PDB-7qu8: ADGRG3/GPR97 Extracellular Region

ID or keywords:

Entry

Database: PDB / ID: 7qu8

Title

ADGRG3/GPR97 Extracellular Region

Components

Adhesion G protein-coupled receptor G3

Keywords

IMMUNE SYSTEM / aGPCR / GAIN domain / ADGRG family

Function / homology

Function and homology information

negative regulation of CREB transcription factor activity / negative regulation of non-canonical NF-kappaB signal transduction / specific granule membrane / regulation of cell migration / B cell differentiation / G protein-coupled receptor activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / heparin binding / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.37 Å

Authors

Zheng-Gerard, C. / Chu, T.Y. / El Omari, K. / Lin, H.H. / Seiradake, E.

Funding support

European Union, 2items

Citation

Journal: Nat Commun / Year: 2022
Title: GPR97-mediated PAR2 transactivation via a mPR3-associated macromolecular complex induces inflammatory activation of human neutrophils
Authors: Chu, T.Y. / Zheng-Gerard, C. / Huang, K.Y. / Chang, Y.C. / Chen, Y.W. / Yi, K.Y. / Lo, Y.L. / Chiang, N.Y. / Chen, H.Y. / Stacey, M. / Gordon, S. / Tseng, W.Y. / Sun, C.Y. / Wu, Y.M. / Pan, ...

History

Deposition	Jan 17, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 28, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	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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PDBx/mmCIF format	7qu8.cif.gz	196 KB	Display	PDBx/mmCIF format
PDB format	pdb7qu8.ent.gz	151.5 KB	Display	PDB format
PDBx/mmJSON format	7qu8.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7qu8_validation.pdf.gz	457.6 KB	Display	wwPDB validaton report
Full document	7qu8_full_validation.pdf.gz	471.4 KB	Display
Data in XML	7qu8_validation.xml.gz	18.4 KB	Display
Data in CIF	7qu8_validation.cif.gz	23.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qu/7qu8 ftp://data.pdbj.org/pub/pdb/validation_reports/qu/7qu8	HTTPS FTP

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Related structure data

Related structure data	5kvmS 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	#184 - Apr 2015 Glucagon similarity (4)

Deposited unit

A: Adhesion G protein-coupled receptor G3

B: Adhesion G protein-coupled receptor G3

C: Adhesion G protein-coupled receptor G3

D: Adhesion G protein-coupled receptor G3

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

1

A: Adhesion G protein-coupled receptor G3

C: Adhesion G protein-coupled receptor G3

defined by author&software
Evidence: gel filtration, Despite the autoproteolysis site between L249 and T250, the extracellular domain remains globular, and the 2 fragments remain non-covalently associated., native gel ...Evidence: gel filtration, Despite the autoproteolysis site between L249 and T250, the extracellular domain remains globular, and the 2 fragments remain non-covalently associated., native gel electrophoresis, SDS-PAGE showed a mixture of non-autoproteolysed and auto-proteolysed species.
60.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Adhesion G protein-coupled receptor G3

D: Adhesion G protein-coupled receptor G3

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

Unit cell

Length a, b, c (Å)	96.278, 96.278, 172.838
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2

Noncrystallographic symmetry (NCS)

NCS domain:

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

NCS domain segments:

End auth comp-ID: LEU / End label comp-ID: LEU

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	PRO	PRO	A	A	28 - 249	28 - 249
2	2	1	PRO	PRO	B	B	28 - 249	28 - 249
3	3	2	THR	THR	C	C	250 - 260	250 - 260
4	4	2	THR	THR	D	D	250 - 260	250 - 260

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4

#1: Protein	Adhesion G protein-coupled receptor G3 / G-protein coupled receptor 97 / G-protein coupled receptor PGR26 Mass: 30262.635 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ADGRG3, GPR97, PGR26 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q86Y34

#1: Protein

Adhesion G protein-coupled receptor G3 / G-protein coupled receptor 97 / G-protein coupled receptor PGR26

Mass: 30262.635 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: ADGRG3, GPR97, PGR26 / Cell line (production host): HEK293 / Production host:

Homo sapiens (human) / References: UniProt: Q86Y34

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Experiment

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

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Sample preparation

Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 1.8 M Ammonium citrate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 3.37→96.28 Å / Num. obs: 12030 / % possible obs: 99.7 % / Redundancy: 11.6 % / CC_1/2: 0.996 / R_merge(I) obs: 0.027 / R_pim(I) all: 0.083 / R_rim(I) all: 0.028 / Net I/σ(I): 6.5
Reflection shell	Resolution: 3.37→3.64 Å / Redundancy: 12.2 % / R_merge(I) obs: 0.123 / Num. unique obs: 2398 / CC_1/2: 0.521 / R_pim(I) all: 0.036 / R_rim(I) all: 0.129 / % possible all: 99.4

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Processing

Software

Name	Version	Classification
DIALS		data reduction
Aimless		data scaling
PHASER		phasing
BUSTER	2.10.3	refinement
REFMAC	5.8.0267	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5KVM

5kvm

Resolution: 3.37→84.109 Å / Cor.coef. F_o:F_c: 0.899 / Cor.coef. F_o:F_c free: 0.86 / WR_factor R_free: 0.305 / WR_factor R_work: 0.261 / SU B: 85.976 / SU ML: 0.577 / Average fsc free: 0.8152 / Average fsc work: 0.8234 / Cross valid method: THROUGHOUT / ESU R Free: 0.628 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.313	1040	8.662 %	RANDOM
R_work	0.2659	10967	-	-
all	0.27	-	-	-
obs	-	12007	99.371 %	-

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: 134.326 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.001 Å²	-0 Å²	-0 Å²
2-	-	0.001 Å²	-0 Å²
3-	-	-	-0.002 Å²

Refinement step

Cycle: LAST / Resolution: 3.37→84.109 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3640	0	0	0	3640

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.012	3726
X-RAY DIFFRACTION	r_angle_refined_deg	1.229	1.644	5060
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.08	5	462
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.7	21.875	192
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.208	15	634
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.827	15	28
X-RAY DIFFRACTION	r_chiral_restr	0.086	0.2	476
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	2802
X-RAY DIFFRACTION	r_nbd_refined	0.238	0.2	1459
X-RAY DIFFRACTION	r_nbtor_refined	0.301	0.2	2512
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.156	0.2	61
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.313	0.2	44
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.237	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	4.303	8.509	1860
X-RAY DIFFRACTION	r_mcangle_it	7.642	12.761	2318
X-RAY DIFFRACTION	r_scbond_it	3.779	8.76	1865
X-RAY DIFFRACTION	r_scangle_it	6.547	12.96	2741
X-RAY DIFFRACTION	r_lrange_it	15.999	155.358	13767
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.039	0.05	6595
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.019	0.05	227

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	0.03939	0.05011
1	2	B	X-RAY DIFFRACTION	Local ncs	0.03939	0.05011
2	3	C	X-RAY DIFFRACTION	Local ncs	0.01936	0.05009
2	4	D	X-RAY DIFFRACTION	Local ncs	0.01936	0.05009

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
3.37-3.457	0.433	55	0.405	806	0.407	873	0.453	0.49	98.6254	0.402
3.457-3.552	0.35	70	0.371	772	0.369	848	0.535	0.438	99.2924	0.369
3.552-3.655	0.351	73	0.343	734	0.344	815	0.677	0.693	99.0184	0.339
3.655-3.767	0.376	84	0.311	712	0.317	804	0.768	0.82	99.005	0.307
3.767-3.89	0.333	63	0.272	710	0.277	777	0.811	0.862	99.4852	0.264
3.89-4.027	0.293	64	0.271	697	0.272	767	0.873	0.886	99.2177	0.257
4.027-4.178	0.294	71	0.231	653	0.237	726	0.878	0.905	99.7245	0.218
4.178-4.348	0.233	74	0.221	609	0.222	689	0.935	0.934	99.1292	0.209
4.348-4.541	0.274	65	0.206	630	0.212	698	0.901	0.929	99.5702	0.193
4.541-4.762	0.289	55	0.209	584	0.215	643	0.895	0.936	99.3779	0.195
4.762-5.019	0.231	61	0.206	566	0.208	631	0.93	0.939	99.3661	0.193
5.019-5.322	0.253	45	0.225	535	0.228	582	0.932	0.928	99.6564	0.21
5.322-5.688	0.299	47	0.288	518	0.289	566	0.885	0.89	99.8233	0.278
5.688-6.141	0.389	44	0.303	476	0.31	522	0.817	0.86	99.6169	0.285
6.141-6.724	0.435	38	0.269	443	0.281	482	0.85	0.901	99.7925	0.259
6.724-7.512	0.365	43	0.279	408	0.287	453	0.87	0.905	99.5585	0.272
7.512-8.662	0.335	25	0.229	378	0.235	404	0.91	0.938	99.7525	0.236
8.662-10.581	0.218	30	0.223	312	0.222	342	0.95	0.955	100	0.23
10.581-14.846	0.417	16	0.274	259	0.282	277	0.87	0.915	99.278	0.278
14.846-84.109	0.381	17	0.432	165	0.427	184	0.837	0.768	98.913	0.551

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	2.6525	3.9973	-0.7977	8.0212	0.8247	3.1349	-0.1611	0.2476	-0.0372	0.1056	0.0958	0.1061	-0.0087	-0.1509	0.0653	0.3352	0.0116	0.0923	0.5135	-0.026	0.0289	-53.3378	-25.1809	-1.347
2	6.9903	0.3845	-0.4535	0.707	-0.2969	3.1813	0.3006	-0.0169	-0.1703	-0.1151	-0.4115	0.0666	0.0297	0.0584	0.111	0.4955	0.0174	0.05	0.4877	0.1098	0.15	-25.7694	-11.0109	-16.8311
3	0.6619	-1.5698	-1.3369	3.7447	3.173	2.7084	-0.214	-0.0068	-0.1726	0.3392	-0.098	0.4223	0.2926	0.0691	0.312	0.5083	-0.0512	0.1008	0.7652	0.132	0.2386	-41.1695	-22.0317	1.7882
4	1.6585	-2.964	2.0076	6.2806	-5.162	4.9922	0.1431	0.3427	-0.0333	-0.2744	0.1676	0.1449	-0.0706	-0.918	-0.3107	0.7906	0.1	0.1979	0.8229	-0.0321	0.3321	-35.0205	-19.5168	-19.9943

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	{A\|28 - 249}	A	28 - 249
2	X-RAY DIFFRACTION	2	ALL	{B\|28 - 249}	B	28 - 249
3	X-RAY DIFFRACTION	3	ALL	{C\|250 - 260}	C	250 - 260
4	X-RAY DIFFRACTION	4	ALL	{D\|250 - 260}	D	250 - 260

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