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- PDB-3n7p: Crystal structure of the ectodomain complex of the CGRP receptor,... -

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Basic information

Entry
Database: PDB / ID: 3n7p
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 / positive regulation of protein glycosylation / adrenomedullin binding / 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 / positive regulation of protein glycosylation / adrenomedullin binding / 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 / G protein-coupled receptor activity / protein localization to plasma membrane / 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 / cell surface receptor signaling pathway / 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
Receptor activity-modifying protein 1 / Calcitonin gene-related peptide type 1 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)99,83724
Polymers98,3008
Non-polymers1,53716
Water95553
1
A: Calcitonin gene-related peptide type 1 receptor
R: Receptor activity-modifying protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1518
Polymers24,5752
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-95 kcal/mol
Surface area11760 Å2
MethodPISA
2
B: Calcitonin gene-related peptide type 1 receptor
D: Receptor activity-modifying protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1518
Polymers24,5752
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-87 kcal/mol
Surface area11770 Å2
MethodPISA
3
C: Calcitonin gene-related peptide type 1 receptor
F: Receptor activity-modifying protein 1


Theoretical massNumber of molelcules
Total (without water)24,5752
Polymers24,5752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-11 kcal/mol
Surface area9390 Å2
MethodPISA
4
E: Receptor activity-modifying protein 1
J: Calcitonin gene-related peptide type 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9596
Polymers24,5752
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-84 kcal/mol
Surface area9890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.000, 118.000, 225.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 13572.389 Da / Num. of mol.: 4 / 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.: 4 / 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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 4.61 Å3/Da / Density % sol: 73.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1-1.3M ammonium sulfate, 6-8% dioxane, 60-80mM MES pH 6.5, 10mM Tris pH8.5 and 200mM sodium nitrate. The crystals were transfered to 2.1M NaMalonate (pH 7.0) prior to freezing in liquid ...Details: 1-1.3M ammonium sulfate, 6-8% dioxane, 60-80mM MES pH 6.5, 10mM Tris pH8.5 and 200mM sodium nitrate. The crystals were transfered 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

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 5.0.210.9804
SYNCHROTRONALS 5.0.221
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDSep 29, 2006
ADSC QUANTUM 3152CCDSep 29, 2006
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.98041
211
ReflectionResolution: 2.8→50 Å / Num. obs: 39158 / % possible obs: 84.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 17.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
2.8-2.92.40.31936
2.9-3.022.60.28754.2
3.02-3.152.80.26479.8
3.15-3.323.30.21596.7
3.32-3.533.60.15798.8
3.53-3.83.60.10898.1
3.8-4.183.60.07697.8
4.18-4.793.50.05896.8
4.79-6.033.30.05195.8
6.03-503.50.03793.1

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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
HKL-2000data scaling
SHARPphasing
BUSTER2.9.2refinement
RefinementResolution: 2.8→27.12 Å / Cor.coef. Fo:Fc: 0.8959 / Cor.coef. Fo:Fc free: 0.8721 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2408 1845 4.96 %RANDOM
Rwork0.2138 ---
obs0.2151 37201 --
Displacement parametersBiso mean: 97.39 Å2
Baniso -1Baniso -2Baniso -3
1--15.5692 Å20 Å20 Å2
2---15.5692 Å20 Å2
3---31.1385 Å2
Refine analyzeLuzzati coordinate error obs: 0.532 Å
Refinement stepCycle: LAST / Resolution: 2.8→27.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5324 0 80 53 5457
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0095654HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.067758HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1772SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes132HARMONIC2
X-RAY DIFFRACTIONt_gen_planes871HARMONIC5
X-RAY DIFFRACTIONt_it5654HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.44
X-RAY DIFFRACTIONt_other_torsion21.29
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion724SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies6HARMONIC1
X-RAY DIFFRACTIONt_utility_distance20HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6195SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.3524 48 4.75 %
Rwork0.2832 962 -
all0.2864 1010 -
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)
12.6612-1.66422.02760.56-2.18145.67560.001-0.5805-0.05580.25390.0899-0.2256-0.22060.1078-0.0909-0.2245-0.0422-0.12090.16870.0039-0.198662.170845.935736.8736
25.2767-0.9099-2.0913.26852.15346.28730.032-0.60110.2810.28190.08270.18380.0056-0.1084-0.1147-0.3007-0.06760.00670.1283-0.0157-0.272637.855156.965236.0082
3-2.1761.6252-1.65682.66872.13991.17430.0763-0.2160.1010.0873-0.0185-0.097-0.1785-0.0796-0.0578-0.1034-0.24170.09370.1397-0.1214-0.156521.667378.033665.4585
44.3164-1.199-0.29732.02170.23753.49570.1822-0.0641-0.0738-0.21270.0716-0.19370.2080.5965-0.2538-0.2767-0.0485-0.06640.1183-0.0253-0.194863.069546.9219.4082
53.8769-0.06240.33423.92420.43315.38160.16980.1744-0.217-0.5185-0.0844-0.2045-0.04120.5619-0.0854-0.06480.23360.08240.0164-0.1108-0.296362.575144.7246-19.914
63.15370.99550.06582.89853.37343.19460.01010.07690.3221-0.0013-0.0772-0.0933-0.35930.01920.0671-0.1769-0.24560.11250.1716-0.1105-0.021232.567579.255951.4906
73.87590.9153-1.03642.1049-0.18926.12480.1450.3438-0.1027-0.2331-0.1185-0.2343-0.30060.3627-0.0265-0.13060.0334-0.0174-0.0781-0.035-0.226255.282252.5889-4.3181
84.501-1.3576-0.22510.3731-0.06052.31280.363-0.13040.087-0.2296-0.0139-0.0091-0.1533-0.4593-0.3491-0.2135-0.0535-0.03760.04410.0117-0.139737.122753.807218.885
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A29-A128 }A29 - 128
2X-RAY DIFFRACTION2{ B31-B129 }B31 - 129
3X-RAY DIFFRACTION3{ C35-C57 C66-C75 C|81-C91 C101-C124 }C35 - 57
4X-RAY DIFFRACTION3{ C35-C57 C66-C75 C|81-C91 C101-C124 }C66 - 75
5X-RAY DIFFRACTION3{ C35-C57 C66-C75 C|81-C91 C101-C124 }C81 - 91
6X-RAY DIFFRACTION3{ C35-C57 C66-C75 C|81-C91 C101-C124 }C101 - 124
7X-RAY DIFFRACTION4{ D27-D116 }D27 - 116
8X-RAY DIFFRACTION5{ E27-E105 }E27 - 105
9X-RAY DIFFRACTION6{ F27-F105 }F27 - 105
10X-RAY DIFFRACTION7{ J32-J128 }J32 - 128
11X-RAY DIFFRACTION8{ R27-R117 }R27 - 117

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