[English] 日本語
Yorodumi
- PDB-5t04: STRUCTURE OF CONSTITUTIVELY ACTIVE NEUROTENSIN RECEPTOR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5t04
TitleSTRUCTURE OF CONSTITUTIVELY ACTIVE NEUROTENSIN RECEPTOR
Components
  • ARG-ARG-PRO-TYR-ILE-LEU
  • Neurotensin receptor type 1,Endolysin,Neurotensin receptor type 1
KeywordsSIGNALING PROTEIN / MEMBRANE PROTEIN / G PROTEIN-COUPLED RECEPTOR / GPCR / NEUROTENSIN RECEPTOR / NTSR1 / agonist
Function / homology
Function and homology information


response to antipsychotic drug / Peptide ligand-binding receptors / neuropeptide receptor binding / G protein-coupled neurotensin receptor activity / inositol phosphate catabolic process / symmetric synapse / response to mineralocorticoid / D-aspartate import across plasma membrane / positive regulation of gamma-aminobutyric acid secretion / regulation of membrane depolarization ...response to antipsychotic drug / Peptide ligand-binding receptors / neuropeptide receptor binding / G protein-coupled neurotensin receptor activity / inositol phosphate catabolic process / symmetric synapse / response to mineralocorticoid / D-aspartate import across plasma membrane / positive regulation of gamma-aminobutyric acid secretion / regulation of membrane depolarization / positive regulation of arachidonate secretion / neuron spine / L-glutamate import across plasma membrane / regulation of respiratory gaseous exchange / positive regulation of inhibitory postsynaptic potential / neuropeptide hormone activity / hyperosmotic response / negative regulation of systemic arterial blood pressure / positive regulation of glutamate secretion / negative regulation of release of sequestered calcium ion into cytosol / digestive tract development / G alpha (q) signalling events / response to corticosterone / positive regulation of inositol phosphate biosynthetic process / response to lipid / cellular response to lithium ion / temperature homeostasis / detection of temperature stimulus involved in sensory perception of pain / response to axon injury / neuropeptide signaling pathway / viral release from host cell by cytolysis / transport vesicle / axon terminus / peptidoglycan catabolic process / response to amphetamine / cellular response to dexamethasone stimulus / positive regulation of release of sequestered calcium ion into cytosol / dendritic shaft / blood vessel diameter maintenance / liver development / adult locomotory behavior / learning / response to cocaine / cellular response to nerve growth factor stimulus / terminal bouton / visual learning / cytoplasmic side of plasma membrane / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / response to estradiol / dendritic spine / perikaryon / host cell cytoplasm / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / defense response to bacterium / positive regulation of apoptotic process / receptor ligand activity / membrane raft / axon / negative regulation of gene expression / neuronal cell body / dendrite / positive regulation of gene expression / protein-containing complex binding / negative regulation of apoptotic process / cell surface / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Neurotensin/neuromedin N / Neurotensin/neuromedin N precursor / Neurotensin receptor / Neurotensin type 1 receptor / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily ...Neurotensin/neuromedin N / Neurotensin/neuromedin N precursor / Neurotensin receptor / Neurotensin type 1 receptor / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / G-protein coupled receptors family 1 signature. / Lysozyme-like domain superfamily / 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
DI(HYDROXYETHYL)ETHER / 3,3',3''-phosphanetriyltripropanoic acid / Endolysin / Neurotensin/neuromedin N / Neurotensin receptor type 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsKrumm, B. / Botos, I. / Grisshammer, R.
CitationJournal: Sci Rep / Year: 2016
Title: Structure and dynamics of a constitutively active neurotensin receptor.
Authors: Krumm, B.E. / Lee, S. / Bhattacharya, S. / Botos, I. / White, C.F. / Du, H. / Vaidehi, N. / Grisshammer, R.
History
DepositionAug 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Neurotensin receptor type 1,Endolysin,Neurotensin receptor type 1
B: ARG-ARG-PRO-TYR-ILE-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0937
Polymers58,4322
Non-polymers6615
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-5 kcal/mol
Surface area23190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.190, 75.710, 83.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Neurotensin receptor type 1,Endolysin,Neurotensin receptor type 1 / NTR1 / High-affinity levocabastine-insensitive neurotensin receptor / NTRH / Lysis protein / ...NTR1 / High-affinity levocabastine-insensitive neurotensin receptor / NTRH / Lysis protein / Lysozyme / Muramidase / NTR1 / High-affinity levocabastine-insensitive neurotensin receptor / NTRH


Mass: 57613.445 Da / Num. of mol.: 1
Fragment: unp residues 43-268; 2-161; 297-396,unp residues 43-268; 2-161; 297-396,unp residues 43-268; 2-161; 297-396
Mutation: A86L, G215A, F358A, V360A, R12G, C54T, C97A, Q122N, Q123N, I137R,A86L, G215A, F358A, V360A, R12G, C54T, C97A, Q122N, Q123N, I137R,A86L, G215A, F358A, V360A, R12G, C54T, C97A, Q122N, Q123N, I137R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: Ntsr1, Ntsr / Plasmid: PFASTBAC1 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): CABBAGE LOOPER / References: UniProt: P20789, UniProt: P00720, lysozyme
#2: Protein/peptide ARG-ARG-PRO-TYR-ILE-LEU


Mass: 819.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: P20068*PLUS
#3: Chemical ChemComp-TCE / 3,3',3''-phosphanetriyltripropanoic acid / 3-[bis(2-carboxyethyl)phosphanyl]propanoic acid


Mass: 250.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15O6P
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.2 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 13-16% (v/v) PEG 400, 80 mM TrisHCl pH 8.5-9.0, 1.9 mM TCEP, 68-91 mM lithium acetate, 0.9 mM Neurotensin
PH range: 8.5-9.0

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1901
2901
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-D11.0332
SYNCHROTRONAPS 23-ID-B21.0332
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELJun 25, 2015
MARMOSAIC 300 mm CCD2CCDFeb 26, 2015
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.03321
21
ReflectionResolution: 3.3→38.141 Å / Num. obs: 10042 / % possible obs: 97.3 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 8.3
Reflection shellResolution: 3.3→3.56 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.6 / % possible all: 88.3

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XEE

4xee


Resolution: 3.3→38.141 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 30.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2833 1484 7.99 %
Rwork0.253 --
obs0.2555 18582 97.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→38.141 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3660 0 43 0 3703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023781
X-RAY DIFFRACTIONf_angle_d0.4945130
X-RAY DIFFRACTIONf_dihedral_angle_d12.5612228
X-RAY DIFFRACTIONf_chiral_restr0.039597
X-RAY DIFFRACTIONf_plane_restr0.005634
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3003-3.40680.36241240.35231354X-RAY DIFFRACTION86
3.4068-3.52850.36281280.32241375X-RAY DIFFRACTION88
3.5285-3.66960.29431260.30671610X-RAY DIFFRACTION99
3.6696-3.83650.34271360.29731596X-RAY DIFFRACTION100
3.8365-4.03860.33941530.28141594X-RAY DIFFRACTION100
4.0386-4.29130.29781240.25681607X-RAY DIFFRACTION100
4.2913-4.62210.31591470.24971571X-RAY DIFFRACTION100
4.6221-5.08630.2911570.24611574X-RAY DIFFRACTION100
5.0863-5.820.3767990.26821635X-RAY DIFFRACTION100
5.82-7.32410.2851410.25311594X-RAY DIFFRACTION100
7.3241-38.14390.17541490.18831588X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 228.6574 Å / Origin y: 16.6097 Å / Origin z: 96.5727 Å
111213212223313233
T0.6506 Å2-0.0298 Å20.0376 Å2-0.3866 Å20.0691 Å2--0.609 Å2
L1.7744 °21.0331 °22.1998 °2-0.6489 °21.3564 °2--3.5909 °2
S-0.0182 Å °-0.0725 Å °0.0265 Å °0.1158 Å °-0.0393 Å °0.0096 Å °-0.1396 Å °-0.1072 Å °0.0805 Å °
Refinement TLS groupSelection details: all

+
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