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- PDB-8d51: Parathyroid hormone 1 receptor extracellular domain complexed wit... -

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Basic information

Entry
Database: PDB / ID: 8d51
TitleParathyroid hormone 1 receptor extracellular domain complexed with a peptide ligand containing beta-3-homotryptophan
Components
  • PTHrP[1-36]
  • Parathyroid hormone/parathyroid hormone-related peptide receptor
KeywordsSIGNALING PROTEIN / parathyroid hormone 1 receptor / signaling / beta-amino acid
Function / homology
Function and homology information


negative regulation of chondrocyte development / regulation of chondrocyte differentiation / parathyroid hormone receptor activity / cAMP metabolic process / Class B/2 (Secretin family receptors) / G protein-coupled peptide receptor activity / negative regulation of chondrocyte differentiation / osteoblast development / peptide hormone receptor binding / positive regulation of inositol phosphate biosynthetic process ...negative regulation of chondrocyte development / regulation of chondrocyte differentiation / parathyroid hormone receptor activity / cAMP metabolic process / Class B/2 (Secretin family receptors) / G protein-coupled peptide receptor activity / negative regulation of chondrocyte differentiation / osteoblast development / peptide hormone receptor binding / positive regulation of inositol phosphate biosynthetic process / bone mineralization / peptide hormone binding / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / epidermis development / chondrocyte differentiation / bone resorption / cell maturation / skeletal system development / female pregnancy / hormone activity / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / intracellular calcium ion homeostasis / cell-cell signaling / regulation of gene expression / G alpha (s) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / basolateral plasma membrane / in utero embryonic development / cell surface receptor signaling pathway / cell population proliferation / receptor complex / apical plasma membrane / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / positive regulation of cell population proliferation / nucleolus / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular region / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Parathyroid hormone-related protein / Parathyroid hormone/parathyroid hormone-related protein / Parathyroid hormone family / Parathyroid hormone family signature. / Parathyroid hormone / GPCR, family 2, parathyroid hormone receptor / G-protein coupled receptors family 2 signature 1. / : / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. ...Parathyroid hormone-related protein / Parathyroid hormone/parathyroid hormone-related protein / Parathyroid hormone family / Parathyroid hormone family signature. / Parathyroid hormone / GPCR, family 2, parathyroid hormone receptor / G-protein coupled receptors family 2 signature 1. / : / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / Hormone receptor domain / 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
Parathyroid hormone-related protein / Parathyroid hormone/parathyroid hormone-related peptide receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYu, Z. / Kreitler, D.F. / Gellman, S.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM056414 United States
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: Harnessing Aromatic-Histidine Interactions through Synergistic Backbone Extension and Side Chain Modification.
Authors: Yu, Z. / Kreitler, D.F. / Chiu, Y.T.T. / Xu, R. / Bruchs, A.T. / Bingman, C.A. / Gellman, S.H.
History
DepositionJun 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Parathyroid hormone/parathyroid hormone-related peptide receptor
B: PTHrP[1-36]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9454
Polymers14,8182
Non-polymers1272
Water63135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.472, 58.472, 206.331
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11B-101-

ZN

21A-305-

HOH

31B-204-

HOH

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Components

#1: Protein Parathyroid hormone/parathyroid hormone-related peptide receptor / PTH/PTHrP type I receptor / PTH/PTHr receptor / Parathyroid hormone 1 receptor / PTH1 receptor


Mass: 11995.670 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTH1R, PTHR, PTHR1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q03431
#2: Protein/peptide PTHrP[1-36]


Mass: 2822.272 Da / Num. of mol.: 1 / Mutation: I31 substituted with beta-3-tryptophan / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P12272
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
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: 2.35 Å3/Da / Density % sol: 47.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 28 % v/v PEG Smear Low, 0.1 M tris-HCl pH 8, 0.15 M Sodium citrate, 1% ethylene glycol, 1 mM ZnSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920105 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 6, 2022 / Details: KB
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920105 Å / Relative weight: 1
ReflectionResolution: 1.997→49.179 Å / Num. obs: 7236 / % possible obs: 75.2 % / Redundancy: 5.4 % / Biso Wilson estimate: 53.73 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.027 / Rrim(I) all: 0.063 / Net I/σ(I): 12.6
Reflection shellResolution: 1.997→2.206 Å / Rmerge(I) obs: 0.831 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 362 / CC1/2: 0.843 / Rpim(I) all: 0.628 / Rrim(I) all: 0.947

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Processing

Software
NameVersionClassification
PHENIX1.18rc7_3834refinement
autoPROCdata processing
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H3G

3h3g


Resolution: 2→36.14 Å / SU ML: 0.2019 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 36.5025
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2463 514 7.11 %
Rwork0.2218 6718 -
obs0.2236 7232 75.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.45 Å2
Refinement stepCycle: LAST / Resolution: 2→36.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms966 0 5 35 1006
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021002
X-RAY DIFFRACTIONf_angle_d0.44191367
X-RAY DIFFRACTIONf_chiral_restr0.0387139
X-RAY DIFFRACTIONf_plane_restr0.004179
X-RAY DIFFRACTIONf_dihedral_angle_d11.4291345
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.20.3262240.3467317X-RAY DIFFRACTION14.5
2.2-2.520.36461460.3171847X-RAY DIFFRACTION84.34
2.52-3.170.29571610.2832228X-RAY DIFFRACTION99.83
3.17-36.140.21671830.19132326X-RAY DIFFRACTION99.6
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)
15.483292798540.3417047563991.079225764615.286552578271.216558840072.74237003689-0.3493404699191.381196857841.6652266908-2.44212507092-0.100492783238-0.892356963815-1.655644859540.998780878916-0.01274478539371.33275143408-0.1707071252340.2821743916070.8530186717880.2750408061120.51928054459710.759530474918.61534815847.57126808405
24.895223475431.725615250214.040238012733.005592729572.138065080213.71328809144-0.2230315143910.6852030277390.467535860305-0.2656619266850.481813188948-0.818337554537-0.4766540346720.968825235057-0.07227909907030.569432254706-0.1795546174310.1349768104790.542718587601-0.02687720225890.54918845083517.653031499419.284972046518.7995237911
37.720801884411.649078939552.21730226274.695956480110.7727430144033.67163923912-0.416938138877-0.1285809535341.42913490562-1.015827057780.0460432281855-0.847216875486-0.8004115769480.6073283200380.1231080916730.576847234391-0.09397018474440.04193940904630.3159517259790.001386189987370.72395766408812.889594543322.700975034124.7253622596
45.561438743651.14440830821.505295814595.625186789951.846038140587.010682168310.163652738011-0.3471452024750.304512423745-0.5466249114910.0014044368699-0.346049114881-0.395153288164-0.2986134619510.0406267413870.433444786955-0.0791314001901-0.02471489507570.4232367736580.0491950943280.4459281149048.5729414100715.706563081323.8592046762
55.161554379661.332124044762.429488918212.148995224593.10570709494.813048915080.407602122929-0.230100751261-0.881040349302-0.523582023695-0.2143678284151.125270568421.17166130636-1.05857255880.3544681963780.708048404415-0.0385445715431-0.02068123496231.030696016930.05270237388120.803763637111-2.7276765341313.286690937922.8004475163
62.36057393092.11416985269-0.4024716093395.114023967682.011393250785.14836447415-0.07608308112770.05455421353380.369768821071-0.985723309982-0.1741381985850.612774561849-0.276188931262-1.114154067990.09702311294150.659172553259-0.0140405351305-0.1272372860140.7008528781070.09130755234820.407044877515-2.159305968557.189030262411.216465555
79.67927897158-2.60247419272-0.7560946322258.405833254975.811093586354.805739244430.464720221642-0.6907268875480.2296535208220.627755362899-0.439656917994-1.072081112371.25196725578-0.1415489969950.07363393862640.479319938744-0.174941561909-0.1648781529980.6536956848980.1414860539640.7585657281246.930087654387.3072983025223.6270224988
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 32 through 57 )AA32 - 571 - 26
22chain 'A' and (resid 58 through 116 )AA58 - 11627 - 41
33chain 'A' and (resid 117 through 130 )AA117 - 13042 - 55
44chain 'A' and (resid 131 through 167 )AA131 - 16756 - 92
55chain 'A' and (resid 168 through 174 )AA168 - 17493 - 99
66chain 'B' and (resid 16 through 29 )BB16 - 291 - 14
77chain 'B' and (resid 30 through 36 )BB30 - 3615 - 21

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