5JTB

Crystal structure of the chimeric protein of A2aAR-BRIL with bound iodide ions

PDB DOI: https://doi.org/10.2210/pdb5JTB/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens, Escherichia coli
Expression System: Spodoptera frugiperda
Mutation(s): Yes
Membrane Protein: Yes PDBTMMemProtMD

Deposited: 2016-05-09 Released: 2017-05-31
Deposition Author(s): Melnikov, I., Polovinkin, V., Shevtsov, M., Borshchevskiy, V., Cherezov, V., Popov, A., Gordeliy, V.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.294
R-Value Work: 0.234
R-Value Observed: 0.238

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Fast iodide-SAD phasing for high-throughput membrane protein structure determination.

Melnikov, I., Polovinkin, V., Kovalev, K., Gushchin, I., Shevtsov, M., Shevchenko, V., Mishin, A., Alekseev, A., Rodriguez-Valera, F., Borshchevskiy, V., Cherezov, V., Leonard, G.A., Gordeliy, V., Popov, A.

(2017) Sci Adv 3: e1602952-e1602952

PubMed: 28508075 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1126/sciadv.1602952
Primary Citation of Related Structures:
5JGP, 5JRF, 5JSI, 5JTB

PubMed Abstract:
We describe a fast, easy, and potentially universal method for the de novo solution of the crystal structures of membrane proteins via iodide-single-wavelength anomalous diffraction (I-SAD). The potential universality of the method is based on a common feature of membrane proteins-the availability at the hydrophobic-hydrophilic interface of positively charged amino acid residues with which iodide strongly interacts. We demonstrate the solution using I-SAD of four crystal structures representing different classes of membrane proteins, including a human G protein-coupled receptor (GPCR), and we show that I-SAD can be applied using data collection strategies based on either standard or serial x-ray crystallography techniques.

Organizational Affiliation

European Synchrotron Radiation Facility, 38043 Grenoble, France.

Macromolecule Content

Total Structure Weight: 56.07 kDa
Atom Count: 3,436
Modelled Residue Count: 388
Deposited Residue Count: 447
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a	A	447	Homo sapiens, Escherichia coli	Mutation(s): 3 Gene Names: ADORA2A, ADORA2, cybC Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7 Go to UniProtKB: P0ABE7
Find proteins for P29274 (Homo sapiens) Explore P29274 Go to UniProtKB: P29274
PHAROS: P29274 GTEx: ENSG00000128271
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P0ABE7P29274
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CLR Query on CLR Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A], E [auth A]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]
OLB Query on OLB Download Ideal Coordinates CCD File SDF format, chain X [auth A] MOL2 format, chain X [auth A] mmCIF format, chain X [auth A]	X [auth A]	(2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C₂₁ H₄₀ O₄ RZRNAYUHWVFMIP-QJRAZLAKSA-N		Interactions Focus chain X [auth A] Interactions & Density Focus chain X [auth A]
OLC Query on OLC Download Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A]	R [auth A] S [auth A] T [auth A] U [auth A] V [auth A] R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C₂₁ H₄₀ O₄ RZRNAYUHWVFMIP-GDCKJWNLSA-N		Interactions Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Interactions & Density Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A]
ZMA Query on ZMA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	4-{2-[(7-amino-2-furan-2-yl[1,2,4]triazolo[1,5-a][1,3,5]triazin-5-yl)amino]ethyl}phenol C₁₆ H₁₅ N₇ O₂ PWTBZOIUWZOPFT-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
OLA Query on OLA Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A]	N [auth A], O [auth A], P [auth A], Q [auth A]	OLEIC ACID C₁₈ H₃₄ O₂ ZQPPMHVWECSIRJ-KTKRTIGZSA-N		Interactions Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A]
IOD Query on IOD Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain I [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain I [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain I [auth A]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A]	L [auth A], M [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain L [auth A] Focus chain M [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
ZMA	BindingDB: 5JTB	Ki: min: 0.1, max: 395 (nM) from 18 assay(s)
		Kd: min: 0.22, max: 286 (nM) from 2 assay(s)
		IC50: min: 0.68, max: 81 (nM) from 7 assay(s)