5D5B

In meso X-ray crystallography structure of the Beta2-adrenergic receptor at 100 K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.242 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history


Literature

In meso in situ serial X-ray crystallography of soluble and membrane proteins at cryogenic temperatures.

Huang, C.Y.Olieric, V.Ma, P.Howe, N.Vogeley, L.Liu, X.Warshamanage, R.Weinert, T.Panepucci, E.Kobilka, B.Diederichs, K.Wang, M.Caffrey, M.

(2016) Acta Crystallogr D Struct Biol 72: 93-112

  • DOI: https://doi.org/10.1107/S2059798315021683
  • Primary Citation of Related Structures:  
    5D52, 5D53, 5D54, 5D56, 5D57, 5D58, 5D59, 5D5A, 5D5B, 5D5C, 5D5D, 5D5E, 5D5F

  • PubMed Abstract: 

    Here, a method for presenting crystals of soluble and membrane proteins growing in the lipid cubic or sponge phase for in situ diffraction data collection at cryogenic temperatures is introduced. The method dispenses with the need for the technically demanding and inefficient crystal-harvesting step that is an integral part of the lipid cubic phase or in meso method of growing crystals. Crystals are dispersed in a bolus of mesophase sandwiched between thin plastic windows. The bolus contains tens to hundreds of crystals, visible with an in-line microscope at macromolecular crystallography synchrotron beamlines and suitably disposed for conventional or serial crystallographic data collection. Wells containing the crystal-laden boluses are removed individually from hermetically sealed glass plates in which crystallization occurs, affixed to pins on goniometer bases and excess precipitant is removed from around the mesophase. The wells are snap-cooled in liquid nitrogen, stored and shipped in Dewars, and manually or robotically mounted on a goniometer in a cryostream for diffraction data collection at 100 K, as is performed routinely with standard, loop-harvested crystals. The method is a variant on the recently introduced in meso in situ serial crystallography (IMISX) method that enables crystallographic measurements at cryogenic temperatures where crystal lifetimes are enormously enhanced whilst reducing protein consumption dramatically. The new approach has been used to generate high-resolution crystal structures of a G-protein-coupled receptor, α-helical and β-barrel transporters and an enzyme as model integral membrane proteins. Insulin and lysozyme were used as test soluble proteins. The quality of the data that can be generated by this method was attested to by performing sulfur and bromine SAD phasing with two of the test proteins.


  • Organizational Affiliation

    Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College, Dublin 2, D02 R590, Ireland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2 adrenergic receptor,Endolysin,Beta-2 adrenergic receptor500Homo sapiensTequatrovirus T4Mutation(s): 0 
Gene Names: ADRB2ADRB2RB2AR
EC: 3.2.1.17
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P07550 (Homo sapiens)
Explore P07550 
Go to UniProtKB:  P07550
PHAROS:  P07550
GTEx:  ENSG00000169252 
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP00720P07550
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose
B
2N/A
Glycosylation Resources
GlyTouCan:  G66120GK
GlyCosmos:  G66120GK
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLR
Query on CLR

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
CAU
Query on CAU

Download Ideal Coordinates CCD File 
C [auth A](2S)-1-(9H-Carbazol-4-yloxy)-3-(isopropylamino)propan-2-ol
C18 H22 N2 O2
BQXQGZPYHWWCEB-ZDUSSCGKSA-N
PLM
Query on PLM

Download Ideal Coordinates CCD File 
I [auth A]PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
J [auth A]
K [auth A]
L [auth A]
M [auth A]
N [auth A]
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
BU1
Query on BU1

Download Ideal Coordinates CCD File 
D [auth A]1,4-BUTANEDIOL
C4 H10 O2
WERYXYBDKMZEQL-UHFFFAOYSA-N
ACM
Query on ACM

Download Ideal Coordinates CCD File 
E [auth A]ACETAMIDE
C2 H5 N O
DLFVBJFMPXGRIB-UHFFFAOYSA-N
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.242 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107α = 90
b = 170β = 106.25
c = 40.5γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Science Foundation IrelandIreland12/IA/1255

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-13
    Type: Initial release
  • Version 1.1: 2016-03-02
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-01-10
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-11-06
    Changes: Structure summary