[English] 日本語
Yorodumi
- PDB-6vi4: Nanobody-Enabled Monitoring of Kappa Opioid Receptor States -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vi4
TitleNanobody-Enabled Monitoring of Kappa Opioid Receptor States
Components
  • Kappa opioid receptor
  • Nanobody 6
KeywordsMEMBRANE PROTEIN / G protein-coupled opioid receptor
Function / homology
Function and homology information


dynorphin receptor activity / response to acrylamide / regulation of saliva secretion / sensory perception of temperature stimulus / positive regulation of eating behavior / adenylate cyclase-inhibiting opioid receptor signaling pathway / G protein-coupled opioid receptor activity / negative regulation of luteinizing hormone secretion / G protein-coupled opioid receptor signaling pathway / positive regulation of dopamine secretion ...dynorphin receptor activity / response to acrylamide / regulation of saliva secretion / sensory perception of temperature stimulus / positive regulation of eating behavior / adenylate cyclase-inhibiting opioid receptor signaling pathway / G protein-coupled opioid receptor activity / negative regulation of luteinizing hormone secretion / G protein-coupled opioid receptor signaling pathway / positive regulation of dopamine secretion / sensory perception / positive regulation of potassium ion transmembrane transport / conditioned place preference / maternal behavior / receptor serine/threonine kinase binding / neuropeptide binding / positive regulation of p38MAPK cascade / eating behavior / behavioral response to cocaine / estrous cycle / neuropeptide signaling pathway / MECP2 regulates neuronal receptors and channels / axon terminus / sensory perception of pain / T-tubule / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / Peptide ligand-binding receptors / sarcoplasmic reticulum / locomotory behavior / cellular response to glucose stimulus / response to nicotine / response to insulin / synaptic vesicle membrane / response to estrogen / presynaptic membrane / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / chemical synaptic transmission / cellular response to lipopolysaccharide / postsynaptic membrane / perikaryon / response to ethanol / defense response to virus / neuron projection / immune response / dendrite / mitochondrion / nucleoplasm / membrane / plasma membrane / cytosol
Similarity search - Function
Kappa opioid receptor / Opioid receptor / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Serpentine type 7TM GPCR chemoreceptor Srsx / 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) ...Kappa opioid receptor / Opioid receptor / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Serpentine type 7TM GPCR chemoreceptor Srsx / 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
CHOLESTEROL / Chem-JDC / Kappa-type opioid receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsChe, T. / Roth, B.L.
Funding support1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)
CitationJournal: Nat Commun / Year: 2020
Title: Nanobody-enabled monitoring of kappa opioid receptor states.
Authors: Che, T. / English, J. / Krumm, B.E. / Kim, K. / Pardon, E. / Olsen, R.H.J. / Wang, S. / Zhang, S. / Diberto, J.F. / Sciaky, N. / Carroll, F.I. / Steyaert, J. / Wacker, D. / Roth, B.L.
History
DepositionJan 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Kappa opioid receptor
B: Kappa opioid receptor
C: Nanobody 6
D: Nanobody 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,4097
Polymers99,0914
Non-polymers1,3183
Water00
1
B: Kappa opioid receptor
C: Nanobody 6
hetero molecules

A: Kappa opioid receptor
D: Nanobody 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,4097
Polymers99,0914
Non-polymers1,3183
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_544x+1/2,-y-1,-z-1/21
Unit cell
Length a, b, c (Å)102.394, 108.191, 155.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

-
Components

#1: Protein Kappa opioid receptor / KOR-1


Mass: 34815.398 Da / Num. of mol.: 2 / Mutation: I135L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OPRK1, OPRK / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P41145
#2: Antibody Nanobody 6


Mass: 14730.255 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-JDC / (3R)-7-hydroxy-N-{(2S)-1-[(3R,4R)-4-(3-hydroxyphenyl)-3,4-dimethylpiperidin-1-yl]-3-methylbutan-2-yl}-1,2,3,4-tetrahydroisoquinoline-3-carboxamide


Mass: 465.628 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H39N3O3 / Feature type: SUBJECT OF INVESTIGATION / Comment: antagonist*YM
#4: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.33 Å3/Da / Density % sol: 71.63 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 100 mM Tris pH 7.0, 360-400 mM Ammonium citrate dibasic, 28-32% PEG400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.298→30.013 Å / Num. obs: 26340 / % possible obs: 99.1 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.182 / Rpim(I) all: 0.075 / Rrim(I) all: 0.198 / Χ2: 0.721 / Net I/σ(I): 3.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.3-3.396.61.11419980.480.4541.210.41499.2
3.39-3.496.80.88919800.6150.3590.9640.43199.6
3.49-3.66.90.74420040.7280.2980.8060.4499.3
3.6-3.736.90.5920090.8360.2370.6390.46899.5
3.73-3.886.90.43819960.8980.1750.4740.50199.5
3.88-4.056.70.3320110.9430.1350.3580.57599.4
4.05-4.276.10.2420100.9510.1040.2630.63699
4.27-4.536.30.1920130.9720.080.2080.78399.3
4.53-4.886.30.14920230.9840.0630.1620.91199.2
4.88-5.3770.13820420.9910.0550.1490.89499.4
5.37-6.1470.15720430.9850.0620.1690.74199.3
6.14-7.726.60.11420650.990.0480.1240.94698.6
7.72-3060.05921460.9960.0270.0661.7197.7

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DJH

4djh


Resolution: 3.3→30.01 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2714 1282 4.88 %
Rwork0.2418 25000 -
obs0.2433 26282 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 163.64 Å2 / Biso mean: 87.3078 Å2 / Biso min: 41.6 Å2
Refinement stepCycle: final / Resolution: 3.3→30.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5951 0 96 0 6047
Biso mean--87.17 --
Num. residues----794
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016180
X-RAY DIFFRACTIONf_angle_d1.3448449
X-RAY DIFFRACTIONf_dihedral_angle_d16.3642105
X-RAY DIFFRACTIONf_chiral_restr0.0851027
X-RAY DIFFRACTIONf_plane_restr0.0081026
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3-3.430.38771230.31082674279797
3.43-3.590.31181620.27342731289399
3.59-3.770.31411540.25652743289799
3.77-4.010.32111470.23692753290099
4.01-4.320.24081250.22332790291599
4.32-4.750.24491490.21272757290699
4.75-5.440.24661410.21082809295099
5.44-6.830.25421200.28462857297799
6.84-30.010.2651610.24272886304798

+
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://pdbjlvh1.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