[English] 日本語
Yorodumi
- PDB-4bv0: High Resolution Structure of Evolved Agonist-bound Neurotensin Re... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4bv0
TitleHigh Resolution Structure of Evolved Agonist-bound Neurotensin Receptor 1 Mutant without Lysozyme Fusion
Components
  • NEUROTENSIN RECEPTOR TYPE 1
  • NEUROTENSIN/NEUROMEDIN N
KeywordsSIGNALING PROTEIN / G PROTEIN COUPLED RECEPTOR / MEMBRANE PROTEIN
Function / homology
Function and homology information


regulation of locomotion involved in locomotory behavior / Peptide ligand-binding receptors / positive regulation of locomotion / neuropeptide receptor binding / 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 locomotion involved in locomotory behavior / Peptide ligand-binding receptors / positive regulation of locomotion / neuropeptide receptor binding / 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 / response to antipsychotic drug / neuron spine / L-glutamate import across plasma membrane / regulation of behavioral fear response / regulation of respiratory gaseous exchange / neuropeptide hormone activity / 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 / digestive tract development / G alpha (q) signalling events / hyperosmotic response / positive regulation of glutamate secretion / response to mineralocorticoid / response to food / response to corticosterone / cellular response to lithium ion / temperature homeostasis / positive regulation of inositol phosphate biosynthetic process / response to lipid / response to stress / detection of temperature stimulus involved in sensory perception of pain / associative learning / conditioned place preference / neuropeptide signaling pathway / cellular response to dexamethasone stimulus / response to axon injury / transport vesicle / axon terminus / positive regulation of release of sequestered calcium ion into cytosol / response to amphetamine / blood vessel diameter maintenance / dendritic shaft / adult locomotory behavior / learning / response to cocaine / liver development / cellular response to nerve growth factor stimulus / visual learning / cytoplasmic side of plasma membrane / terminal bouton / response to estradiol / perikaryon / dendritic spine / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of apoptotic process / membrane raft / receptor ligand activity / axon / negative regulation of gene expression / neuronal cell body / dendrite / positive regulation of gene expression / negative regulation of apoptotic process / protein-containing complex binding / 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 / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. ...Neurotensin/neuromedin N / Neurotensin/neuromedin N precursor / Neurotensin receptor / Neurotensin type 1 receptor / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / 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) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Neurotensin/neuromedin N / Neurotensin receptor type 1
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsEgloff, P. / Hillenbrand, M. / Scott, D.J. / Schlinkmann, K.M. / Heine, P. / Balada, S. / Batyuk, A. / Mittl, P. / Schuetz, M. / Plueckthun, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structure of Signaling-Competent Neurotensin Receptor 1 Obtained by Directed Evolution in Escherichia Coli
Authors: Egloff, P. / Hillenbrand, M. / Klenk, C. / Batyuk, A. / Heine, P. / Balada, S. / Schlinkmann, K.M. / Scott, D.J. / Schuetz, M. / Plueckthun, A.
History
DepositionJun 24, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Feb 26, 2014Group: Database references
Revision 1.3Jun 20, 2018Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.page_last / _diffrn_source.pdbx_synchrotron_beamline
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.5Nov 13, 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
B: NEUROTENSIN RECEPTOR TYPE 1
C: NEUROTENSIN/NEUROMEDIN N
D: NEUROTENSIN/NEUROMEDIN N


Theoretical massNumber of molelcules
Total (without water)77,6134
Polymers77,6134
Non-polymers00
Water00
1
A: NEUROTENSIN RECEPTOR TYPE 1
C: NEUROTENSIN/NEUROMEDIN N


Theoretical massNumber of molelcules
Total (without water)38,8072
Polymers38,8072
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-8.1 kcal/mol
Surface area14650 Å2
MethodPISA
2
B: NEUROTENSIN RECEPTOR TYPE 1
D: NEUROTENSIN/NEUROMEDIN N


Theoretical massNumber of molelcules
Total (without water)38,8072
Polymers38,8072
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-7.1 kcal/mol
Surface area14950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.580, 91.560, 208.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A
211CHAIN B
112CHAIN C
212CHAIN D

NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (-0.488, -0.155, -0.859), (-0.1464, -0.9556, 0.2556), (-0.8604, 0.2505, 0.4437)
Vector: -4.465, -30.54, 2.75)

-
Components

#1: Protein NEUROTENSIN RECEPTOR TYPE 1 / NEUROTENSIN RECEPTOR 1 TM86VDIC3B / NT-R-1 / NTR1 / HIGH-AFFINITY LEVOCABASTINE-INSENSITIVE ...NEUROTENSIN RECEPTOR 1 TM86VDIC3B / NT-R-1 / NTR1 / HIGH-AFFINITY LEVOCABASTINE-INSENSITIVE NEUROTENSIN RECEPTOR / NTRH


Mass: 37719.238 Da / Num. of mol.: 2 / Fragment: RESIDUES 50-390 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: THERMOSTABLE MUTANT WITH INTRACELLULAR LOOP 3 DELETION B (T279-I295)
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PEP-TM86VDIC3III / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): TUNER / References: UniProt: P20789
#2: Protein/peptide NEUROTENSIN/NEUROMEDIN N / LARGE NEUROMEDIN N / NMN-125 / NEUROMEDIN N / NN / NMN / NEUROTENSIN / NT / TAIL PEPTIDE


Mass: 1087.277 Da / Num. of mol.: 2 / Fragment: C-TERMINUS, RESIDUES 157-162
Source method: isolated from a genetically manipulated source
Details: THE SEQUENCE RRPYIL CORRESPONDS TO RESIDUES 8-13 OF THE NEUROTENSIN C-TERMINUS. THE FULL CRYSTALLIZED CONSTRUCT WAS GPGGRRPYIL (THE N-TERMINAL GPGG IS AN ARTIFICIAL LINKER).
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P20068
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.73 Å3/Da / Density % sol: 67.03 % / Description: NONE
Crystal growpH: 9.4
Details: 22.5% (V/V) PEG600, 0.5 M NACL, 50 MM GLYCINE PH 9.4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Type: SLS / Wavelength: 1
DetectorType: DECTRIS PILATUS / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 21665 / % possible obs: 99.2 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.55
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 0.51 / % possible all: 97

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZEV

3zev


Resolution: 3.1→19.88 Å / SU ML: 0.77 / σ(F): 1.35 / Phase error: 45.01 / Stereochemistry target values: ML / Details: PHENIX AND REFMAC WERE USED
RfactorNum. reflection% reflection
Rfree0.3105 1036 5 %
Rwork0.284 --
obs-20680 95.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4865 0 0 0 4865
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034985
X-RAY DIFFRACTIONf_angle_d0.6516794
X-RAY DIFFRACTIONf_dihedral_angle_d10.1051725
X-RAY DIFFRACTIONf_chiral_restr0.046821
X-RAY DIFFRACTIONf_plane_restr0.003818
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDType
11AX-RAY DIFFRACTIONPOSITIONAL
12BX-RAY DIFFRACTIONPOSITIONAL
21CX-RAY DIFFRACTIONPOSITIONAL
22DX-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1002-3.2630.44841370.44852589X-RAY DIFFRACTION89
3.263-3.46650.44711400.45342635X-RAY DIFFRACTION92
3.4665-3.73250.47621330.42682512X-RAY DIFFRACTION86
3.7325-4.10510.34581510.33792899X-RAY DIFFRACTION99
4.1051-4.69230.29041550.23952934X-RAY DIFFRACTION100
4.6923-5.88620.28641560.26282967X-RAY DIFFRACTION100
5.8862-19.87650.26551640.23753108X-RAY DIFFRACTION100

+
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