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- PDB-4l6r: Structure of the class B human glucagon G protein coupled receptor -

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Basic information

Entry
Database: PDB / ID: 4l6r
TitleStructure of the class B human glucagon G protein coupled receptor
ComponentsSoluble cytochrome b562 and Glucagon receptor chimera
KeywordsMEMBRANE PROTEIN / Human glucagon receptor / diabetes / GPCR network / PSI-Biology / novel protein engineering / Structural Genomics / Protein Structure Initiative / GPCR / membrane
Function / homology
Function and homology information


regulation of glycogen metabolic process / glucagon receptor activity / response to starvation / peptide hormone binding / response to nutrient / cellular response to glucagon stimulus / guanyl-nucleotide exchange factor activity / cellular response to starvation / generation of precursor metabolites and energy / electron transport chain ...regulation of glycogen metabolic process / glucagon receptor activity / response to starvation / peptide hormone binding / response to nutrient / cellular response to glucagon stimulus / guanyl-nucleotide exchange factor activity / cellular response to starvation / generation of precursor metabolites and energy / electron transport chain / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / regulation of blood pressure / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Glucagon signaling in metabolic regulation / Glucagon-type ligand receptors / glucose homeostasis / G alpha (s) signalling events / G alpha (q) signalling events / periplasmic space / electron transfer activity / cell surface receptor signaling pathway / iron ion binding / heme binding / 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 / Cytochrome c/b562 / G-protein coupled receptors family 2 signature 1. / : / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / Hormone receptor domain / GPCR family 2, extracellular hormone receptor domain superfamily ...GPCR, family 2, glucagon receptor / GPCR, family 2, glucagon-like peptide-1/glucagon receptor / Cytochrome c/b562 / G-protein coupled receptors family 2 signature 1. / : / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / Hormone receptor domain / 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. / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Soluble cytochrome b562 / Glucagon receptor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsSiu, F.Y. / He, M. / de Graaf, C. / Han, G.W. / Yang, D. / Zhang, Z. / Zhou, C. / Xu, Q. / Wacker, D. / Joseph, J.S. ...Siu, F.Y. / He, M. / de Graaf, C. / Han, G.W. / Yang, D. / Zhang, Z. / Zhou, C. / Xu, Q. / Wacker, D. / Joseph, J.S. / Liu, W. / Lau, J. / Cherezov, V. / Katritch, V. / Wang, M.W. / Stevens, R.C. / GPCR Network (GPCR)
CitationJournal: Nature / Year: 2013
Title: Structure of the human glucagon class B G-protein-coupled receptor.
Authors: Siu, F.Y. / He, M. / de Graaf, C. / Han, G.W. / Yang, D. / Zhang, Z. / Zhou, C. / Xu, Q. / Wacker, D. / Joseph, J.S. / Liu, W. / Lau, J. / Cherezov, V. / Katritch, V. / Wang, M.W. / Stevens, R.C.
History
DepositionJun 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references
Revision 1.2Aug 7, 2013Group: Database references
Revision 1.3Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Soluble cytochrome b562 and Glucagon receptor chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2572
Polymers48,1511
Non-polymers1061
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.615, 66.651, 163.331
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN.

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Components

#1: Protein Soluble cytochrome b562 and Glucagon receptor chimera / Cytochrome b-562 / GL-R


Mass: 48150.840 Da / Num. of mol.: 1 / Fragment: UNP residues 23-128 and 123-434 / Mutation: M7W, H102I, R106L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Gene: cybC, GCGR_Human, GCGR / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P0ABE7, UniProt: P47871
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
Has protein modificationY
Sequence detailsGLY430-PRO432 ARE CLONING-SITE RESIDUES AND LEU433-GLN438 ARE PRECISION CLEAVAGE-SITE RESIDUES.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 14

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Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 61.56 %
Crystal growTemperature: 293 K / pH: 6
Details: 100 mM MES pH 6.0, 140-200 mM NaK tartrate tetrahydrate, 9-17% (v/v) PEG 400, 0.35-0.55% (v/v) Jeffamine M-600 pH 7.0, 200 uM NNC0640, Lipidic Cubic Phase (LCP), temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 1, 2012 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 9067 / % possible obs: 93.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 110.45 Å2 / Rmerge(I) obs: 0.0105 / Net I/σ(I): 22.6
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.882 / Mean I/σ(I) obs: 1.5 / % possible all: 90.2

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
PHASERphasing
BUSTER2.10.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2Z73

2z73


Resolution: 3.3→33.12 Å / Cor.coef. Fo:Fc: 0.8834 / Cor.coef. Fo:Fc free: 0.8424 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: 1. THE DIFFRACTION DATA ARE ANISOTROPIC. THE RESOLUTION LIMITS OF A*, B*, AND C* AXES ARE 3.3, 3.4 AND 3.3A, RESPECTIVELY. DIFFRAC DATA WERE INCLUDED IN REFINEMENT TO 3.3A IN THE A* AND C* ...Details: 1. THE DIFFRACTION DATA ARE ANISOTROPIC. THE RESOLUTION LIMITS OF A*, B*, AND C* AXES ARE 3.3, 3.4 AND 3.3A, RESPECTIVELY. DIFFRAC DATA WERE INCLUDED IN REFINEMENT TO 3.3A IN THE A* AND C* DIRECTIONS, WITH AN OVERALL EFFECTIVE AND REPORTED RESOLUTION OF 3.4A. 2. THE DENSITIES AT THE BOTTOM OF HELIX VI AND VII NEAR LYS349 WERE MODELLED AS A PEG-400 FRAGMENT (PEG) MOLECULE FROM THE CRYSTALLIZATION CONDITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.3385 430 4.79 %RANDOM
Rwork0.2835 ---
obs0.2862 8981 91.59 %-
Displacement parametersBiso mean: 126.83 Å2
Baniso -1Baniso -2Baniso -3
1--1.1296 Å20 Å20 Å2
2--21.5553 Å20 Å2
3----20.4256 Å2
Refine analyzeLuzzati coordinate error obs: 1.234 Å
Refinement stepCycle: LAST / Resolution: 3.3→33.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3049 0 7 0 3056
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013118HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.044228HARMONIC2.5
X-RAY DIFFRACTIONt_dihedral_angle_d1432SINUSOIDAL15
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes65HARMONIC2
X-RAY DIFFRACTIONt_gen_planes459HARMONIC5
X-RAY DIFFRACTIONt_it3118HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.79
X-RAY DIFFRACTIONt_other_torsion1.81
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion403SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3725SEMIHARMONIC4
LS refinement shellResolution: 3.3→3.69 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3136 118 5.11 %
Rwork0.2812 2190 -
all0.283 2308 -
obs-2190 91.59 %
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)
116.63092.34383.42996.08510.679914.87710.1704-0.1676-0.540.7744-0.1591-0.9671-0.00460.2207-0.01120.1043-0.2881-0.16360.0470.1298-0.539516.41764.5252-2.0054
20.94660.61681.80621.27892.0355.40020.34330.0555-0.26350.10790.3087-0.299-0.36081.0885-0.652-0.379-0.20480.05270.6079-0.1883-0.607916.1524-11.4685-44.8801
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1001 - A|1106 }A1001 - 1106
2X-RAY DIFFRACTION2{ A|123 - A|429 }A123 - 429

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