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- PDB-4lf3: Inhibitory Mechanism of an Allosteric Antibody Targeting the Gluc... -

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Basic information

Entry
Database: PDB / ID: 4lf3
TitleInhibitory Mechanism of an Allosteric Antibody Targeting the Glucagon Receptor
Components
  • Fab heavy chainFragment antigen-binding
  • Fab light chainFragment antigen-binding
  • Glucagon receptor
KeywordsIMMUNE SYSTEM / Fab fragment / GCGR
Function / homology
Function and homology information


regulation of glycogen metabolic process / glucagon receptor activity / response to starvation / cellular response to glucagon stimulus / exocytosis / peptide hormone binding / cellular response to starvation / hormone-mediated signaling pathway / response to nutrient / guanyl-nucleotide exchange factor activity ...regulation of glycogen metabolic process / glucagon receptor activity / response to starvation / cellular response to glucagon stimulus / exocytosis / peptide hormone binding / cellular response to starvation / hormone-mediated signaling pathway / response to nutrient / guanyl-nucleotide exchange factor activity / generation of precursor metabolites and energy / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / Glucagon signaling in metabolic regulation / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Glucagon-type ligand receptors / regulation of blood pressure / glucose homeostasis / G alpha (s) signalling events / G alpha (q) signalling events / cell surface receptor signaling pathway / endosome / positive regulation of gene expression / membrane / plasma membrane
Similarity search - Function
GPCR, family 2, extracellular hormone receptor domain / GPCR, family 2, glucagon receptor / Hormone receptor fold / GPCR, family 2, glucagon-like peptide-1/glucagon receptor / G-protein coupled receptors family 2 signature 1. / Hormone receptor domain / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / GPCR family 2, extracellular hormone receptor domain superfamily ...GPCR, family 2, extracellular hormone receptor domain / GPCR, family 2, glucagon receptor / Hormone receptor fold / GPCR, family 2, glucagon-like peptide-1/glucagon receptor / G-protein coupled receptors family 2 signature 1. / Hormone receptor domain / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / GPCR family 2, extracellular hormone receptor domain superfamily / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / Few Secondary Structures / Irregular / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.735 Å
AuthorsMurray, J.M. / Mukund, S.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Inhibitory mechanism of an allosteric antibody targeting the glucagon receptor.
Authors: Mukund, S. / Shang, Y. / Clarke, H.J. / Madjidi, A. / Corn, J.E. / Kates, L. / Kolumam, G. / Chiang, V. / Luis, E. / Murray, J. / Zhang, Y. / Hotzel, I. / Koth, C.M. / Allan, B.B.
History
DepositionJun 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2Jan 1, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fab heavy chain
B: Fab light chain
C: Glucagon receptor
D: Fab heavy chain
E: Fab light chain
F: Glucagon receptor


Theoretical massNumber of molelcules
Total (without water)119,2316
Polymers119,2316
Non-polymers00
Water1,838102
1
A: Fab heavy chain
B: Fab light chain
C: Glucagon receptor


Theoretical massNumber of molelcules
Total (without water)59,6163
Polymers59,6163
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Fab heavy chain
E: Fab light chain
F: Glucagon receptor


Theoretical massNumber of molelcules
Total (without water)59,6163
Polymers59,6163
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.928, 62.777, 116.432
Angle α, β, γ (deg.)90.000, 106.040, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.858691, -0.005308, 0.512467), (-0.004429, -0.999986, -0.002935), (0.512475, 0.000251, -0.858702)-14.9113, -28.5179, 56.242802
2given(0.859228, -0.001551, 0.51159), (-0.008335, -0.999905, 0.010968), (0.511524, -0.013688, -0.85916)-14.7913, -29.1805, 55.934299
3given(0.855034, 0.011903, 0.518435), (0.005818, -0.999894, 0.013362), (0.518539, -0.008408, -0.855012)-14.8813, -29.0529, 55.9174

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Components

#1: Antibody Fab heavy chain / Fragment antigen-binding


Mass: 23263.811 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Anti GCGR mAb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#2: Antibody Fab light chain / Fragment antigen-binding


Mass: 25000.998 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Anti GCGR mAb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#3: Protein Glucagon receptor / / GL-R


Mass: 11350.929 Da / Num. of mol.: 2 / Fragment: GCGR ECD (UNP residues 29-123) / Mutation: G40S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GCGR / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P47871
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.21 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl, 0.2 M NaCl, PEG3350, pH 8.5, vapor diffusion, hanging drop, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: ADSC / Detector: CCD / Date: Apr 25, 2011
RadiationProtocol: SINGLE / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.735→55.95 Å / Num. all: 35933 / Num. obs: 35933 / % possible obs: 92.6 % / Redundancy: 2.9 % / Rsym value: 0.066 / Net I/σ(I): 12.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.735-2.882.60.3672.11366251740.36792.4
2.88-3.0630.2383.31517051290.23895.8
3.06-3.2730.1594.91427447710.15995.3
3.27-3.5330.09681299443980.09694
3.53-3.872.90.07110.81137439730.07192.8
3.87-4.322.70.04715.7952434850.04789.6
4.32-4.993.10.03420.9969631640.03491.2
4.99-6.123.10.03418.5826026780.03490.3
6.12-8.652.90.03121.5573820000.03188.4
8.65-55.953.20.02227.1372611610.02288.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 41.76
Highest resolutionLowest resolution
Rotation2.73 Å55.95 Å
Translation2.73 Å55.95 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
PHASER2.1.4phasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4ERS

4ers


Resolution: 2.735→55.95 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 1.02 / Cross valid method: Random / σ(F): 1.35 / Phase error: 26.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2635 1788 4.98 %
Rwork0.2088 --
obs0.2116 35910 92.16 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.147 Å2 / ksol: 0.363 e/Å3
Displacement parametersBiso max: 172.47 Å2 / Biso mean: 52.4367 Å2 / Biso min: 4.97 Å2
Baniso -1Baniso -2Baniso -3
1-2.0451 Å2-0 Å2-4.5211 Å2
2---5.59 Å20 Å2
3---3.5449 Å2
Refinement stepCycle: LAST / Resolution: 2.735→55.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8368 0 0 102 8470
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018586
X-RAY DIFFRACTIONf_angle_d1.53811655
X-RAY DIFFRACTIONf_chiral_restr0.0921264
X-RAY DIFFRACTIONf_plane_restr0.0091499
X-RAY DIFFRACTIONf_dihedral_angle_d16.2343077
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.735-2.80870.44071440.35742520266490
2.8087-2.89140.4351250.33472673279894
2.8914-2.98470.31831450.26052705285095
2.9847-3.09130.29561310.23422683281496
3.0913-3.21510.31061330.22112711284495
3.2151-3.36140.27261500.22122647279795
3.3614-3.53860.27291390.22052662280193
3.5386-3.76030.25231490.21622615276493
3.7603-4.05050.25531260.19512556268289
4.0505-4.4580.20771380.16532589272790
4.458-5.10270.21761370.15692595273291
5.1027-6.42740.24591340.19612582271690
6.4274-55.96130.22931370.19182584272187
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
11.05340.065-0.12571.02160.16020.6468-0.03760.05110.26230.0425-0.0506-0.2421-0.25020.08290.02610.3051-0.0619-0.06050.0860.04520.143210.314710.266311.8661
21.10730.07470.20850.9250.20740.609-0.0042-0.12650.09290.26170.072-0.1445-0.22510.01830.0260.49920.0244-0.09840.0943-0.1080.20578.44668.003818.382
31.9011-0.11990.35880.2652-0.46040.8102-0.25090.1788-0.16470.03220.3182-0.8864-0.0404-0.18350.07870.4451-0.1632-0.16190.3901-0.08280.493731.78869.871718.9562
40.7042-0.51920.02962.75750.87391.3294-0.10630.2459-0.0145-0.42550.0633-0.4284-0.05750.4930.13890.4874-0.21640.14680.6128-0.13290.789442.8976-7.361112.4502
51.2945-0.34090.00352.207-0.12071.3025-0.16110.3762-0.399-0.5210.1099-0.90570.01990.24040.04580.5676-0.32850.13770.6467-0.09620.647943.7195-5.53519.4414
62.1899-0.1097-0.11461.0162-0.24341.34850.3054-0.2497-0.0146-0.07330.0331-0.33780.0556-0.14570.04940.3823-0.0985-0.02240.10730.06990.14758.6462-17.909717.7933
70.94270.16010.95391.5983-0.07380.99660.0871-0.06960.0381-0.07820.05030.0504-0.1087-0.14150.03070.2841-0.04140.03550.03050.0633-0.09311.4929-12.310312.9121
80.8030.21970.49230.7509-0.07180.99830.0323-0.2191-0.11380.23140.101-0.4521-0.07130.1992-0.09270.2445-0.024-0.08760.1684-0.05350.251228.9064-11.996621.1241
92.73411.14111.03321.9448-0.4461.46080.0943-0.75-0.25070.682-0.37760.37070.2302-0.54650.00590.4872-0.10940.19630.66170.18570.4526-29.9805-4.436714.6247
102.29680.53450.97731.527-0.12863.30390.0494-0.175-0.4258-0.12880.03610.4873-0.0266-0.4739-0.0880.28510.01360.04460.18420.02790.3045-23.861-2.00010.7323
111.18-0.09840.24490.9066-0.26420.6180.0126-0.0528-0.30080.1306-0.0116-0.23320.111-0.07560.01160.1138-0.02430.05690.12040.00980.1888-1.2475-38.972751.1355
120.871-0.52630.40130.6339-0.13290.52660.10060.0971-0.2143-0.1324-0.063-0.12750.10730.08940.01550.08310.01840.05520.0298-0.03860.21180.5356-36.781844.5604
131.6777-0.3629-0.45230.2085-0.14660.5784-0.0582-0.1347-0.0794-0.03180.1081-0.5957-0.0334-0.1599-0.33220.11910.07240.07290.21850.09070.426320.7784-39.072556.0265
140.0033-0.07260.03811.2231-0.56290.3749-0.0263-0.16130.00350.1903-0.1883-0.6565-0.2210.06830.2540.16710.0978-0.15880.24110.07560.470727.0539-21.45467.0659
151.29040.10260.32381.87830.02241.0755-0.0621-0.20470.05010.4804-0.0326-0.3604-0.09250.1186-0.00150.28690.144-0.18020.37040.07760.436326.2408-23.269870.072
160.99770.4970.44720.9268-0.02591.90840.09240.08930.10340.02820.1259-0.3751-0.04260.0137-0.05720.06440.00570.05670.11640.11050.17280.5641-10.832245.1964
170.8381-0.1714-0.45551.2809-0.31810.90560.19070.18630.175-0.2225-0.03250.1558-0.0632-0.04710.11880.14980.05690.07990.18670.06650.1791-6.4382-17.355839.6304
181.629-0.2752-0.40832.13620.45250.2742-0.03630.01840.05610.0026-0.0111-0.0116-0.0159-0.1435-0.01240.08020.01080.07540.10130.07370.1371-8.6207-16.057447.7578
191.26460.5874-0.02850.96530.31670.4481-0.00840.22870.0118-0.08460.0194-0.18410.03040.1342-0.05440.10840.04440.04750.1580.03210.11043.4082-21.143547.9345
201.7145-0.2167-0.32911.83010.09880.8618-0.07920.03970.0598-0.1087-0.0522-0.53670.09580.18740.04180.04720.03690.13210.2201-0.01870.483228.6937-14.315755.0711
212.9375-0.52570.00533.99880.26111.41740.46480.72520.1045-1.14790.0464-0.2652-0.5387-0.25280.13160.5938-0.0189-0.22370.87230.20310.4762-34.7314-24.025928.1382
222.38540.0627-0.87121.4012-0.40491.7302-0.18670.3930.2711-0.09660.0890.5506-0.02-0.44440.06450.1832-0.0068-0.030.20730.00940.3063-36.1744-26.800442.8006
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1:38)A1 - 38
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 39:102)A39 - 102
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 103:113)A103 - 113
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 114:150)A114 - 150
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 151:214)A151 - 214
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 215:231)B215 - 231
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 232:313)B232 - 313
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 314:445)B314 - 445
9X-RAY DIFFRACTION9CHAIN C AND (RESSEQ 29:47)C29 - 47
10X-RAY DIFFRACTION10CHAIN C AND (RESSEQ 48:123)C48 - 123
11X-RAY DIFFRACTION11CHAIN D AND (RESSEQ 1:38)D1 - 38
12X-RAY DIFFRACTION12CHAIN D AND (RESSEQ 39:102)D39 - 102
13X-RAY DIFFRACTION13CHAIN D AND (RESSEQ 103:113)D103 - 113
14X-RAY DIFFRACTION14CHAIN D AND (RESSEQ 114:150)D114 - 150
15X-RAY DIFFRACTION15CHAIN D AND (RESSEQ 151:214)D151 - 214
16X-RAY DIFFRACTION16CHAIN E AND (RESSEQ 215:231)E215 - 231
17X-RAY DIFFRACTION17CHAIN E AND (RESSEQ 232:253)E232 - 253
18X-RAY DIFFRACTION18CHAIN E AND (RESSEQ 254:313)E254 - 313
19X-RAY DIFFRACTION19CHAIN E AND (RESSEQ 314:363)E314 - 363
20X-RAY DIFFRACTION20CHAIN E AND (RESSEQ 364:445)E364 - 445
21X-RAY DIFFRACTION21CHAIN F AND (RESSEQ 30:47)F30 - 47
22X-RAY DIFFRACTION22CHAIN F AND (RESSEQ 48:123)F48 - 123

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