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- PDB-3n7s: Crystal structure of the ectodomain complex of the CGRP receptor,... -

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Basic information

Entry
Database: PDB / ID: 3n7s
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 / cell surface receptor signaling pathway / lysosome / receptor complex / 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. / Hormone receptor domain ...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. / 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. / DNA polymerase; domain 1 / Few Secondary Structures / Irregular / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-3N6 / Chem-3N7 / Receptor activity-modifying protein 1 / Calcitonin gene-related peptide type 1 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 / 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 / _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)50,1807
Polymers48,8684
Non-polymers1,3123
Water2,360131
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
Buried area2170 Å2
ΔGint-13 kcal/mol
Surface area9830 Å2
MethodPISA
2
B: Calcitonin gene-related peptide type 1 receptor
C: Receptor activity-modifying protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8774
Polymers24,4342
Non-polymers4422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-29 kcal/mol
Surface area10900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.305, 119.131, 137.158
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-218-

HOH

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Components

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Protein , 2 types, 4 molecules ABCD

#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

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Non-polymers , 4 types, 134 molecules

#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-3N7 / N~4~-(5-cyclopropyl-1H-pyrazol-3-yl)-N~2~-1H-indazol-5-yl-6-methylpyrimidine-2,4-diamine


Mass: 346.389 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18N8
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 3.06 Å3/Da / Density % sol: 59.85 %
Crystal growTemperature: 298 K / 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, 0.4 M potassium thiocyanate. The crystals were transferred to 2.1M NaMalonate (pH 7.0) prior to freezing in liquid nitrogen, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 22, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→100 Å / Num. obs: 30529 / % possible obs: 86.9 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.073 / Χ2: 1.214 / Net I/σ(I): 12.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.1-2.183.10.42417820.90651.5
2.18-2.263.60.38622030.92863.7
2.26-2.3740.31325130.99272.5
2.37-2.494.20.27629431.00984.3
2.49-2.654.50.23333431.03396.3
2.65-2.8550.234811.08699.9
2.85-3.145.10.11735221.152100
3.14-3.595.10.06135021.29999.9
3.59-4.5250.04435631.76599.8
4.52-1004.80.02936771.37199.3

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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
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→46.17 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.919 / Occupancy max: 1 / Occupancy min: 0.58 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1509 4.95 %RANDOM
Rwork0.208 ---
obs0.209 30514 --
Displacement parametersBiso max: 120.26 Å2 / Biso mean: 42.815 Å2 / Biso min: 15.17 Å2
Baniso -1Baniso -2Baniso -3
1--8.952 Å20 Å20 Å2
2--2.732 Å20 Å2
3---6.22 Å2
Refine analyzeLuzzati coordinate error obs: 0.323 Å
Refinement stepCycle: LAST / Resolution: 2.1→46.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2900 0 85 131 3116
Refine LS restraints
Refine-IDTypeNumberWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d9862
X-RAY DIFFRACTIONt_trig_c_planes1022
X-RAY DIFFRACTIONt_gen_planes4615
X-RAY DIFFRACTIONt_it308820
X-RAY DIFFRACTIONt_nbd05
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion3725
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_contact37034
X-RAY DIFFRACTIONt_bond_d308820.008
X-RAY DIFFRACTIONt_angle_deg420421.02
X-RAY DIFFRACTIONt_omega_torsion2.91
X-RAY DIFFRACTIONt_other_torsion20.95
LS refinement shellResolution: 2.1→2.17 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.26 78 4.83 %
Rwork0.245 1537 -
all0.246 1615 -
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)
12.8727-0.29411.89632.0028-0.6243.6114-0.1564-0.15380.40010.3073-0.0172-0.0324-0.5358-0.08480.17360.06910.0989-0.0698-0.1078-0.0573-0.080521.167231.680168.2154
21.26471.09670.49323.69350.51832.62310.0384-0.01510.02550.04320.0118-0.03350.2921-0.0431-0.05020.0309-0.0372-0.008-0.0688-0.0104-0.096135.31480.236289.5793
30.6539-0.00040.21922.467-0.26832.18970.05110.08050.0784-0.0674-0.04810.0942-0.13970.1596-0.0030.0072-0.00520.0328-0.05170.0044-0.069637.135318.005589.1422
43.4125-1.62371.05472.8741-0.24142.14730.0630.1305-0.2221-0.2506-0.01540.2370.2373-0.0294-0.04760.07970.0669-0.0106-0.0908-0.0144-0.084718.669918.54555.5648
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|32 - A|57 A|61 - A|128 }A32 - 57
2X-RAY DIFFRACTION1{ A|32 - A|57 A|61 - A|128 }A61 - 128
3X-RAY DIFFRACTION2{ B|32 - B|55 B|60 - B|129 }B32 - 55
4X-RAY DIFFRACTION2{ B|32 - B|55 B|60 - B|129 }B60 - 129
5X-RAY DIFFRACTION3{ C|26 - C|115 }C26 - 115
6X-RAY DIFFRACTION4{ D|27 - D|111 }D27 - 111

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