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- PDB-5xez: Structure of the Full-length glucagon class B G protein-coupled r... -

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Basic information

Entry
Database: PDB / ID: 5xez
TitleStructure of the Full-length glucagon class B G protein-coupled receptor
Components
  • (Antibody, mAb1, ...) x 2
  • Glucagon receptor,Endolysin,Glucagon receptor
KeywordsSIGNALING PROTEIN / Human GCGR receptor / Class B / 7TM domain / membrane / LCP / XFEL
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 / viral release from host cell by cytolysis / cellular response to starvation / hormone-mediated signaling pathway / 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 / viral release from host cell by cytolysis / cellular response to starvation / hormone-mediated signaling pathway / guanyl-nucleotide exchange factor activity / peptidoglycan catabolic process / response to nutrient / 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 / cell wall macromolecule catabolic process / glucose homeostasis / lysozyme / lysozyme activity / G alpha (s) signalling events / G alpha (q) signalling events / host cell cytoplasm / cell surface receptor signaling pathway / endosome / defense response to bacterium / positive regulation of gene expression / membrane / plasma membrane
Similarity search - Function
GPCR, family 2, glucagon receptor / 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, glucagon receptor / 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. / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme-like domain superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-97V / Endolysin / Glucagon receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsZhang, H. / Qiao, A. / Yang, D. / Yang, L. / Dai, A. / de Graaf, C. / Reedtz-Runge, S. / Dharmarajan, V. / Zhang, H. / Han, G.W. ...Zhang, H. / Qiao, A. / Yang, D. / Yang, L. / Dai, A. / de Graaf, C. / Reedtz-Runge, S. / Dharmarajan, V. / Zhang, H. / Han, G.W. / Grant, T. / Sierra, R. / Weierstall, U. / Nelson, G. / Liu, W. / Wu, Y. / Ma, L. / Cai, X. / Lin, G. / Wu, X. / Geng, Z. / Dong, Y. / Song, G. / Griffin, P. / Lau, J. / Cherezov, V. / Yang, H. / Hanson, M. / Stevens, R. / Jiang, H. / Wang, M. / Zhao, Q. / Wu, B.
CitationJournal: Nature / Year: 2017
Title: Structure of the full-length glucagon class B G-protein-coupled receptor.
Authors: Zhang, H. / Qiao, A. / Yang, D. / Yang, L. / Dai, A. / de Graaf, C. / Reedtz-Runge, S. / Dharmarajan, V. / Zhang, H. / Han, G.W. / Grant, T.D. / Sierra, R.G. / Weierstall, U. / Nelson, G. / ...Authors: Zhang, H. / Qiao, A. / Yang, D. / Yang, L. / Dai, A. / de Graaf, C. / Reedtz-Runge, S. / Dharmarajan, V. / Zhang, H. / Han, G.W. / Grant, T.D. / Sierra, R.G. / Weierstall, U. / Nelson, G. / Liu, W. / Wu, Y. / Ma, L. / Cai, X. / Lin, G. / Wu, X. / Geng, Z. / Dong, Y. / Song, G. / Griffin, P.R. / Lau, J. / Cherezov, V. / Yang, H. / Hanson, M.A. / Stevens, R.C. / Zhao, Q. / Jiang, H. / Wang, M.W. / Wu, B.
History
DepositionApr 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucagon receptor,Endolysin,Glucagon receptor
B: Glucagon receptor,Endolysin,Glucagon receptor
C: Antibody, mAb1, heavy chain
D: Antibody, mAb1, light chain
H: Antibody, mAb1, heavy chain
L: Antibody, mAb1, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,98516
Polymers228,0526
Non-polymers3,93310
Water0
1
A: Glucagon receptor,Endolysin,Glucagon receptor
C: Antibody, mAb1, heavy chain
D: Antibody, mAb1, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,0948
Polymers114,0263
Non-polymers2,0685
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glucagon receptor,Endolysin,Glucagon receptor
H: Antibody, mAb1, heavy chain
L: Antibody, mAb1, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,8918
Polymers114,0263
Non-polymers1,8655
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.610, 245.330, 96.150
Angle α, β, γ (deg.)90.00, 90.01, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22H
13D
23L

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A27 - 575
2010B27 - 575
1020C215 - 445
2020H215 - 445
1030D1 - 214
2030L1 - 214

NCS ensembles :
ID
1
2
3

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Components

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Antibody , 2 types, 4 molecules CHDL

#2: Antibody Antibody, mAb1, heavy chain /


Mass: 24977.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Antibody Antibody, mAb1, light chain /


Mass: 23263.811 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)

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Protein / Non-polymers , 2 types, 4 molecules AB

#1: Protein Glucagon receptor,Endolysin,Glucagon receptor / GL-R / Lysis protein / Lysozyme / Muramidase / GL-R


Mass: 65784.070 Da / Num. of mol.: 2
Fragment: UNP RESIDUES 27-256,UNP RESIDUES 2-161,UNP RESIDUES 260-432
Mutation: C54T, C97A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: GCGR, e, T4Tp126 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P47871, UniProt: D9IEF7, lysozyme
#6: Chemical ChemComp-97V / 4-{[(4-cyclohexylphenyl){[3-(methylsulfonyl)phenyl]carbamoyl}amino]methyl}-N-(1H-tetrazol-5-yl)benzamide


Mass: 573.666 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H31N7O4S

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Sugars , 2 types, 8 molecules

#4: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 3.76 Å3/Da / Density % sol: 73.47 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 100mM HEPES, pH7.0, 300mM potassium phosphate monobasic, 25% PEG500DME, 100mM gly-gly-glycine

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.3 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Aug 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.501
11h,-k,-l20.499
ReflectionResolution: 3→50 Å / Num. obs: 67598 / % possible obs: 100 % / Redundancy: 198 % / Net I/σ(I): 4.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4L6R

4l6r


Resolution: 3→31.78 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.877 / SU B: 16.114 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.287 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24327 3311 4.9 %RANDOM
Rwork0.20953 ---
obs0.21123 63632 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 78.21 Å2
Baniso -1Baniso -2Baniso -3
1--5.16 Å20 Å2-4.17 Å2
2---8.98 Å2-0 Å2
3---14.14 Å2
Refinement stepCycle: 1 / Resolution: 3→31.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14804 0 264 0 15068
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01915459
X-RAY DIFFRACTIONr_bond_other_d0.0030.0214214
X-RAY DIFFRACTIONr_angle_refined_deg1.4141.96121051
X-RAY DIFFRACTIONr_angle_other_deg1.0933.00132618
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6351926
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.22423.635630
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.494152370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3281581
X-RAY DIFFRACTIONr_chiral_restr0.0740.22374
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217492
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023637
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5377.3987728
X-RAY DIFFRACTIONr_mcbond_other1.5367.3987727
X-RAY DIFFRACTIONr_mcangle_it2.76611.099646
X-RAY DIFFRACTIONr_mcangle_other2.76611.0919647
X-RAY DIFFRACTIONr_scbond_it1.1147.3757731
X-RAY DIFFRACTIONr_scbond_other1.1147.3757731
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.05511.05111406
X-RAY DIFFRACTIONr_long_range_B_refined4.64358.91816544
X-RAY DIFFRACTIONr_long_range_B_other4.64358.92116545
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A476360.12
12B476360.12
21C260600.04
22H260600.04
31D245680.02
32L245680.02
LS refinement shellResolution: 2.999→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 243 -
Rwork0.348 4636 -
obs--98.79 %
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)
10.0496-0.2049-0.02170.89090.09510.01310.0018-0.0044-0.0184-0.0177-0.00270.0561-0.01220.00580.00090.14680.0150.00810.0333-0.00160.023545.5063.77522.3363
20.051-0.2466-0.00911.38670.01190.04190.04590.01660.0032-0.1522-0.0744-0.12980.0131-0.03640.02850.1074-0.0076-0.01120.0386-0.00480.095341.534-121.7155-51.7952
30.06230.0072-0.02970.39260.19240.2579-0.009800.01050.07430.0099-0.0490.04020.0893-0.00010.02090.0108-0.01620.1066-0.00730.023968.8318-64.7005-28.5842
40.19010.00350.00460.20050.29770.4659-0.00170.0299-0.01070.0182-0.00450.0010.0020.02270.00620.0579-0.0075-0.01970.0573-0.00450.009652.8869-66.0296-36.1679
50.10210.05040.12140.3486-0.11080.2588-0.0087-0.03290.01810.0140.01110.0469-0.0157-0.0921-0.00240.01510.01910.00110.10420.00130.016121.4712-57.0794-76.7088
60.10030.0649-0.01090.1838-0.14850.28730.00260.00410.0176-0.0182-0.0111-0.02430.0046-0.05170.00850.03910.01420.00480.0621-0.00070.024537.5043-55.5903-84.1117
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 1161
2X-RAY DIFFRACTION2B24 - 1161
3X-RAY DIFFRACTION3C215 - 445
4X-RAY DIFFRACTION4D1 - 214
5X-RAY DIFFRACTION5H215 - 445
6X-RAY DIFFRACTION6L1 - 214

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