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 

wwPDB Validation 3D Report Full Report



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: 10.1107/S2059798315021683
  • Primary Citation of Related Structures:  
    5D5A, 5D5C, 5D5B, 5D5E, 5D5D, 5D57, 5D56, 5D59, 5D58, 5D53

  • 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2 adrenergic receptor,Endolysin,Beta-2 adrenergic receptorA500Homo sapiensEscherichia virus T4Mutation(s): 0 
Gene Names: ADRB2ADRB2RB2AR
EC: 3.2.1.17
Find proteins for P07550 (Homo sapiens)
Explore P07550 
Go to UniProtKB:  P07550
NIH Common Fund Data Resources
PHAROS  P07550
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose
B
2 N/A
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CLR
Query on CLR

Download CCD File 
A
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
CAU
Query on CAU

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A
(2S)-1-(9H-Carbazol-4-yloxy)-3-(isopropylamino)propan-2-ol
C18 H22 N2 O2
BQXQGZPYHWWCEB-ZDUSSCGKSA-N
 Ligand Interaction
PLM
Query on PLM

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A
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
BU1
Query on BU1

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A
1,4-BUTANEDIOL
C4 H10 O2
WERYXYBDKMZEQL-UHFFFAOYSA-N
 Ligand Interaction
ACM
Query on ACM

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A
ACETAMIDE
C2 H5 N O
DLFVBJFMPXGRIB-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900018
Query on PRD_900018
Bbeta-maltoseOligosaccharide /  Nutrient

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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

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Science Foundation IrelandIreland12/IA/1255

Revision History 

  • 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