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- PDB-8d52: Parathyroid hormone 1 receptor extracellular domain complexed wit... -

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Basic information

Entry
Database: PDB / ID: 8d52
TitleParathyroid hormone 1 receptor extracellular domain complexed with a peptide ligand containing (2-naphthyl)-beta-3-homoalanine
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 / G protein-coupled peptide receptor activity / negative regulation of chondrocyte differentiation / Class B/2 (Secretin family receptors) / osteoblast development / positive regulation of inositol phosphate biosynthetic process / peptide hormone receptor binding ...negative regulation of chondrocyte development / regulation of chondrocyte differentiation / parathyroid hormone receptor activity / cAMP metabolic process / G protein-coupled peptide receptor activity / negative regulation of chondrocyte differentiation / Class B/2 (Secretin family receptors) / osteoblast development / positive regulation of inositol phosphate biosynthetic process / peptide hormone receptor binding / bone mineralization / peptide hormone binding / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / epidermis development / bone resorption / chondrocyte differentiation / cell maturation / skeletal system development / female pregnancy / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / hormone activity / intracellular calcium ion homeostasis / cell-cell signaling / phospholipase C-activating G protein-coupled receptor signaling pathway / regulation of gene expression / G alpha (s) signalling events / basolateral plasma membrane / in utero embryonic development / cell population proliferation / receptor complex / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / apical plasma membrane / negative regulation of cell population proliferation / positive regulation of cell population proliferation / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular region / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
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: 2.02 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 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_validate_peptide_omega.auth_comp_id_1 / _pdbx_validate_peptide_omega.auth_comp_id_2 / _pdbx_validate_peptide_omega.auth_seq_id_1 / _pdbx_validate_peptide_omega.auth_seq_id_2 / _pdbx_validate_peptide_omega.omega / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Dec 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)14,9564
Polymers14,8292
Non-polymers1272
Water79344
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.383, 57.383, 205.208
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-317-

HOH

31B-208-

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: 2833.294 Da / Num. of mol.: 1
Mutation: I31 substituted by (2-naphthyl)-beta-3-homoalanine
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.: 44 / 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: 2.34 Å3/Da / Density % sol: 47.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion / 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: 2.02→68.403 Å / Num. obs: 7246 / % possible obs: 81.1 % / Redundancy: 4.2 % / Biso Wilson estimate: 42.74 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.088 / Net I/σ(I): 9.1
Reflection shellResolution: 2.02→2.163 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.123 / Num. unique obs: 361 / CC1/2: 0.551 / Rpim(I) all: 0.791 / % possible all: 22.1

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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: 2.02→48.3 Å / SU ML: 0.2504 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.8938
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.244 544 7.51 %
Rwork0.2042 6700 -
obs0.2072 7244 81.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.52 Å2
Refinement stepCycle: LAST / Resolution: 2.02→48.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms932 0 52 44 1028
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00481015
X-RAY DIFFRACTIONf_angle_d0.88171383
X-RAY DIFFRACTIONf_chiral_restr0.0717140
X-RAY DIFFRACTIONf_plane_restr0.0035181
X-RAY DIFFRACTIONf_dihedral_angle_d13.1949351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.220.3823500.3092611X-RAY DIFFRACTION30.17
2.22-2.540.30991530.27771895X-RAY DIFFRACTION93.56
2.55-3.210.33431670.24092062X-RAY DIFFRACTION99.91
3.21-48.30.19961740.17422132X-RAY DIFFRACTION99.05
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)
16.538422226792.822022668293.72543314478.427066858122.495229746559.84906351368-0.9346817532330.6211669475270.803976176645-1.551564752660.590809706223-0.32948119611-1.36904024850.8086577910030.3897598591710.600199801914-0.07508974273430.06031107700350.3781838693140.08551933293670.4781461111816.9417.4776.352
23.313657577151.445702743551.881182249543.71286506890.7631251542993.60119720693-0.4202487477780.6761899654880.151615400257-0.6590490272740.589840596485-1.11552026255-0.9276514985841.34883169098-0.1339701153280.449894949631-0.1960099739730.09083041325730.515976351154-0.02125396302260.64882595816317.9520.99619.715
36.858272929210.2597678060512.798790103836.303268812840.2153324841239.997984198750.159403400751-0.2969240083260.606961051445-0.130658204209-0.085240993932-0.205860979108-0.2622203468190.0366335267709-0.07559202978770.284280823644-0.0279251997019-0.03232884227240.194095529906-0.07714375005440.353992483938.05316.58524.024
45.26252406775-2.409586286521.215929165572.008234866975.239209665712.006033697370.180462214349-0.682514999711-0.8126120926710.493599993996-0.2214200650521.550800396480.765561844065-2.056360015930.04313698938760.467779271395-0.0446507499768-0.01029935481980.714705931220.02530327117580.850443575544-3.31313.18222.308
58.971435957715.68967741483-4.935435627497.123224761213.103091457482.03287339276-0.3022967717610.4487032932890.739656078429-0.6614453660020.1668697422910.481272436877-0.831302131391-0.9109884140430.1554104284120.3378376508690.0303171479606-0.05500334876250.2903158445830.0208640050080.343200360606-2.477.3411.227
64.446892362144.000743753761.723652561193.58527078451.535613031380.6624649060740.249848705165-0.756674027241-0.02268974527980.745315898676-0.216512613836-0.7886169347280.781876676118-0.09139572899720.2476921650730.474199827215-0.0825914974707-0.2057925843780.3917294441690.02515132336370.5795787350926.3637.00422.385
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 30:53 )A30 - 53
2X-RAY DIFFRACTION2( CHAIN A AND RESID 54:124 )A54 - 124
3X-RAY DIFFRACTION3( CHAIN A AND RESID 125:168 )A125 - 168
4X-RAY DIFFRACTION4( CHAIN A AND RESID 169:174 )A169 - 174
5X-RAY DIFFRACTION5( CHAIN B AND RESID 15:29 )B15 - 29
6X-RAY DIFFRACTION6( CHAIN B AND RESID 30:35 )B30 - 35

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