6LPK

A2AR crystallized in EROCOC17+4, LCP-SFX at 293 K

PDB DOI: https://doi.org/10.2210/pdb6LPK/pdb

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

Deposited: 2020-01-10 Released: 2020-11-25
Deposition Author(s): Ihara, K., Hato, M., Nakane, T., Yamashita, K., Kimura-Someya, T., Hosaka, T., Ishizuka-Katsura, Y., Tanaka, R., Tanaka, T., Sugahara, M., Hirata, K., Yamamoto, M., Nureki, O., Tono, K., Nango, E., Iwata, S., Shirouzu, M.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.209
R-Value Work: 0.177
R-Value Observed: 0.179

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Isoprenoid-chained lipid EROCOC 17+4 : a new matrix for membrane protein crystallization and a crystal delivery medium in serial femtosecond crystallography.

Ihara, K., Hato, M., Nakane, T., Yamashita, K., Kimura-Someya, T., Hosaka, T., Ishizuka-Katsura, Y., Tanaka, R., Tanaka, T., Sugahara, M., Hirata, K., Yamamoto, M., Nureki, O., Tono, K., Nango, E., Iwata, S., Shirouzu, M.

(2020) Sci Rep 10: 19305-19305

PubMed: 33168855 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41598-020-76277-x
Primary Citation of Related Structures:
6LPJ, 6LPK, 6LPL

PubMed Abstract:
In meso crystallization of membrane proteins relies on the use of lipids capable of forming a lipidic cubic phase (LCP). However, almost all previous crystallization trials have used monoacylglycerols, with 1-(cis-9-octadecanoyl)-rac-glycerol (MO) being the most widely used lipid. We now report that EROCOC ₁₇₊₄ mixed with 10% (w/w) cholesterol (Fig. 1) serves as a new matrix for crystallization and a crystal delivery medium in the serial femtosecond crystallography of Adenosine A _2A receptor (A _2AR). The structures of EROCOC ₁₇₊₄-matrix grown A _2AR crystals were determined at 2.0 Å resolution by serial synchrotron rotation crystallography at a cryogenic temperature, and at 1.8 Å by LCP-serial femtosecond crystallography, using an X-ray free-electron laser at 4 and 20 °C sample temperatures, and are comparable to the structure of the MO-matrix grown A _2AR crystal (PDB ID: 4EIY). Moreover, X-ray scattering measurements indicated that the EROCOC ₁₇₊₄/water system did not form the crystalline L _C phase at least down to - 20 °C, in marked contrast to the equilibrium MO/water system, which transforms into the crystalline L _C phase below about 17 °C. As the L _C phase formation within the LCP-matrix causes difficulties in protein crystallography experiments in meso, this feature of EROCOC ₁₇₊₄ will expand the utility of the in meso method.

Organizational Affiliation

RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.

Macromolecule Content

Total Structure Weight: 56.06 kDa
Atom Count: 3,583
Modelled Residue Count: 390
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
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli) Go to UniProtKB: P0ABE7
Find proteins for P29274 (Homo sapiens) Go to UniProtKB: P29274
PHAROS: P29274 GTEx: ENSG00000128271
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 12 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ER0 (Subject of Investigation/LOI) Query on ER0 Download Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain X [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain X [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain X [auth A]	Q [auth A], X [auth A]	[(2~{R},3~{S})-2,3,4-tris(oxidanyl)butyl] (5~{R},9~{R},13~{R})-5,9,13,17-tetramethyloctadecanoate C₂₆ H₅₂ O₅ RSTFOCYJXCUQHZ-UUFXTFJOSA-N		Interactions Focus chain Q [auth A] Focus chain X [auth A]
CLR Query on CLR Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	D [auth A], E [auth A], F [auth A]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [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]
8K6 Query on 8K6 Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] MOL2 format, chain K [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] mmCIF format, chain K [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A]	K [auth A], S [auth A], T [auth A]	Octadecane C₁₈ H₃₈ RZJRJXONCZWCBN-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain S [auth A] Focus chain T [auth A]
MYS Query on MYS Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain AA [auth A] SDF format, chain H [auth A] SDF format, chain O [auth A] SDF format, chain R [auth A] SDF format, chain Y [auth A] MOL2 format, chain J [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain H [auth A] MOL2 format, chain O [auth A] MOL2 format, chain R [auth A] MOL2 format, chain Y [auth A] mmCIF format, chain J [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain H [auth A] mmCIF format, chain O [auth A] mmCIF format, chain R [auth A] mmCIF format, chain Y [auth A]	AA [auth A] H [auth A] J [auth A] O [auth A] R [auth A] AA [auth A], H [auth A], J [auth A], O [auth A], R [auth A], Y [auth A]	PENTADECANE C₁₅ H₃₂ YCOZIPAWZNQLMR-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain H [auth A] Focus chain J [auth A] Focus chain O [auth A] Focus chain R [auth A] Focus chain Y [auth A]
TRD Query on TRD Download Ideal Coordinates CCD File SDF format, chain BA [auth A] SDF format, chain W [auth A] SDF format, chain Z [auth A] SDF format, chain U [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain W [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain U [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain W [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain U [auth A]	BA [auth A], U [auth A], W [auth A], Z [auth A]	TRIDECANE C₁₃ H₂₈ IIYFAKIEWZDVMP-UHFFFAOYSA-N		Interactions Focus chain BA [auth A] Focus chain U [auth A] Focus chain W [auth A] Focus chain Z [auth A]
D12 Query on D12 Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	DODECANE C₁₂ H₂₆ SNRUBQQJIBEYMU-UHFFFAOYSA-N		Interactions Focus chain G [auth A]
UND Query on UND Download Ideal Coordinates CCD File SDF format, chain P [auth A] MOL2 format, chain P [auth A] mmCIF format, chain P [auth A]	P [auth A]	UNDECANE C₁₁ H₂₄ RSJKGSCJYJTIGS-UHFFFAOYSA-N		Interactions Focus chain P [auth A]
D10 Query on D10 Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain L [auth A]
OCT Query on OCT Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain V [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain V [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain V [auth A]	M [auth A], N [auth A], V [auth A]	N-OCTANE C₈ H₁₈ TVMXDCGIABBOFY-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain V [auth A]
HEX Query on HEX Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	HEXANE C₆ H₁₄ VLKZOEOYAKHREP-UHFFFAOYSA-N		Interactions Focus chain I [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
ZMA	BindingDB: 6LPK	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)