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- PDB-6ln2: Crystal structure of full length human GLP1 receptor in complex w... -

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Basic information

Entry
Database: PDB / ID: 6ln2
TitleCrystal structure of full length human GLP1 receptor in complex with Fab fragment (Fab7F38)
Components
  • Fab7F38_heavy chain
  • Fab7F38_light chain
  • Glucagon-like peptide 1 receptor,Rubredoxin,Glucagon-like peptide 1 receptor
KeywordsMEMBRANE PROTEIN / Full length Human GLP1 receptor / Class B / Fab7F38 / TMD / NAM PF06372222 / LCP
Function / homology
Function and homology information


alkane catabolic process / glucagon-like peptide 1 receptor activity / glucagon receptor activity / hormone secretion / positive regulation of blood pressure / post-translational protein targeting to membrane, translocation / regulation of heart contraction / response to psychosocial stress / peptide hormone binding / activation of adenylate cyclase activity ...alkane catabolic process / glucagon-like peptide 1 receptor activity / glucagon receptor activity / hormone secretion / positive regulation of blood pressure / post-translational protein targeting to membrane, translocation / regulation of heart contraction / response to psychosocial stress / peptide hormone binding / activation of adenylate cyclase activity / negative regulation of blood pressure / cAMP-mediated signaling / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Glucagon-type ligand receptors / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / transmembrane signaling receptor activity / positive regulation of cytosolic calcium ion concentration / G alpha (s) signalling events / electron transfer activity / learning or memory / cell surface receptor signaling pathway / iron ion binding / membrane / plasma membrane
Similarity search - Function
: / GPCR, family 2, glucagon-like peptide-1 receptor / Rubredoxin / Rubredoxin, iron-binding site / Rubredoxin signature. / Rubredoxin domain / Rubredoxin / GPCR, family 2, glucagon-like peptide-1/glucagon receptor / Rubredoxin-like domain / Rubredoxin-like domain profile. ...: / GPCR, family 2, glucagon-like peptide-1 receptor / Rubredoxin / Rubredoxin, iron-binding site / Rubredoxin signature. / Rubredoxin domain / Rubredoxin / GPCR, family 2, glucagon-like peptide-1/glucagon receptor / Rubredoxin-like domain / Rubredoxin-like domain profile. / 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.
Similarity search - Domain/homology
Chem-97Y / Rubredoxin / Glucagon-like peptide 1 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Clostridium pasteurianum (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsWu, F. / Yang, L. / Hang, K. / Laursen, M. / Wu, L. / Han, G.W. / Ren, Q. / Roed, N.K. / Lin, G. / Hanson, M. ...Wu, F. / Yang, L. / Hang, K. / Laursen, M. / Wu, L. / Han, G.W. / Ren, Q. / Roed, N.K. / Lin, G. / Hanson, M. / Jiang, H. / Wang, M. / Reedtz-Runge, S. / Song, G. / Stevens, R.C.
CitationJournal: Nat Commun / Year: 2020
Title: Full-length human GLP-1 receptor structure without orthosteric ligands.
Authors: Wu, F. / Yang, L. / Hang, K. / Laursen, M. / Wu, L. / Han, G.W. / Ren, Q. / Roed, N.K. / Lin, G. / Hanson, M.A. / Jiang, H. / Wang, M.W. / Reedtz-Runge, S. / Song, G. / Stevens, R.C.
History
DepositionDec 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 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-like peptide 1 receptor,Rubredoxin,Glucagon-like peptide 1 receptor
B: Fab7F38_light chain
C: Fab7F38_heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,2066
Polymers102,4043
Non-polymers8023
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-41 kcal/mol
Surface area41000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.040, 64.660, 322.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN.

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Components

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Antibody , 2 types, 2 molecules BC

#2: Antibody Fab7F38_light chain


Mass: 23307.939 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Antibody Fab7F38_heavy chain


Mass: 24476.268 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Glucagon-like peptide 1 receptor,Rubredoxin,Glucagon-like peptide 1 receptor / GLP-1R / Rd / GLP-1R


Mass: 54619.996 Da / Num. of mol.: 1
Mutation: S193C,I196F,S225A,M233C,S271A,I317C,G318I,K346A,C347F,G361C,E387D
Source method: isolated from a genetically manipulated source
Details: The fusion protein of GLP1 receptor (UNP residues 24-260), Rubredoxin (UNP residues 1-54) and GLP1 receptor (UNP residues 262-439)
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Clostridium pasteurianum (bacteria)
Gene: GLP1R / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P43220, UniProt: P00268
#4: 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.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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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Non-polymers , 2 types, 2 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-97Y / N-{4-[(R)-(3,3-dimethylcyclobutyl)({6-[4-(trifluoromethyl)-1H-imidazol-1-yl]pyridin-3-yl}amino)methyl]benzene-1-carbonyl}-beta-alanine


Mass: 515.527 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H28F3N5O3 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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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: 3.21 Å3/Da / Density % sol: 61.66 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 200-300 mM Ammonium formate, 36% PEG 400, 5%-10% (w/v) Guanidine hydrochloride
PH range: pH 6.2-6.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→45.7 Å / Num. obs: 22019 / % possible obs: 97.8 % / Redundancy: 4.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.116 / Net I/σ(I): 6.5
Reflection shellResolution: 3.2→3.37 Å / Rmerge(I) obs: 0.626 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3109 / CC1/2: 0.526 / % possible all: 96.7

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NX2

5nx2


Resolution: 3.2→30 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.886 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.453
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1098 4.99 %RANDOM
Rwork0.213 ---
obs0.215 21990 97 %-
Displacement parametersBiso max: 261 Å2 / Biso mean: 136.81 Å2 / Biso min: 58.31 Å2
Baniso -1Baniso -2Baniso -3
1--27.2666 Å20 Å20 Å2
2--21.8594 Å20 Å2
3---5.4073 Å2
Refine analyzeLuzzati coordinate error obs: 0 Å
Refinement stepCycle: final / Resolution: 3.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6472 0 52 0 6524
Biso mean--160.86 --
Num. residues----876
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2848SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes109HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1011HARMONIC5
X-RAY DIFFRACTIONt_it6720HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion911SEMIHARMONIC5
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_contact8084SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6720HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg9229HARMONIC20.94
X-RAY DIFFRACTIONt_omega_torsion3.54
X-RAY DIFFRACTIONt_other_torsion2.9
LS refinement shellResolution: 3.2→3.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.258 135 4.74 %
Rwork0.244 2711 -
all0.245 2846 -
obs--95.89 %
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)
10.33690.42690.98760.6010.06615.72180.1417-0.12190.15230.0815-0.19150.01860.1344-0.38460.04990.60790.03210.1003-0.4806-0.0846-0.429320.530230.334773.4657
20.7241-0.5759-0.20613.5183-0.70680.98440.01040.07310.2354-0.09880.0733-0.06890.17880.1585-0.0837-0.26780.0043-0.04080.0244-0.00270.338615.508159.76490.3
31.0976-0.7520.05284.2593-0.9722.1476-0.2367-0.30230.09030.68340.21960.32060.1887-0.47010.0171-0.30470.0180.0517-0.1408-0.05630.1137.266461.800516.3734
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A29 - 474
2X-RAY DIFFRACTION2{ B|* }B1 - 213
3X-RAY DIFFRACTION3{ C|* }C1 - 226

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