[English] 日本語
Yorodumi
- PDB-7uzp: parathyroid hormone 1 receptor extracellular domain complexed wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7uzp
Titleparathyroid hormone 1 receptor extracellular domain complexed with a peptide ligand containing three beta-amino acids
Components
  • PTHrP[1-36] 24,28,31 XCP
  • Parathyroid hormone/parathyroid hormone-related peptide receptor
KeywordsSIGNALING PROTEIN / parathyroid hormone 1 receptor / signaling / beta-amino acid
Function / homology
Function and homology information


parathyroid hormone receptor activity / Class B/2 (Secretin family receptors) / G protein-coupled peptide receptor activity / osteoblast development / positive regulation of inositol phosphate biosynthetic process / bone mineralization / peptide hormone binding / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / chondrocyte differentiation / bone resorption ...parathyroid hormone receptor activity / Class B/2 (Secretin family receptors) / G protein-coupled peptide receptor activity / osteoblast development / positive regulation of inositol phosphate biosynthetic process / bone mineralization / peptide hormone binding / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / chondrocyte differentiation / bone resorption / cell maturation / skeletal system development / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / intracellular calcium ion homeostasis / basolateral plasma membrane / G alpha (s) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / 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 / nucleolus / protein homodimerization activity / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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, 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/parathyroid hormone-related peptide receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 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
Revision 2.1Feb 28, 2024Group: Refinement description / Category: software / Item: _software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Parathyroid hormone/parathyroid hormone-related peptide receptor
B: PTHrP[1-36] 24,28,31 XCP
C: Parathyroid hormone/parathyroid hormone-related peptide receptor
D: PTHrP[1-36] 24,28,31 XCP
E: Parathyroid hormone/parathyroid hormone-related peptide receptor
F: PTHrP[1-36] 24,28,31 XCP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5149
Polymers44,3246
Non-polymers1903
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9070 Å2
ΔGint-66 kcal/mol
Surface area20260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.650, 58.949, 77.924
Angle α, β, γ (deg.)90.000, 117.570, 90.000
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
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.: 3
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] 24,28,31 XCP


Mass: 2779.161 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.51 %
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

-
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: 2.29→34.54 Å / Num. obs: 18565 / % possible obs: 99.7 % / Redundancy: 7.501 % / Biso Wilson estimate: 41.05 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1 / Rrim(I) all: 0.107 / Χ2: 0.873 / Net I/σ(I): 12.62 / Num. measured all: 139252 / Scaling rejects: 24
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
2.29-2.357.0580.8362.549733138013790.7710.90399.9
2.35-2.417.6050.6533.299864130212970.8450.70199.6
2.41-2.487.6520.573.739993130613060.8910.612100
2.48-2.567.5690.4654.529711129012830.9090.49999.5
2.56-2.647.6280.3775.469093119411920.9490.40499.8
2.64-2.747.6310.2837.18989118011780.9680.30499.8
2.74-2.847.6050.2288.288677114211410.9840.24499.9
2.84-2.967.6550.1849.918459111111050.9890.19899.5
2.96-3.097.610.1312.878044105810570.9940.13999.9
3.09-3.247.6070.11714.5675699959950.9930.126100
3.24-3.417.5780.08717.1572529619570.9970.09499.6
3.41-3.627.6340.07320.3769709149130.9970.07899.9
3.62-3.877.5070.06922.6163218448420.9970.07499.8
3.87-4.187.5140.06423.8960948148110.9970.06999.6
4.18-4.587.4720.06125.2754627387310.9980.06699.1
4.58-5.127.4250.06425.1549976756730.9970.06999.7
5.12-5.917.3750.06925.2644036005970.9960.07499.5
5.91-7.247.1860.07525.635504964940.9970.08199.6
7.24-10.246.940.07726.5527624043980.9960.08398.5
10.24-34.546.060.0824.9613092262160.9930.08795.6

-
Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
autoPROC1.0.5 (20210420)data reduction
XDSFeb 5, 2021 (BUILT 20210322)data reduction
Aimless0.7.7data scaling
pointless1.12.10data scaling
autoPROC1.0.5 (20210420)data scaling
PHASERphasing
XSCALEJan 10, 2022 BUILT=20220220data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FJ3

6fj3


Resolution: 2.29→34.54 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2427 960 5.19 %
Rwork0.209 17520 -
obs0.2107 18480 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 224.55 Å2 / Biso mean: 60.6824 Å2 / Biso min: 22.37 Å2
Refinement stepCycle: final / Resolution: 2.29→34.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3010 0 21 146 3177
Biso mean--67.24 45.65 -
Num. residues----368
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.29-2.410.36861300.278524842614100
2.41-2.570.26591400.269625162656100
2.57-2.760.29251450.249524512596100
2.76-3.040.29291320.226724832615100
3.04-3.480.25481220.216725402662100
3.48-4.380.2161410.17124922633100
4.39-34.540.20811500.19552554270499
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)
13.0091-2.0113-4.64255.65761.82677.6532-0.28421.4534-0.7169-0.46820.23290.62070.7383-0.81070.10170.5666-0.1722-0.09170.6386-0.10710.4999-18.868918.28077.2463
27.37190.7982-2.14683.8926-1.16295.85660.0480.9110.04510.1105-0.06920.4992-0.1484-0.81830.07240.3117-0.0837-0.0740.46980.02040.4698-26.273920.793120.8551
39.155-0.4727-4.867.58392.24768.035-0.4429-0.1236-0.5959-0.01680.3242-0.13590.33280.18130.0810.2076-0.0407-0.05630.27990.04440.4298-15.22319.532524.1576
42.45852.1054-3.06536.8098-0.72986.7411-0.74090.7002-1.3032-0.92960.4123-0.59980.19440.74580.44420.4911-0.07850.07510.514-0.21020.5763-2.202222.37310.9729
54.3481-2.1333.68652.4237-1.31814.4591-0.7947-0.9932-0.34950.01120.3191-0.896-0.87830.98610.39590.2829-0.00190.00990.6196-0.07040.5518-10.056626.575325.0203
69.6931-4.57064.62394.2637-5.56867.45940.48910.57-0.4837-2.1033-0.5941-0.84831.11150.73710.2810.72170.08870.13450.5256-0.00590.538317.51419.69557.3468
77.5033-3.13734.90026.0677-3.13713.61780.5523-0.404-0.5798-0.8654-0.36-0.37440.6067-0.0206-0.20580.46530.10060.03850.50390.01620.523519.515312.0320.4831
85.09310.4991-0.96797.2671-4.33857.90660.11470.00130.21980.4385-0.1963-0.546-0.32130.22430.06040.22220.0289-0.06160.2571-0.01570.353514.944322.496324.2136
92.172-1.17781.29369.48160.68872.262-0.30190.61140.1437-1.3940.2694-0.50090.0655-0.5187-0.08040.40190.0232-0.01790.37420.03650.39146.171532.745911.2284
108.5824-4.0031-5.49999.33515.67745.5657-0.31520.06430.74341.71090.43350.26950.3542-1.6174-0.17470.61260.11850.09110.3840.07130.58196.125923.459425.0719
117.18063.84444.71634.55774.51584.7345-0.77840.76661.1145-1.86420.16991.0852-1.00450.53570.53290.8603-0.0468-0.07510.60860.09810.5414-1.375651.34217.4499
126.211.42610.49198.51380.5714.5275-0.67660.11040.7959-0.91780.62080.1111-0.74910.4830.01470.4753-0.0497-0.01610.28330.02010.4483.823256.054620.8808
137.64261.58974.49756.05793.10399.22610.0544-0.28180.3334-0.0586-0.13420.43-0.1147-0.23730.06140.3351-0.01450.02190.1979-0.02060.4293-1.827448.424924.2731
147.5125.10315.38514.92395.03515.14770.3116-1.156-0.61010.2039-0.30351.7770.1265-1.16370.09480.3811-0.107-0.0130.5408-0.02750.603-10.187839.388722.9288
157.94532.4594-1.36022.91662.75725.55360.18190.5539-0.3017-0.7703-0.06650.72470.5341-0.81090.01140.487-0.0177-0.16950.4039-0.02010.4244-6.976834.638211.1726
162.54383.454-2.3286.101-2.71652.37820.5729-0.4039-0.89890.4364-0.15070.54971.4340.7392-0.48480.5714-0.052-0.08670.4208-0.00650.55040.764539.130225.0393
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 57 )A30 - 57
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 80 )A58 - 80
3X-RAY DIFFRACTION3chain 'A' and (resid 81 through 130 )A81 - 130
4X-RAY DIFFRACTION4chain 'B' and (resid 15 through 29 )B15 - 29
5X-RAY DIFFRACTION5chain 'B' and (resid 30 through 36 )B30 - 36
6X-RAY DIFFRACTION6chain 'C' and (resid 30 through 57 )C30 - 57
7X-RAY DIFFRACTION7chain 'C' and (resid 58 through 80 )C58 - 80
8X-RAY DIFFRACTION8chain 'C' and (resid 81 through 130 )C81 - 130
9X-RAY DIFFRACTION9chain 'D' and (resid 15 through 29 )D15 - 29
10X-RAY DIFFRACTION10chain 'D' and (resid 30 through 36 )D30 - 36
11X-RAY DIFFRACTION11chain 'E' and (resid 30 through 57 )E30 - 57
12X-RAY DIFFRACTION12chain 'E' and (resid 58 through 80 )E58 - 80
13X-RAY DIFFRACTION13chain 'E' and (resid 81 through 123 )E81 - 123
14X-RAY DIFFRACTION14chain 'E' and (resid 124 through 130 )E124 - 130
15X-RAY DIFFRACTION15chain 'F' and (resid 16 through 29 )F16 - 29
16X-RAY DIFFRACTION16chain 'F' and (resid 30 through 36 )F30 - 36

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more