[English] 日本語
Yorodumi
- PDB-6z8n: Crystal structure of the neurotensin receptor 1 in complex with t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6z8n
TitleCrystal structure of the neurotensin receptor 1 in complex with the small-molecule full agonist SRI-9829
ComponentsNeurotensin receptor type 1,Neurotensin receptor type 1,Neurotensin receptor type 1,Neurotensin receptor type 1,Neurotensin receptor 1 (NTSR1),Neurotensin receptor 1 (NTSR1)
KeywordsMEMBRANE PROTEIN / GPCR-ligand complex / rNTSR1 / SRI-9829 / full agonist
Function / homology
Function and homology information


Peptide ligand-binding receptors / positive regulation of locomotion / G protein-coupled neurotensin receptor activity / regulation of inositol trisphosphate biosynthetic process / inositol phosphate catabolic process / symmetric synapse / D-aspartate import across plasma membrane / positive regulation of gamma-aminobutyric acid secretion / regulation of membrane depolarization / positive regulation of arachidonate secretion ...Peptide ligand-binding receptors / positive regulation of locomotion / G protein-coupled neurotensin receptor activity / regulation of inositol trisphosphate biosynthetic process / inositol phosphate catabolic process / symmetric synapse / D-aspartate import across plasma membrane / positive regulation of gamma-aminobutyric acid secretion / regulation of membrane depolarization / positive regulation of arachidonate secretion / vocalization behavior / neuron spine / L-glutamate import across plasma membrane / regulation of behavioral fear response / regulation of respiratory gaseous exchange / cAMP biosynthetic process / positive regulation of inhibitory postsynaptic potential / negative regulation of systemic arterial blood pressure / negative regulation of release of sequestered calcium ion into cytosol / G alpha (q) signalling events / positive regulation of glutamate secretion / response to food / temperature homeostasis / response to lipid / positive regulation of inositol phosphate biosynthetic process / detection of temperature stimulus involved in sensory perception of pain / response to stress / associative learning / conditioned place preference / neuropeptide signaling pathway / axon terminus / positive regulation of release of sequestered calcium ion into cytosol / dendritic shaft / adult locomotory behavior / learning / cytoplasmic side of plasma membrane / terminal bouton / perikaryon / dendritic spine / positive regulation of apoptotic process / membrane raft / axon / neuronal cell body / dendrite / positive regulation of gene expression / negative regulation of apoptotic process / protein-containing complex binding / cell surface / identical protein binding / plasma membrane
Similarity search - Function
Neurotensin receptor / Neurotensin type 1 receptor / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
Chem-SR9 / Neurotensin receptor type 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.803 Å
AuthorsDeluigi, M. / Klipp, A. / Hilge, M. / Merklinger, L. / Klenk, C. / Plueckthun, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_182334 Switzerland
CitationJournal: Sci Adv / Year: 2021
Title: Complexes of the neurotensin receptor 1 with small-molecule ligands reveal structural determinants of full, partial, and inverse agonism.
Authors: Deluigi, M. / Klipp, A. / Klenk, C. / Merklinger, L. / Eberle, S.A. / Morstein, L. / Heine, P. / Mittl, P.R.E. / Ernst, P. / Kamenecka, T.M. / He, Y. / Vacca, S. / Egloff, P. / Honegger, A. / Pluckthun, A.
History
DepositionJun 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 17, 2021Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Neurotensin receptor type 1,Neurotensin receptor type 1,Neurotensin receptor type 1,Neurotensin receptor type 1,Neurotensin receptor 1 (NTSR1),Neurotensin receptor 1 (NTSR1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5552
Polymers53,0891
Non-polymers4661
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area20820 Å2
Unit cell
Length a, b, c (Å)76.665, 213.971, 94.052
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Neurotensin receptor type 1,Neurotensin receptor type 1,Neurotensin receptor type 1,Neurotensin receptor type 1,Neurotensin receptor 1 (NTSR1),Neurotensin receptor 1 (NTSR1) / NTR1 / High-affinity levocabastine-insensitive neurotensin receptor / NTRH


Mass: 53089.223 Da / Num. of mol.: 1
Mutation: S83G,A86L,T101R,H103D,H105Y,L119F,M121L,E124D,R143K,D150E,A161V,R167L,R213L,V234L,K235R,V240L,I253A,I260A,N262R,K263R,H305R,C332V,F342A,T354S,F358V,S362A
Source method: isolated from a genetically manipulated source
Details: Residues 60-371 represent the rat neurotensin receptor 1 mutant H4 (NTSR1-H4). Residues 273 to 290 were deleted for crystallisation purposes. Residues 372 to 380 form a linker connecting ...Details: Residues 60-371 represent the rat neurotensin receptor 1 mutant H4 (NTSR1-H4). Residues 273 to 290 were deleted for crystallisation purposes. Residues 372 to 380 form a linker connecting NTSR1 with the DARPin crystallisation chaperone. Residues 381 to 536 represent the DARPin crystallisation chaperone that is related to 5LW2. Residues 537 to 539 represent a short linker connecting the DARPin crystallisation chaperone with the HRV 3C protease recognition sequence. Residues 540 to 544 are part of the HRV 3C protease recognition sequence visible in the electron density.,Residues 60-371 represent the rat neurotensin receptor 1 mutant H4 (NTSR1-H4). Residues 273 to 290 were deleted for crystallisation purposes. Residues 372 to 380 form a linker connecting NTSR1 with the DARPin crystallisation chaperone. Residues 381 to 536 represent the DARPin crystallisation chaperone that is related to 5LW2. Residues 537 to 539 represent a short linker connecting the DARPin crystallisation chaperone with the HRV 3C protease recognition sequence. Residues 540 to 544 are part of the HRV 3C protease recognition sequence visible in the electron density.
Source: (gene. exp.) Rattus norvegicus (Norway rat), (gene. exp.) synthetic construct (others)
Gene: Ntsr1, Ntsr / Production host: Escherichia coli (E. coli) / References: UniProt: P20789
#2: Chemical ChemComp-SR9 / (2~{S})-4-methyl-2-[(1-quinolin-8-ylsulfonylindol-3-yl)carbonylamino]pentanoic acid


Mass: 465.522 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H23N3O5S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.51 Å3/Da / Density % sol: 64.92 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase / pH: 6.8
Details: 100 mM HEPES 370-520 mM Na citrate 32% (v/v) PEG400 10 uM SRI-9829

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999998 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999998 Å / Relative weight: 1
ReflectionResolution: 2.803→29.595 Å / Num. obs: 13189 / % possible obs: 90.4 % / Redundancy: 5.2 % / CC1/2: 0.982 / Rmerge(I) obs: 0.208 / Rpim(I) all: 0.099 / Rrim(I) all: 0.232 / Net I/σ(I): 5.1
Reflection shellResolution: 2.803→3.127 Å / Rmerge(I) obs: 1.866 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 660 / CC1/2: 0.32 / Rpim(I) all: 0.82 / Rrim(I) all: 2.05
Serial crystallography sample deliveryMethod: fixed target

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YVR

6yvr


Resolution: 2.803→29.595 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.89 / WRfactor Rfree: 0.307 / WRfactor Rwork: 0.296 / SU B: 19.62 / SU ML: 0.364 / Average fsc free: 0.8412 / Average fsc work: 0.8649 / Cross valid method: FREE R-VALUE / ESU R Free: 0.501
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2986 659 5.01 %
Rwork0.277 12495 -
all0.278 --
obs-13154 67.623 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 65.825 Å2
Baniso -1Baniso -2Baniso -3
1-0.576 Å20 Å20 Å2
2---0.928 Å20 Å2
3---0.353 Å2
Refinement stepCycle: LAST / Resolution: 2.803→29.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3302 0 33 0 3335
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0010.0133416
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173029
X-RAY DIFFRACTIONr_angle_refined_deg1.1691.6124706
X-RAY DIFFRACTIONr_angle_other_deg1.1161.5696889
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.255458
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.11822.742124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55315419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.921158
X-RAY DIFFRACTIONr_chiral_restr0.0310.2479
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024064
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02740
X-RAY DIFFRACTIONr_nbd_refined0.1740.2779
X-RAY DIFFRACTIONr_symmetry_nbd_other0.150.22678
X-RAY DIFFRACTIONr_nbtor_refined0.1520.21718
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21571
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.275
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1090.28
X-RAY DIFFRACTIONr_nbd_other0.110.232
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1490.22
X-RAY DIFFRACTIONr_mcbond_it1.0087.6791837
X-RAY DIFFRACTIONr_mcbond_other1.0077.6791838
X-RAY DIFFRACTIONr_mcangle_it1.83511.5162295
X-RAY DIFFRACTIONr_mcangle_other1.83511.5172295
X-RAY DIFFRACTIONr_scbond_it0.6837.5611578
X-RAY DIFFRACTIONr_scbond_other0.6837.5621579
X-RAY DIFFRACTIONr_scangle_it1.2911.3442411
X-RAY DIFFRACTIONr_scangle_other1.28911.3452412
X-RAY DIFFRACTIONr_lrange_it5.863142.84514322
X-RAY DIFFRACTIONr_lrange_other5.866142.8514308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.803-2.8760.420.51443X-RAY DIFFRACTION3.1938
2.876-2.9540.33460.4113X-RAY DIFFRACTION8.4758
2.954-3.040.399120.389191X-RAY DIFFRACTION15.1493
3.04-3.1330.306240.334295X-RAY DIFFRACTION24.6713
3.133-3.2360.246210.347455X-RAY DIFFRACTION37.6285
3.236-3.350.362380.346713X-RAY DIFFRACTION60.8097
3.35-3.4760.338500.328993X-RAY DIFFRACTION88.1657
3.476-3.6180.362650.2981047X-RAY DIFFRACTION98.5816
3.618-3.7780.339600.2921039X-RAY DIFFRACTION99.009
3.778-3.9620.248380.272989X-RAY DIFFRACTION98.6551
3.962-4.1760.266450.268949X-RAY DIFFRACTION99.4995
4.176-4.4290.331500.256891X-RAY DIFFRACTION99.4715
4.429-4.7350.3430.263863X-RAY DIFFRACTION98.9083
4.735-5.1130.308350.259798X-RAY DIFFRACTION99.5221
5.113-5.60.377410.297721X-RAY DIFFRACTION99.4778
5.6-6.2590.335350.359672X-RAY DIFFRACTION99.4374
6.259-7.2230.303300.325595X-RAY DIFFRACTION98.8924
7.223-8.8360.219230.231504X-RAY DIFFRACTION98.1378
8.836-12.4540.211270.181405X-RAY DIFFRACTION99.3103
12.454-29.5950.287140.303219X-RAY DIFFRACTION87.9245

+
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