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- PDB-7uzo: Parathyroid hormone 1 receptor extracellular domain complexed wit... -

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Basic information

Entry
Database: PDB / ID: 7uzo
TitleParathyroid hormone 1 receptor extracellular domain complexed with a peptide ligand containing one beta-amino acid
Components
  • Parathyroid hormone/parathyroid hormone-related peptide receptor
  • Peptide from Parathyroid hormone-related protein
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 / cAMP metabolic process / negative regulation of chondrocyte differentiation / Class B/2 (Secretin family receptors) / osteoblast development / peptide hormone receptor binding / bone mineralization / epidermis development / skeletal system development ...negative regulation of chondrocyte development / regulation of chondrocyte differentiation / cAMP metabolic process / negative regulation of chondrocyte differentiation / Class B/2 (Secretin family receptors) / osteoblast development / peptide hormone receptor binding / bone mineralization / epidermis development / skeletal system development / female pregnancy / adenylate cyclase-activating G protein-coupled receptor signaling pathway / hormone activity / cell-cell signaling / G alpha (s) signalling events / regulation of gene expression / negative regulation of cell population proliferation / positive regulation of cell population proliferation / Golgi apparatus / extracellular space / extracellular region / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
Parathyroid hormone-related protein / Parathyroid hormone/parathyroid hormone-related protein / Parathyroid hormone family / Parathyroid hormone family signature. / Parathyroid hormone
Similarity search - Domain/homology
Parathyroid hormone-related protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsYu, Z. / Bruchs, A.T. / Bingman, C.A. / 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: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Altered signaling at the PTH receptor via modified agonist contacts with the extracellular domain provides a path to prolonged agonism in vivo.
Authors: Liu, S. / Yu, Z. / Daley, E.J. / Bingman, C.A. / Bruchs, A.T. / Gardella, T.J. / Gellman, S.H.
History
DepositionMay 9, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: 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
Revision 1.2Oct 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 / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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: Peptide from Parathyroid hormone-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6703
Polymers14,6052
Non-polymers651
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-10 kcal/mol
Surface area7660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.023, 56.023, 100.823
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-101-

ZN

21B-212-

HOH

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Components

#1: Protein Parathyroid hormone/parathyroid hormone-related peptide receptor


Mass: 11823.531 Da / Num. of mol.: 1 / Fragment: amino-terminal extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTH1R, PTHR, PTHR1 / Production host: Escherichia coli (E. coli)
#2: Protein/peptide Peptide from Parathyroid hormone-related protein / / PTHrP[1-36] 31 XCP


Mass: 2781.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P12272
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.06 Å3/Da / Density % sol: 40.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 28 % v/v PEG Smear Low, 0.1 M tris-HCl pH 8, 0.15 M Sodium citrate, 1% ethylene glycol, 0.4 mM ZnSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.3→28.01 Å / Num. obs: 29018 / % possible obs: 99.5 % / Redundancy: 10.059 % / Biso Wilson estimate: 18.01 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.044 / Rrim(I) all: 0.047 / Χ2: 0.949 / Net I/σ(I): 22.57 / Num. measured all: 291893
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.3-1.335.0940.9041.710545218820700.6451.00894.6
1.33-1.376.7180.6912.7213845208320610.8340.74998.9
1.37-1.418.850.583.9617938202720270.9110.616100
1.41-1.4510.4160.4345.7920779199519950.9620.457100
1.45-1.511.2290.3128.4221392190519050.9790.327100
1.5-1.5511.2780.22311.6121225188218820.9890.234100
1.55-1.6111.3060.17714.2620452180918090.9920.186100
1.61-1.6811.290.13917.8919250170517050.9950.146100
1.68-1.7511.2580.1122.0418688166016600.9960.115100
1.75-1.8411.1490.08626.917716158915890.9970.09100
1.84-1.9410.9650.07132.116568151115110.9980.075100
1.94-2.0510.8180.05637.1415340141814180.9990.059100
2.05-2.1910.6280.0541.8114358135113510.9990.052100
2.19-2.3710.5460.04644.4412940122712270.9990.049100
2.37-2.610.4760.04346.8312194116411640.9990.046100
2.6-2.910.5710.044911036104410440.9990.042100
2.9-3.3510.5520.03850.7594868998990.9990.04100
3.35-4.110.6930.03452.3382767747740.9990.036100
4.1-5.8110.890.03253.4466106076070.9990.034100
5.81-28.0110.1720.03551.0932553253200.9980.03798.5

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Processing

Software
NameVersionClassification
PHENIXPHENIX 1.20.1_4487refinement
XDSFeb 5, 2021data reduction
XSCALEFeb 5, 2021data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6fj3

6fj3


Resolution: 1.3→28.01 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 24.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.182 1414 4.87 %
Rwork0.1573 27612 -
obs0.1585 29018 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.74 Å2 / Biso mean: 27.9406 Å2 / Biso min: 12.83 Å2
Refinement stepCycle: final / Resolution: 1.3→28.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1021 0 1 143 1165
Biso mean--15.72 34.41 -
Num. residues----124
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3-1.340.34181070.27942633274095
1.34-1.40.2551480.224727832931100
1.4-1.460.2321290.218327972926100
1.46-1.540.24141490.183927422891100
1.54-1.630.2241440.200827732917100
1.63-1.760.21841500.172927912941100
1.76-1.940.2011530.193927612914100
1.94-2.220.15471380.156627942932100
2.22-2.790.16491480.15327722920100
2.79-28.010.16441480.129727662914100
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)
16.6525-3.58264.23443.5277-3.05824.5718-0.2802-0.44660.12040.23160.2520.1124-0.2713-0.36790.050.14710.01520.0380.1529-0.0150.113-12.563119.5276-7.7031
25.0922-0.51332.17581.8172-0.61053.5966-0.07990.1153-0.01010.01190.01570.0015-0.10790.05780.08080.11940.00220.02750.099-0.00040.0853-7.413818.7059-19.699
37.2808-0.51834.03923.36-0.33126.4483-0.2139-0.35250.0680.48930.1549-0.629-0.18280.38390.02050.16880.0162-0.03070.1646-0.0030.20963.00727.0568-7.8051
47.27523.11870.14284.5876-3.73598.5507-0.03520.3514-0.8606-0.8383-0.2056-0.76080.79740.30340.37810.24580.05990.01220.2067-0.010.2931-6.11669.2062-20.6993
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 72 )A30 - 72
2X-RAY DIFFRACTION2chain 'A' and (resid 73 through 130 )A73 - 130
3X-RAY DIFFRACTION3chain 'B' and (resid 15 through 29 )B15 - 29
4X-RAY DIFFRACTION4chain 'B' and (resid 30 through 36 )B30 - 36

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