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- PDB-5k5t: Crystal structure of the inactive form of human calcium-sensing r... -

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Basic information

Entry
Database: PDB / ID: 5k5t
TitleCrystal structure of the inactive form of human calcium-sensing receptor extracellular domain
ComponentsExtracellular calcium-sensing receptor
KeywordsSIGNALING PROTEIN / Venus Flytrap module / cysteine rich domain / homodimer
Function / homology
Function and homology information


bile acid secretion / chemosensory behavior / cellular response to peptide / response to fibroblast growth factor / cellular response to vitamin D / phosphatidylinositol phospholipase C activity / Class C/3 (Metabotropic glutamate/pheromone receptors) / calcium ion import / positive regulation of positive chemotaxis / fat pad development ...bile acid secretion / chemosensory behavior / cellular response to peptide / response to fibroblast growth factor / cellular response to vitamin D / phosphatidylinositol phospholipase C activity / Class C/3 (Metabotropic glutamate/pheromone receptors) / calcium ion import / positive regulation of positive chemotaxis / fat pad development / amino acid binding / cellular response to hepatocyte growth factor stimulus / branching morphogenesis of an epithelial tube / positive regulation of calcium ion import / regulation of calcium ion transport / cellular response to low-density lipoprotein particle stimulus / detection of calcium ion / anatomical structure morphogenesis / axon terminus / positive regulation of vasoconstriction / JNK cascade / chloride transmembrane transport / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / ossification / G protein-coupled receptor activity / response to ischemia / cellular response to glucose stimulus / intracellular calcium ion homeostasis / positive regulation of insulin secretion / vasodilation / integrin binding / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / cellular response to hypoxia / G alpha (q) signalling events / basolateral plasma membrane / transmembrane transporter binding / positive regulation of ERK1 and ERK2 cascade / G protein-coupled receptor signaling pathway / apical plasma membrane / neuronal cell body / calcium ion binding / positive regulation of cell population proliferation / positive regulation of gene expression / protein kinase binding / cell surface / protein homodimerization activity / identical protein binding / plasma membrane
Similarity search - Function
GPCR, family 3, extracellular calcium-sensing receptor-related / G-protein coupled receptors family 3 signature 1. / G-protein coupled receptors family 3 signature 2. / GPCR, family 3, nine cysteines domain / GPCR, family 3, nine cysteines domain superfamily / Nine Cysteines Domain of family 3 GPCR / GPCR, family 3, conserved site / G-protein coupled receptors family 3 signature 3. / GPCR, family 3 / GPCR family 3, C-terminal ...GPCR, family 3, extracellular calcium-sensing receptor-related / G-protein coupled receptors family 3 signature 1. / G-protein coupled receptors family 3 signature 2. / GPCR, family 3, nine cysteines domain / GPCR, family 3, nine cysteines domain superfamily / Nine Cysteines Domain of family 3 GPCR / GPCR, family 3, conserved site / G-protein coupled receptors family 3 signature 3. / GPCR, family 3 / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR / G-protein coupled receptors family 3 profile. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
Extracellular calcium-sensing receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsGeng, Y. / Mosyak, L. / Kurinov, I. / Zuo, H. / Sturchler, E. / Cheng, T.C. / Subramanyam, P. / Brown, A.P. / Brennan, S.C. / Mun, H.-C. ...Geng, Y. / Mosyak, L. / Kurinov, I. / Zuo, H. / Sturchler, E. / Cheng, T.C. / Subramanyam, P. / Brown, A.P. / Brennan, S.C. / Mun, H.-C. / Bush, M. / Chen, Y. / Nguyen, T. / Cao, B. / Chang, D. / Quick, M. / Conigrave, A. / Colecraft, H.M. / McDonald, P. / Fan, Q.R.
Funding support United States, 2items
OrganizationGrant numberCountry
American Heart Association15GRNT25420002 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM112973 United States
CitationJournal: Elife / Year: 2016
Title: Structural mechanism of ligand activation in human calcium-sensing receptor.
Authors: Geng, Y. / Mosyak, L. / Kurinov, I. / Zuo, H. / Sturchler, E. / Cheng, T.C. / Subramanyam, P. / Brown, A.P. / Brennan, S.C. / Mun, H.C. / Bush, M. / Chen, Y. / Nguyen, T.X. / Cao, B. / ...Authors: Geng, Y. / Mosyak, L. / Kurinov, I. / Zuo, H. / Sturchler, E. / Cheng, T.C. / Subramanyam, P. / Brown, A.P. / Brennan, S.C. / Mun, H.C. / Bush, M. / Chen, Y. / Nguyen, T.X. / Cao, B. / Chang, D.D. / Quick, M. / Conigrave, A.D. / Colecraft, H.M. / McDonald, P. / Fan, Q.R.
History
DepositionMay 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jul 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_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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 / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Extracellular calcium-sensing receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,10412
Polymers69,2281
Non-polymers1,87711
Water77543
1
A: Extracellular calcium-sensing receptor
hetero molecules

A: Extracellular calcium-sensing receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,20924
Polymers138,4552
Non-polymers3,75322
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_554-x+1/2,y,-z-1/21
Buried area9870 Å2
ΔGint-107 kcal/mol
Surface area55810 Å2
MethodPISA
2
A: Extracellular calcium-sensing receptor
hetero molecules

A: Extracellular calcium-sensing receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,20924
Polymers138,4552
Non-polymers3,75322
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area8810 Å2
ΔGint-84 kcal/mol
Surface area56860 Å2
MethodPISA
3
A: Extracellular calcium-sensing receptor
hetero molecules

A: Extracellular calcium-sensing receptor
hetero molecules

A: Extracellular calcium-sensing receptor
hetero molecules

A: Extracellular calcium-sensing receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)284,41748
Polymers276,9104
Non-polymers7,50744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area21350 Å2
ΔGint-177 kcal/mol
Surface area110010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.330, 150.150, 214.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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Components

#1: Protein Extracellular calcium-sensing receptor / CaSR / Parathyroid cell calcium-sensing receptor 1 / PCaR1


Mass: 69227.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASR, GPRC2A, PCAR1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P41180
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 3.79 Å3/Da / Density % sol: 67.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.5 M Li2SO4, 100 mM Tris pH 8.5, 2 mM CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.1→107.21 Å / Biso Wilson estimate: 130.17 Å2
Reflection shellResolution: 3.1→3.6 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→107.21 Å / Cor.coef. Fo:Fc: 0.9241 / Cor.coef. Fo:Fc free: 0.918 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.397
RfactorNum. reflection% reflectionSelection details
Rfree0.2386 845 5.05 %RANDOM
Rwork0.2222 ---
obs0.223 16747 89.53 %-
Displacement parametersBiso mean: 110.92 Å2
Baniso -1Baniso -2Baniso -3
1--5.1523 Å20 Å20 Å2
2--3.0765 Å20 Å2
3---2.0758 Å2
Refine analyzeLuzzati coordinate error obs: 0.755 Å
Refinement stepCycle: LAST / Resolution: 3.1→107.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4564 0 114 43 4721
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084800HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.156526HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1663SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes127HARMONIC2
X-RAY DIFFRACTIONt_gen_planes700HARMONIC5
X-RAY DIFFRACTIONt_it4800HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.62
X-RAY DIFFRACTIONt_other_torsion16.69
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion643SEMIHARMONIC5
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_contact5388SEMIHARMONIC4
LS refinement shellResolution: 3.1→3.31 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3562 83 5.05 %
Rwork0.2681 1560 -
all0.2726 1643 -
obs--89.53 %
Refinement TLS params.Method: refined / Origin x: 5.4621 Å / Origin y: -18.773 Å / Origin z: -43.8814 Å
111213212223313233
T0.003 Å2-0.0086 Å20.0368 Å2--0.0144 Å2-0.0311 Å2---0.0085 Å2
L0.6923 °20.213 °2-0.4193 °2-0.3836 °2-0.1036 °2--0.237 °2
S-0.0037 Å °0.0095 Å °-0.0105 Å °-0.0124 Å °0.0025 Å °0.0282 Å °0.0044 Å °0.0057 Å °0.0012 Å °
Refinement TLS groupSelection details: { A|* }

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