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- PDB-5fbk: Crystal structure of the extracellular domain of human calcium se... -

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Basic information

Entry
Database: PDB / ID: 5fbk
TitleCrystal structure of the extracellular domain of human calcium sensing receptor
ComponentsExtracellular calcium-sensing receptor
KeywordsSIGNALING PROTEIN / membrane protein / G-protein coupled receptor / ectodomain
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 / response to ischemia / G protein-coupled receptor activity / 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. / Response regulator / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BICARBONATE ION / CYCLOMETHYLTRYPTOPHAN / Extracellular calcium-sensing receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsZhang, T. / Zhang, C. / Miller, C.L. / Zou, J. / Moremen, K.W. / Brown, E.M. / Yang, J.J. / Hu, J.
CitationJournal: Sci Adv / Year: 2016
Title: Structural basis for regulation of human calcium-sensing receptor by magnesium ions and an unexpected tryptophan derivative co-agonist.
Authors: Zhang, C. / Zhang, T. / Zou, J. / Miller, C.L. / Gorkhali, R. / Yang, J.Y. / Schilmiller, A. / Wang, S. / Huang, K. / Brown, E.M. / Moremen, K.W. / Hu, J. / Yang, J.J.
History
DepositionDec 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_struct_oper_list / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _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_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Extracellular calcium-sensing receptor
B: Extracellular calcium-sensing receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,04123
Polymers128,4312
Non-polymers2,61021
Water5,819323
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8310 Å2
ΔGint-87 kcal/mol
Surface area38740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.872, 82.916, 94.256
Angle α, β, γ (deg.)90.000, 105.100, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A22 - 531
2010B22 - 531

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Components

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Protein / Sugars , 2 types, 10 molecules AB

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


Mass: 64215.383 Da / Num. of mol.: 2 / Fragment: UNP residues 20-541
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASR, GPRC2A, PCAR1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P41180
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
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

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Non-polymers , 5 types, 336 molecules

#2: Chemical ChemComp-TCR / CYCLOMETHYLTRYPTOPHAN


Type: L-peptide linking / Mass: 216.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H12N2O2
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-BCT / BICARBONATE ION / Bicarbonate


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.51 Å3/Da / Density % sol: 51.02 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% PEG 8000, 200 mM MgCl2, 10 mM CaCl2 and 100 mM Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9785 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 74547 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.043 / Rrim(I) all: 0.076 / Χ2: 0.975 / Net I/av σ(I): 18.063 / Net I/σ(I): 9 / Num. measured all: 284906
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allΧ2% possible allRrim(I) all
2.1-2.183.80.91373810.6310.5410.915100
2.18-2.263.80.66374350.7620.3930.9391000.771
2.26-2.373.80.47574210.8620.2810.9321000.552
2.37-2.493.80.3474080.9180.2010.9651000.395
2.49-2.653.80.2474270.9590.1421.0011000.279
2.65-2.853.80.1574560.9820.0891.0371000.175
2.85-3.143.80.09174650.9910.0540.9641000.106
3.14-3.593.80.06874520.9940.040.991000.079
3.59-4.523.80.04175130.9980.0240.9799.90.047
4.52-403.70.02975890.9980.0171.0499.80.034

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementResolution: 2.1→37.77 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.335 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2227 2000 2.7 %RANDOM
Rwork0.1901 ---
obs0.191 72544 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 123.01 Å2 / Biso mean: 44.987 Å2 / Biso min: 21.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å2-1.7 Å2
2--1.45 Å2-0 Å2
3----0.49 Å2
Refinement stepCycle: final / Resolution: 2.1→37.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7417 0 161 323 7901
Biso mean--64.88 46.14 -
Num. residues----954
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0197766
X-RAY DIFFRACTIONr_bond_other_d0.0040.027093
X-RAY DIFFRACTIONr_angle_refined_deg1.3791.9610569
X-RAY DIFFRACTIONr_angle_other_deg0.981316207
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8075949
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.52524.029350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.497151174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1731538
X-RAY DIFFRACTIONr_chiral_restr0.0790.21180
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028837
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021853
X-RAY DIFFRACTIONr_mcbond_it2.6664.423817
X-RAY DIFFRACTIONr_mcbond_other2.6664.4213816
X-RAY DIFFRACTIONr_mcangle_it4.1096.6174759
Refine LS restraints NCS

Ens-ID: 1 / Number: 25787 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.096→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 143 -
Rwork0.305 5182 -
all-5325 -
obs--97.8 %

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