PDB-4ers: A Molecular Basis for Negative Regulation of the Glucagon Receptor

ID or keywords:

Entry

Database: PDB / ID: 4ers

Title

A Molecular Basis for Negative Regulation of the Glucagon Receptor

Components

Fab heavy chain
Fab light chain
Glucagon receptor

Keywords

IMMUNE SYSTEM / Glucagon receptor / Class-B GPCR / Fab / Glycosylation / Extra-cellular

Function / homology

Function and homology information

regulation of glycogen metabolic process / glucagon receptor activity / cellular response to glucagon stimulus / exocytosis / response to starvation / peptide hormone binding / cellular response to starvation / hormone-mediated signaling pathway / response to nutrient / guanyl-nucleotide exchange factor activity ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.637 Å

Authors

Murray, J.M. / Koth, C.M. / Mukund, S.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Molecular basis for negative regulation of the glucagon receptor.
Authors: Koth, C.M. / Murray, J.M. / Mukund, S. / Madjidi, A. / Minn, A. / Clarke, H.J. / Wong, T. / Chiang, V. / Luis, E. / Estevez, A. / Rondon, J. / Zhang, Y. / Hotzel, I. / Allan, B.B.

History

Deposition	Apr 20, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 29, 2012	Provider: repository / Type: Initial release
Revision 1.1	Oct 17, 2012	Group: Database references
Revision 1.2	Dec 5, 2012	Group: Derived calculations
Revision 1.3	Jul 29, 2020	Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id Description: Carbohydrate remediation / Provider: repository / Type: Remediation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ers.cif.gz	119 KB	Display	PDBx/mmCIF format
PDB format	pdb4ers.ent.gz	94.8 KB	Display	PDB format
PDBx/mmJSON format	4ers.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4ers_validation.pdf.gz	472 KB	Display	wwPDB validaton report
Full document	4ers_full_validation.pdf.gz	487.9 KB	Display
Data in XML	4ers_validation.xml.gz	23.5 KB	Display
Data in CIF	4ers_validation.cif.gz	31.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/er/4ers ftp://data.pdbj.org/pub/pdb/validation_reports/er/4ers	HTTPS FTP

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Related structure data

Similar structure data	1yqv-d 4lf3-1 4lf3-2 5bvp-d 5w1m-3 7jtg-d 5vyf-1 3q1s-d 1lk3-2 1wej-2 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	#184 - Apr 2015 Glucagon similarity (18) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #202 - Oct 2016 Dipeptidyl Peptidase 4 similarity (2)

Deposited unit

L: Fab light chain

H: Fab heavy chain

A: Glucagon receptor

hetero molecules

60.1 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Glucagon receptor

hetero molecules

L: Fab light chain

H: Fab heavy chain

defined by author
60.1 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	46.410, 62.250, 104.940
Angle α, β, γ (deg.)	90.000, 93.910, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Antibody

Fab light chain

Mass: 23263.811 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Production host:

Escherichia coli (E. coli)

#2: Antibody

Fab heavy chain

Mass: 24977.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Production host:

Escherichia coli (E. coli)

#3: Protein

Glucagon receptor / GL-R

Mass: 11420.034 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: GCGR / Production host:

Spodoptera frugiperda (fall armyworm) / References: UniProt: P47871

#4: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.53 Å³/Da / Density % sol: 51.48 %
Crystal grow	Method: vapor diffusion / pH: 8.5 Details: 0.1M Tris pH 8.5, 0.2M sodium chloride, 25% (w/v) PEG3350, VAPOR DIFFUSION

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 5.0.1 / Wavelength: 0.9774 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 1, 2010

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9774 Å / Relative weight: 1

Reflection

Resolution: 2.637→43.468 Å / Num. all: 17586 / Num. obs: 17586 / % possible obs: 99.3 % / Redundancy: 3.9 % / B_iso Wilson estimate: 33 Å² / R_sym value: 0.108 / Net I/σ(I): 14.4

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
2.64-2.79	3.8	0.391	1.9	9473	2503	0.391	97.3
2.79-2.96	3.8	0.287	2.6	9065	2410	0.287	98.6
2.96-3.16	3.9	0.2	3.6	8677	2253	0.2	99.4
3.16-3.41	3.9	0.151	4.7	8335	2118	0.151	99.7
3.41-3.74	4	0.107	6.4	7751	1958	0.107	100
3.74-4.18	3.8	0.084	8	6882	1791	0.084	99.9
4.18-4.83	3.7	0.06	11	5736	1566	0.06	100
4.83-5.91	4.2	0.063	9.9	5613	1344	0.063	100
5.91-8.36	4.2	0.058	11.1	4396	1042	0.058	100
8.36-43.468	3.9	0.044	13.1	2339	601	0.044	99.4

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
SCALA	3.3.16	data scaling
PHASER		phasing
PHENIX	1.7.1_743	refinement
PDB_EXTRACT	3.11	data extraction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.637→43.456 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.87 / σ(F): 1.37 / Phase error: 27.19 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2785	895	5.09 %
R_work	0.2311	-	-
obs	0.2335	17571	98.5 %
all	-	17586	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 42.789 Å² / k_sol: 0.372 e/Å³

Displacement parameters

B_iso max: 166.33 Å² / B_iso mean: 42.9567 Å² / B_iso min: 10.28 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.0246 Å²	0 Å²	4.7291 Å²
2-	-	0.5634 Å²	-0 Å²
3-	-	-	-12.0717 Å²

Refinement step

Cycle: LAST / Resolution: 2.637→43.456 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4181	0	28	76	4285

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	4294
X-RAY DIFFRACTION	f_angle_d	0.664	5833
X-RAY DIFFRACTION	f_chiral_restr	0.048	635
X-RAY DIFFRACTION	f_plane_restr	0.005	752
X-RAY DIFFRACTION	f_dihedral_angle_d	13.506	1534

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.637-2.8023	0.3493	156	0.3005	2586	2742	93
2.8023-3.0186	0.3787	150	0.2686	2760	2910	99
3.0186-3.3223	0.2999	141	0.2408	2809	2950	100
3.3223-3.8028	0.2586	144	0.227	2811	2955	100
3.8028-4.7901	0.2596	152	0.1958	2824	2976	100
4.7901-43.4618	0.2334	152	0.2263	2886	3038	100

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	0.4806	0.2524	0.0503	0.6314	-0.1175	0.5424	-0.3251	-0.8691	-0.9243	0.3312	0.2486	0.0859	0.1196	0.1159	0.4851	0.2463	0.1554	0.1361	0.5844	0.3056	0.5444	23.3552	-501.1977	72.6974
2	0.0323	0.2873	-0.1531	2.5014	-1.3724	1.164	-0.0773	-0.1509	-0.2949	0.2197	-0.2231	0.0531	0.0348	0.0533	-0.5437	0.7537	-0.3325	0.4615	0.2195	-0.0265	0.6914	3.3764	-512.5104	77.0415
3	2.0535	-0.0639	-0.8973	0.1273	0.1199	1.507	-0.0681	-0.6355	-0.1713	0.2057	-0.0011	-0.1058	0.4487	0.357	-0.0517	0.1755	0.04	0.0267	0.199	-0.02	0.1597	11.1575	-495.7564	75.6066
4	0.609	-0.0971	-0.392	0.7346	-0.4648	0.6423	-0.0297	0.1426	0.1029	-0.1357	0.1162	0.1178	0.1518	-0.2418	0.0113	0.7411	-0.4221	0.3461	0.2662	0.0739	0.2014	0.2749	-504.2808	67.2701
5	0.3367	-0.1063	0.0354	0.1593	0.1344	0.1938	-0.0288	0.2162	-0.0292	0.0005	0.1711	0.0466	0.0357	-0.081	0.2486	0.0357	-0.1708	0.0132	0.0688	0.0643	0.2367	8.4963	-492.484	66.3488
6	0.4877	0.0986	-0.1283	0.5523	0.2964	0.3507	0.0765	-0.3209	0.2325	-0.4544	0.1625	0.0234	-0.6306	0.3414	0.0638	0.2612	-0.2928	0.0419	0.1842	-0.0936	0.2408	6.7144	-488.3222	37.1559
7	0.6539	-0.2218	-0.1453	0.5057	0.4589	0.4154	0.1664	-0.1284	-0.2926	-0.3598	0.5182	0.1656	0.2119	-0.4603	-0.1389	0.4721	-0.1435	-0.0753	0.3742	0.12	0.2968	-0.8069	-486.9708	15.8124
8	0.9296	0.9163	-0.0066	2.8209	0.4472	0.4654	-0.2751	-0.0333	-0.0378	-0.6936	0.2512	0.3293	-0.323	-0.3405	-0.0827	0.5012	-0.0606	-0.0814	0.1856	0.0709	0.3007	-11.7899	-503.9777	8.704
9	1.3476	0.7262	0.209	0.8442	0.5693	0.9622	0.2944	0.2654	0.2095	-0.6131	0.1278	0.5664	0.0642	-0.0621	0.143	0.5665	-0.0341	-0.3519	0.2971	0.1545	0.3333	-14.8855	-502.1911	9.4377
10	2.6238	0.7016	0.7113	1.571	0.2703	1.8992	-0.0321	-0.0188	-0.4507	-0.0393	-0.0493	-0.128	0.1119	0.2668	-0.1249	0.1641	0.0683	0.0255	0.1072	0.0379	0.0766	8.4976	-515.4814	36.5769
11	0.4899	-0.2769	0.2835	0.4152	-0.0206	0.6961	-0.0794	0.0921	-0.0098	0.127	0.1494	-0.2928	0.1448	0.2165	-0.039	0.1755	-0.0582	-0.0066	0.3656	-0.1155	0.2058	17.2706	-510.4653	44.8143
12	0.4721	0.3941	0.0944	1.5724	-0.1364	0.8947	-0.1264	0.0329	0.2325	-0.0105	0.0425	0.1416	0.0023	-0.1485	-0.003	0.0591	-0.0049	0.0513	0.1673	-0.0385	0.0905	6.2289	-508.6745	45.8106
13	0.5335	0.3714	0.4431	0.9656	-0.0702	0.4832	-0.2021	0.1041	-0.1504	-0.4422	0.0192	-0.1565	-0.0873	0.0545	0.0263	-0.0152	-0.0067	-0.0172	0.1749	0.0083	0.1058	8.6095	-504.5276	42.5512
14	1.6818	0.7143	0.0484	3.8424	-1.9863	1.5731	0.0254	0.63	0.5137	-0.3376	0.4403	0.5695	-0.3541	-0.4463	-0.0591	0.8783	-0.0019	0.0651	0.6186	0.2005	0.3382	-7.8053	-507.69	-1.5622
15	0.6078	0.3077	-0.4139	1.1682	-0.508	1.2718	-0.2071	0.1477	-0.06	-1.2342	-0.0029	-0.2225	-0.0109	0.4073	-0.0334	0.6424	-0.0884	0.1535	0.2115	0.0086	0.2517	0.2765	-511.3546	7.7839

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'C' and (resseq 28:49)	C	28 - 49
2	X-RAY DIFFRACTION	2	chain 'C' and (resseq 50:59)	C	50 - 59
3	X-RAY DIFFRACTION	3	chain 'C' and (resseq 60:99)	C	60 - 99
4	X-RAY DIFFRACTION	4	chain 'C' and (resseq 100:109)	C	100 - 109
5	X-RAY DIFFRACTION	5	chain 'C' and (resseq 110:123)	C	110 - 123
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 1:102)	A	1 - 102
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 103:113)	A	103 - 113
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 114:150)	A	114 - 150
9	X-RAY DIFFRACTION	9	chain 'A' and (resseq 151:214)	A	151 - 214
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 215:231)	B - A	215 - 231
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 232:246)	B - A	232 - 246
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 247:317)	B - A	247 - 317
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 318:348)	B - A	318 - 348
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 349:363)	B - A	349 - 363
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 364:445)	B - A	364 - 445

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