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- PDB-3n7r: Crystal structure of the ectodomain complex of the CGRP receptor,... -

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Basic information

Entry
Database: PDB / ID: 3n7r
TitleCrystal structure of the ectodomain complex of the CGRP receptor, a Class-B GPCR, reveals the site of drug antagonism
Components
  • Calcitonin gene-related peptide type 1 receptor
  • Receptor activity-modifying protein 1
KeywordsMEMBRANE PROTEIN / GPCR / class B GPCR / antagonist / olcegepant / telcagepant / migraine
Function / homology
Function and homology information


calcitonin gene-related peptide binding / CGRP receptor complex / calcitonin gene-related peptide receptor signaling pathway / adrenomedullin binding / positive regulation of protein glycosylation / cellular response to sucrose stimulus / adrenomedullin receptor activity / adrenomedullin receptor complex / adrenomedullin receptor signaling pathway / amylin receptor activity ...calcitonin gene-related peptide binding / CGRP receptor complex / calcitonin gene-related peptide receptor signaling pathway / adrenomedullin binding / positive regulation of protein glycosylation / cellular response to sucrose stimulus / adrenomedullin receptor activity / adrenomedullin receptor complex / adrenomedullin receptor signaling pathway / amylin receptor activity / calcitonin receptor activity / vascular associated smooth muscle cell proliferation / calcitonin gene-related peptide receptor activity / amylin receptor signaling pathway / Calcitonin-like ligand receptors / regulation of G protein-coupled receptor signaling pathway / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / coreceptor activity / cellular response to hormone stimulus / positive regulation of vascular associated smooth muscle cell proliferation / protein localization to plasma membrane / G protein-coupled receptor activity / intracellular protein transport / adenylate cyclase-activating G protein-coupled receptor signaling pathway / receptor internalization / calcium ion transport / protein transport / heart development / G alpha (s) signalling events / angiogenesis / lysosome / receptor complex / cell surface receptor signaling pathway / endosome / G protein-coupled receptor signaling pathway / cell surface / endoplasmic reticulum / plasma membrane / cytoplasm
Similarity search - Function
Receptor activity modifying family / GPCR, family 2, calcitonin gene-related peptide, type 1 receptor / GPCR, family 2, extracellular hormone receptor domain / Hormone receptor fold / Receptor activity modifying protein / RAMP domain superfamily / Receptor activity modifying family / GPCR, family 2, calcitonin receptor family / G-protein coupled receptors family 2 signature 1. / : ...Receptor activity modifying family / GPCR, family 2, calcitonin gene-related peptide, type 1 receptor / GPCR, family 2, extracellular hormone receptor domain / Hormone receptor fold / Receptor activity modifying protein / RAMP domain superfamily / Receptor activity modifying family / GPCR, family 2, calcitonin receptor family / 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. / DNA polymerase; domain 1 / Few Secondary Structures / Irregular / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-3N6 / Chem-N7R / Receptor activity-modifying protein 1 / Calcitonin gene-related peptide type 1 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsTer Haar, E.
CitationJournal: Structure / Year: 2010
Title: Crystal Structure of the Ectodomain Complex of the CGRP Receptor, a Class-B GPCR, Reveals the Site of Drug Antagonism.
Authors: Ter Haar, E. / Koth, C.M. / Abdul-Manan, N. / Swenson, L. / Coll, J.T. / Lippke, J.A. / Lepre, C.A. / Garcia-Guzman, M. / Moore, J.M.
History
DepositionMay 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 26, 2022Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly / pdbx_struct_assembly / pdbx_struct_assembly_prop / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calcitonin gene-related peptide type 1 receptor
B: Calcitonin gene-related peptide type 1 receptor
C: Receptor activity-modifying protein 1
D: Receptor activity-modifying protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3056
Polymers48,8684
Non-polymers1,4362
Water68538
1
A: Calcitonin gene-related peptide type 1 receptor
D: Receptor activity-modifying protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3043
Polymers24,4342
Non-polymers8701
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Calcitonin gene-related peptide type 1 receptor
C: Receptor activity-modifying protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0013
Polymers24,4342
Non-polymers5671
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.940, 118.200, 133.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Detailschains A & D or chains B & C

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Components

#1: Protein Calcitonin gene-related peptide type 1 receptor / CGRP type 1 receptor / Calcitonin receptor-like receptor


Mass: 13431.703 Da / Num. of mol.: 2 / Fragment: UNP residues 23-133
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALCRL, CALRL_HUMAN, CGRPR / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: Q16602
#2: Protein Receptor activity-modifying protein 1 / Calcitonin-receptor-like receptor activity-modifying protein 1 / CRLR activity-modifying protein 1


Mass: 11002.491 Da / Num. of mol.: 2 / Fragment: Extra-cellular domain residues 26-117
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAMP1, RAMP1_HUMAN / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: O60894
#3: Chemical ChemComp-3N6 / N-{(1S)-5-amino-1-[(4-pyridin-4-ylpiperazin-1-yl)carbonyl]pentyl}-3,5-dibromo-Nalpha-{[4-(2-oxo-1,4-dihydroquinazolin-3 (2H)-yl)piperidin-1-yl]carbonyl}-D-tyrosinamide / Olcegepant


Mass: 869.645 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H47Br2N9O5 / Comment: antagonist*YM
#4: Chemical ChemComp-N7R / N-[(3R,6S)-6-(2,3-difluorophenyl)-2-oxo-1-(2,2,2-trifluoroethyl)azepan-3-yl]-4-(2-oxo-2,3-dihydro-1H-imidazo[4,5-b]pyridin-1-yl)piperidine-1-carboxamide


Mass: 566.523 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H27F5N6O3 / Comment: medication, antagonist*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 3.14 Å3/Da / Density % sol: 60.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: CLR/RAMP1 complex was mixed with Olcegepant prior to crystallization in a 1:4 (protein : compound) molar ratio. Crystals were obtained by mixing 0.6uL protein with 0.3uL reservoir solution ...Details: CLR/RAMP1 complex was mixed with Olcegepant prior to crystallization in a 1:4 (protein : compound) molar ratio. Crystals were obtained by mixing 0.6uL protein with 0.3uL reservoir solution containing 1-1.3M ammonium sulfate, 6-8% dioxane, 60-80mM MES pH 6.5, plus 0.4 M potassium thiocyanate. Telcagepant was soaked into the ligand binding site. The crystal was transferred to 2.1M NaMalonate (pH 7.0) prior to freezing in liquid nitrogen., VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 18, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 10420 / % possible obs: 73.6 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.066 / Χ2: 1.13 / Net I/σ(I): 14.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.9-31.30.4381681.20412.1
3-3.122.10.34661.01933.4
3.12-3.273.10.2547531.24753.9
3.27-3.4440.1769431.35167.9
3.44-3.654.30.13911171.52480.1
3.65-3.944.40.10613031.08592.2
3.94-4.334.40.07613791.0297.6
4.33-4.964.40.06413951.02998.7
4.96-6.244.30.06214131.04798.6
6.24-504.20.03914830.99197.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
BUSTER-TNTBUSTER 2.9.2refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
BUSTER2.9.2refinement
RefinementResolution: 2.9→46.55 Å / Cor.coef. Fo:Fc: 0.8808 / Cor.coef. Fo:Fc free: 0.8411 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2669 491 4.73 %RANDOM
Rwork0.232 ---
obs0.2337 10386 --
Displacement parametersBiso mean: 91.53 Å2
Baniso -1Baniso -2Baniso -3
1--38.2491 Å20 Å20 Å2
2--15.3628 Å20 Å2
3---22.8863 Å2
Refine analyzeLuzzati coordinate error obs: 0.542 Å
Refinement stepCycle: LAST / Resolution: 2.9→46.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2692 0 94 38 2824
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082891HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.033943HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d877SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes96HARMONIC2
X-RAY DIFFRACTIONt_gen_planes451HARMONIC5
X-RAY DIFFRACTIONt_it2891HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.69
X-RAY DIFFRACTIONt_other_torsion21.1
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion360SEMIHARMONIC5
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_contact3362SEMIHARMONIC4
LS refinement shellResolution: 2.9→3.24 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2627 55 4.2 %
Rwork0.2708 1255 -
all0.2704 1310 -
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)
14.6966-0.10632.91040.60632.20392.0397-0.0531-0.11840.29590.14010.08980.0269-0.39620.008-0.03670.24660.1497-0.021-0.12810.0172-0.173422.409231.306667.4817
22.54652.8891.34265.58891.06213.790.01550.04-0.302-0.07090.1796-0.18650.16390.0536-0.1952-0.1144-0.0058-0.07-0.0859-0.026-0.046436.998-0.471986.7207
30.34910.15840.4733.4903-1.24213.52990.05950.09180.108-0.1306-0.18170.1263-0.07840.17140.1222-0.0841-0.00570.0119-0.01290.001-0.066938.055618.480684.5808
41.2901-0.4843-1.12192.23740.63041.9442-0.00830.0598-0.1937-0.12220.23750.08610.0664-0.0886-0.22920.01660.0365-0.0405-0.07330.0422-0.037819.742518.641654.1447
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A32-A56 A63-A128 }A32 - 56
2X-RAY DIFFRACTION1{ A32-A56 A63-A128 }A63 - 128
3X-RAY DIFFRACTION2{ B33-B55 B60-B129 }B33 - 55
4X-RAY DIFFRACTION2{ B33-B55 B60-B129 }B60 - 129
5X-RAY DIFFRACTION3{ C26-C107 }C26 - 107
6X-RAY DIFFRACTION4{ D27-D106 }D27 - 106

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