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Crystal Structure of a nanobody-stabilized active state of the kappa-opioid receptor

UID: 10719

Author(s): Che, Tao, Majumdar, Susruta*, Zaidi, Saheem A., Ondachi, Pauline, McCorvy, John D., Wang, Sheng, Mosier, Philip D., Uprety, Rajendra*, Vardy, Eyal, Krumm, Brian E., Han, Gye W., Lee, Ming-Yue, Pardon, Els, Steyaert, Jan, Huang, Xi-Ping, Strachan, Ryan T., Tribo, Alexandra R., Pasternak, Gavril W.*, Carroll, F. Ivy, Stevens, Raymond C., Cherezov, Vadim, Katritch, Vsevolod, Wacker, Daniel, Roth, Bryan L. * MSK affiliated

Description
This deposit in the Research Collaboratory for Structural Bioinformatics Protein Data Base (PDB) includes x-ray diffraction data used for modeling the crystal structure of a nanobody-stabilized active state of the kappa-opioid receptor. The main summary display for this entry includes information on the experimental data, validation, macromolecules, small molecules, version history and funding information. Data is provided for download as FASTA sequence format, the Protein Data Bases own PDB format, crystallographic information file (.cif), XML, DSN6 Maps, MTZ Map Coefficients, as well as the full validation file in either PDF or XML formats. Additionally, the PDB provides embedded visualization software to display a 3D view of the protein: PDB's Mol* viewer, NGL viewer, and JSmol. PDB provides protein family and gene product annotations, additional details about the experiment parameters, a Protein Feature Viewer (in the Sequence tab) which displays all available features and alignments of known polymer instances, and a genome view which provides graphical summaries of the correspondences between PDB Entity sequences and genomes.
Subject of Study
Escherichia coli
Homo sapiens
Lama glama
Subject(s)
Protein Binding
Receptors, Opioid, kappa
Access via PDB

Research Collaboratory for Structural Bioinformatics Protein Data Base
Accession #: 6B73

Access Restrictions
Free to All
Access Instructions
The RCSB Protein Data Base provides access to 3D structure data for large biological molecules (proteins, DNA, and RNA). Sequence, protein structure, EM, and other data can be downloaded in formats specific to the data they contain.
DOI
10.2210/pdb6B73/pdb
Associated Publications
Che T, Majumdar S, Zaidi S, et al. Structure of the nanobody-stabilized active state of the kappa opioid receptor. Cell. 2018; 172(1-2):55-67.e9.
Data Type
Analytical Chemistry
Equipment Used
APS (Advanced Photon Source) Beamline 23-ID-D

Sector 21 uses canted undulators to provide two independent sources for four ID end stations: 21-ID-D, 21-ID-E, 21-ID-F, and 21-ID-G. All four stations can be used simultaneously and independently. The 21-ID-D station supports macromolecular crystallography, SAD and MAD phasing over a wide energy range from 6.5 keV to 20 keV.

DECTRIS EIGER X 16M

X-ray detector with optimized solid-state sensors and CMOS readout ASICs in hybrid pixel technology

Software Used
BUSTER

Structure refinement package

HKL-3000

The HKL suite is a package of programs intended for the analysis of X-ray diffraction data collected from single crystals, and consists of three programs: XdisplayFfor visualization of the diffraction pattern, Denzofor data reduction and integration, and Scalepackfor merging and scaling of the intensities obtained by Denzoor other programs.

JSmol

HTML5 modality of the Jmol open-source Java viewer for chemical structures in 3D

Mol*

Plugin created by the Protein Data Base to visualize protein structures

NGL

NGL Viewer is a web application for molecular visualization.

PHASER

Phaser is a program for phasing macromolecular crystal structures with maximum likelihood methods.

Dataset Format(s)
PDF, XML, FASTA, PDB, CIF, MTZ, DSN6
Data Tool(s)
X-ray crystallography (XRC)
Dataset Size
696 KB (FASTA), 268 KB (PDB)
Data Catalog Record Updated
2021-07-15