	B	D	1 - 7	1 - 7
12	12	chain 'B' and (resid 8 through 26 )	B	D	8 - 26	8 - 26
13	13	chain 'B' and (resid 27 through 40 )	B	D	27 - 40	27 - 40
14	14	chain 'B' and (resid 41 through 52 )	B	D	41 - 52	41 - 52
15	15	chain 'B' and (resid 53 through 66 )	B	D	53 - 66	53 - 66
16	16	chain 'B' and (resid 67 through 82 )	B	D	67 - 82	67 - 82
17	17	chain 'B' and (resid 83 through 98 )	B	D	83 - 98	83 - 98
18	18	chain 'B' and (resid 99 through 113 )	B	D	99 - 113	99 - 113

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
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

Thousand views of thousand structures

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

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
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

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+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

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
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