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

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Basic information

Entry
Database: PDB / ID: 6pfo
TitleCrystal structure of N-glycosylated human calcitonin receptor extracellular domain in complex with salmon calcitonin (16-32)
Components
  • Calcitonin
  • Maltodextrin-binding protein,Calcitonin receptor
KeywordsSIGNALING PROTEIN / Class B GPCR / GlcNAc
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 cAMP-mediated signaling / positive regulation of calcium-mediated signaling / response to glucocorticoid / regulation of mRNA stability / ossification / osteoclast differentiation / acrosomal vesicle / cilium / adenylate cyclase-activating G protein-coupled receptor signaling pathway / hormone activity / amyloid-beta binding / positive regulation of cytosolic calcium ion concentration / G alpha (s) signalling events / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / axon / positive regulation of gene expression / 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 / : / Calcitonin receptor / Calcitonin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
Oncorhynchus sp. (fish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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 21, 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 / pdbx_struct_assembly_gen / struct_asym / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _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.id / _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_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _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 / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_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: Maltodextrin-binding protein,Calcitonin receptor
B: Maltodextrin-binding protein,Calcitonin receptor
C: Calcitonin
D: Calcitonin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,05611
Polymers112,3914
Non-polymers1,6657
Water11,746652
1
A: Maltodextrin-binding protein,Calcitonin receptor
C: Calcitonin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9805
Polymers56,1952
Non-polymers7853
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-2 kcal/mol
Surface area21970 Å2
MethodPISA
2
B: Maltodextrin-binding protein,Calcitonin receptor
D: Calcitonin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0766
Polymers56,1952
Non-polymers8814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-11 kcal/mol
Surface area22040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.031, 121.031, 263.957
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-902-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A-336 - 137
2010B-336 - 137
1020C16 - 32
2020D16 - 32

NCS ensembles :
ID
1
2

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

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


Mass: 54323.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Gene: malE, ECO26H__750033, CALCR / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: A0A0A8UN35, UniProt: P30988
#2: Protein/peptide Calcitonin /


Mass: 1872.091 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Oncorhynchus sp. (fish) / References: UniProt: Q92163

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Sugars , 2 types, 6 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.: 2
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.: 4
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, 653 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 652 / 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: 2.54 Å3/Da / Density % sol: 51.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 34% Pentaerythritol ethoxylate (15/4 EO/OH), 0.05M Bis-Tris, 0.1M Ammonium sulfate

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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: 1.78→50 Å / Num. obs: 108501 / % possible obs: 99 % / Redundancy: 7.4 % / Net I/σ(I): 29.82
Reflection shellResolution: 1.78→1.81 Å / Num. unique obs: 5201

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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: 1.78→49.86 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 5.837 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.113
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2136 5348 4.9 %RANDOM
Rwork0.1856 ---
obs0.187 103153 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 104.46 Å2 / Biso mean: 32.544 Å2 / Biso min: 14.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20.08 Å20 Å2
2--0.17 Å2-0 Å2
3----0.54 Å2
Refinement stepCycle: final / Resolution: 1.78→49.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7742 0 109 652 8503
Biso mean--42.38 35.04 -
Num. residues----982
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.028334
X-RAY DIFFRACTIONr_bond_other_d0.0020.027522
X-RAY DIFFRACTIONr_angle_refined_deg1.6761.96211362
X-RAY DIFFRACTIONr_angle_other_deg0.9992.99217595
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.35651031
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.31125.104386
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.832151359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9441525
X-RAY DIFFRACTIONr_chiral_restr0.10.21203
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219323
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021666
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A31288
12B31288
21C782
22D782
LS refinement shellResolution: 1.78→1.826 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 351 -
Rwork0.307 7385 -
all-7736 -
obs--97.44 %
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)
10.95710.2910.25341.57360.21341.48590.07840.0413-0.0618-0.013-0.0289-0.0551-0.0172-0.0254-0.04940.0384-0.00680.00650.05820.01490.016629.551-28.588-3.104
24.50760.3095-0.08981.8290.51691.7935-0.06890.2241-0.0867-0.06790.0750.41010.0698-0.6095-0.00620.1738-0.0079-0.0210.47870.07190.1337-5.085-29.782-27.634
31.34170.272-0.45921.33580.18221.2524-0.056-0.02470.00780.09390.05140.09740.2507-0.05270.00450.1540.0010.00630.09940.05620.036239.071-68.7215.074
44.28190.1364-0.3731.04110.01221.2356-0.0659-0.0152-0.00890.00550.067-0.05210.28110.3806-0.00110.20170.1688-0.04730.256-0.04010.019572.427-77.902-18.876
58.20082.72396.66081.44561.27087.1-0.1665-0.28880.46130.0321-0.05680.2549-0.3187-0.4080.22340.1720.1296-0.00770.2618-0.0380.12338.379-17.296-21.747
67.19260.729-1.52880.0798-0.15580.3563-0.0898-0.3938-0.7701-0.0128-0.0686-0.07620.15050.10890.15840.58010.1149-0.0060.17220.03070.084756.252-86.08-12.696
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-336 - 42
2X-RAY DIFFRACTION1A500
3X-RAY DIFFRACTION2A43 - 137
4X-RAY DIFFRACTION2A501 - 502
5X-RAY DIFFRACTION3B-336 - 42
6X-RAY DIFFRACTION3B500
7X-RAY DIFFRACTION4B43 - 137
8X-RAY DIFFRACTION4B501 - 502
9X-RAY DIFFRACTION5C16 - 33
10X-RAY DIFFRACTION6D16 - 33

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