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- PDB-5ii0: Crystal structure of the human calcitonin receptor ectodomain in ... -

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Basic information

Entry
Database: PDB / ID: 5ii0
TitleCrystal structure of the human calcitonin receptor ectodomain in complex with a truncated salmon calcitonin analogue
Components
  • Calcitonin
  • Calcitonin receptor
KeywordsHORMONE / calcitonin / G protein coupled receptor / peptide hormone / ectodomain
Function / homology
Function and homology information


calcitonin binding / amylin receptor complex 1 / amylin receptor complex 2 / cross-receptor inhibition within G protein-coupled receptor heterodimer / amylin receptor complex 3 / amylin receptor activity / calcitonin receptor activity / calcitonin gene-related peptide receptor activity / amylin receptor signaling pathway / positive regulation of adenylate cyclase activity ...calcitonin binding / amylin receptor complex 1 / amylin receptor complex 2 / cross-receptor inhibition within G protein-coupled receptor heterodimer / amylin receptor complex 3 / amylin receptor activity / calcitonin receptor activity / calcitonin gene-related peptide receptor activity / amylin receptor signaling pathway / positive regulation of adenylate cyclase activity / Calcitonin-like ligand receptors / negative regulation of ossification / positive regulation of protein kinase A signaling / response to amyloid-beta / positive regulation of calcium-mediated signaling / response to glucocorticoid / regulation of mRNA stability / ossification / osteoclast differentiation / acrosomal vesicle / adenylate cyclase-activating G protein-coupled receptor signaling pathway / hormone activity / cilium / amyloid-beta binding / positive regulation of cytosolic calcium ion concentration / G alpha (s) signalling events / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / axon / positive regulation of gene expression / extracellular region / plasma membrane
Similarity search - Function
Calcitonin / GPCR, family 2, extracellular hormone receptor domain / GPCR, family 2, calcitonin receptor / Hormone receptor fold / GPCR, family 2, calcitonin receptor family / Calcitonin-like / Calcitonin peptide-like / Calcitonin, conserved site / Calcitonin / CGRP / IAPP family signature. / calcitonin ...Calcitonin / GPCR, family 2, extracellular hormone receptor domain / GPCR, family 2, calcitonin receptor / Hormone receptor fold / GPCR, family 2, calcitonin receptor family / Calcitonin-like / Calcitonin peptide-like / Calcitonin, conserved site / Calcitonin / CGRP / IAPP family signature. / calcitonin / Calcitonin/adrenomedullin / Calcitonin / CGRP / IAPP 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. / Few Secondary Structures / Irregular
Similarity search - Domain/homology
UREA / Calcitonin receptor / Calcitonin / CT protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Oncorhynchus gorbuscha (pink salmon)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.097 Å
AuthorsJohansson, E. / Reedtz-Runge, S.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Type II Turn of Receptor-bound Salmon Calcitonin Revealed by X-ray Crystallography.
Authors: Johansson, E. / Hansen, J.L. / Hansen, A.M. / Shaw, A.C. / Becker, P. / Schaffer, L. / Reedtz-Runge, S.
History
DepositionMar 1, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Jul 6, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Calcitonin receptor
B: Calcitonin receptor
C: Calcitonin receptor
D: Calcitonin
E: Calcitonin
F: Calcitonin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7598
Polymers51,6766
Non-polymers832
Water5,170287
1
A: Calcitonin receptor
D: Calcitonin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2483
Polymers17,2252
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Calcitonin receptor
E: Calcitonin


Theoretical massNumber of molelcules
Total (without water)17,2252
Polymers17,2252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Calcitonin receptor
F: Calcitonin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2853
Polymers17,2252
Non-polymers601
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.558, 113.165, 55.424
Angle α, β, γ (deg.)90.00, 114.79, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-201-

NA

21B-244-

HOH

31B-253-

HOH

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Components

#1: Protein Calcitonin receptor / CT-R


Mass: 14433.183 Da / Num. of mol.: 3 / Fragment: ectodomain UNP residues 25-144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALCR / Variant: isoform II / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P30988
#2: Protein/peptide Calcitonin / calcitonin analogue


Mass: 2791.992 Da / Num. of mol.: 3 / Fragment: UNP residues 8-32 / Source method: obtained synthetically / Source: (synth.) Oncorhynchus gorbuscha (pink salmon) / References: UniProt: Q8QG84, UniProt: Q91970*PLUS
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-URE / UREA


Mass: 60.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4N2O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Hepes, pH 7.5, 4.3 M sodium chloride, 2 M urea

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002+ / Wavelength: 1.54179 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.097→24.84 Å / Num. obs: 31627 / % possible obs: 97 % / Redundancy: 7.5 % / Biso Wilson estimate: 29.59 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 15.99
Reflection shellResolution: 2.097→2.172 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 2.86 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_1938refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N7S

3n7s


Resolution: 2.097→24.84 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0.24 / Phase error: 21.45
RfactorNum. reflection% reflection
Rfree0.2055 1935 6.33 %
Rwork0.1699 --
obs0.1721 30547 96.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.097→24.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2775 0 5 287 3067
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082912
X-RAY DIFFRACTIONf_angle_d1.0973969
X-RAY DIFFRACTIONf_dihedral_angle_d13.8521083
X-RAY DIFFRACTIONf_chiral_restr0.054371
X-RAY DIFFRACTIONf_plane_restr0.006515
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0973-2.14980.2661290.22061874X-RAY DIFFRACTION90
2.1498-2.20780.22441380.19592006X-RAY DIFFRACTION95
2.2078-2.27280.22311360.18431994X-RAY DIFFRACTION95
2.2728-2.34610.24751330.19032012X-RAY DIFFRACTION95
2.3461-2.42990.25471370.18872010X-RAY DIFFRACTION95
2.4299-2.52710.19851310.1872005X-RAY DIFFRACTION95
2.5271-2.6420.25381370.19042024X-RAY DIFFRACTION96
2.642-2.78110.22541370.18472046X-RAY DIFFRACTION97
2.7811-2.95510.21831440.1912083X-RAY DIFFRACTION98
2.9551-3.18280.23071390.17262088X-RAY DIFFRACTION99
3.1828-3.50230.20331440.15592111X-RAY DIFFRACTION100
3.5023-4.00730.18511410.14532100X-RAY DIFFRACTION99
4.0073-5.04190.14011430.14312111X-RAY DIFFRACTION99
5.0419-24.93860.21961460.17682148X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 29.6999 Å / Origin y: 1.4964 Å / Origin z: -1.6102 Å
111213212223313233
T0.2783 Å2-0.0253 Å20.0155 Å2-0.2768 Å2-0.0115 Å2--0.2636 Å2
L0.124 °2-0.1303 °2-0.1136 °2-0.6701 °20.5707 °2--0.802 °2
S-0.0437 Å °-0.0096 Å °-0.0513 Å °0.0488 Å °0.0021 Å °0.043 Å °0.0664 Å °-0.0423 Å °0.0527 Å °
Refinement TLS groupSelection details: all

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