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- PDB-6pgq: Crystal structure of N-glycosylated human calcitonin receptor ext... -

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Basic information

Entry
Database: PDB / ID: 6pgq
TitleCrystal structure of N-glycosylated human calcitonin receptor extracellular domain in complex with salmon calcitonin (22-32)
Components
  • Calcitonin
  • Maltodextrin-binding protein,Calcitonin receptor
KeywordsSIGNALING PROTEIN / class B GPCR / GlcNAc
Function / homology
Function and homology information


calcitonin receptor binding / 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 ...calcitonin receptor binding / 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 / sperm capacitation / positive regulation of protein kinase A signaling / response to amyloid-beta / positive regulation of calcium-mediated signaling / response to glucocorticoid / regulation of mRNA stability / regulation of cytosolic calcium ion concentration / activation of adenylate cyclase activity / ossification / osteoclast differentiation / acrosomal vesicle / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cilium / hormone activity / 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 space / extracellular region / plasma membrane
Similarity search - Function
Calcitonin / GPCR, family 2, calcitonin receptor / 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 ...Calcitonin / GPCR, family 2, calcitonin receptor / 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.
Similarity search - Domain/homology
alpha-maltose / ACETATE ION / : / Calcitonin-1 / Calcitonin receptor / Calcitonin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
Oncorhynchus sp. (fish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsLee, S. / Pioszak, A.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM104251 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103640 United States
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Calcitonin Receptor N-Glycosylation Enhances Peptide Hormone Affinity by Controlling Receptor Dynamics.
Authors: Lee, S.M. / Jeong, Y. / Simms, J. / Warner, M.L. / Poyner, D.R. / Chung, K.Y. / Pioszak, A.A.
History
DepositionJun 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 27, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
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: Maltodextrin-binding protein,Calcitonin receptor
B: Calcitonin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2937
Polymers55,2282
Non-polymers1,0655
Water362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)181.288, 181.288, 181.288
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Maltodextrin-binding protein,Calcitonin receptor / CT-R


Mass: 54078.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Gene: malE, CALCR / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: A0A0A8UN35, UniProt: P30988
#2: Protein/peptide Calcitonin /


Mass: 1149.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Oncorhynchus sp. (fish) / References: UniProt: Q92163, UniProt: P01263*PLUS

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Sugars , 2 types, 4 molecules

#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#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.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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 , 2 types, 3 molecules

#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 4.59 Å3/Da / Density % sol: 73.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 1.94M Ammonium sulfate, 0.1M Sodium acetate, 15% Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 24107 / % possible obs: 99 % / Redundancy: 9.3 % / Net I/σ(I): 21.24
Reflection shellResolution: 2.85→2.9 Å / Num. unique obs: 1167

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→48.45 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / SU B: 28.683 / SU ML: 0.233 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.406 / ESU R Free: 0.269
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2246 1209 5 %RANDOM
Rwork0.1925 ---
obs0.1942 22878 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 160.85 Å2 / Biso mean: 80.839 Å2 / Biso min: 48.25 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.85→48.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3802 0 70 2 3874
Biso mean--84.85 68.17 -
Num. residues----484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.023981
X-RAY DIFFRACTIONr_bond_other_d0.0020.023585
X-RAY DIFFRACTIONr_angle_refined_deg1.8321.9625417
X-RAY DIFFRACTIONr_angle_other_deg1.0882.9878375
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5415482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.35325.165182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.7115637
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9781510
X-RAY DIFFRACTIONr_chiral_restr0.10.2578
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214428
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02788
LS refinement shellResolution: 2.853→2.927 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 87 -
Rwork0.334 1654 -
all-1741 -
obs--99.71 %
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)
12.8702-0.90640.01312.66791.2972.3592-0.0866-0.33410.47460.1690.1638-0.4593-0.18860.135-0.07720.14150.0144-0.0880.0624-0.03230.23526.606-30.2792-18.7223
22.7611-0.0748-2.45652.6262-0.20752.6370.0801-0.0507-0.0634-0.1236-0.1203-0.10560.20310.16520.04020.18330.0242-0.02220.16230.01810.0109-21.5017-24.4044-1.3326
30.2694-1.61221.564510.6247-10.15079.7965-0.01190.22680.1102-0.1155-0.5441-0.83910.14040.73720.5560.32580.0119-0.10190.9997-0.27280.7751-10.3774-16.4896-5.3977
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-334 - 37
2X-RAY DIFFRACTION1A500
3X-RAY DIFFRACTION2A38 - 138
4X-RAY DIFFRACTION2A502
5X-RAY DIFFRACTION2A503
6X-RAY DIFFRACTION2A501
7X-RAY DIFFRACTION3B22 - 33

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