7ZY3

Room temperature structure of Archaerhodopsin-3 obtained 110 ns after photoexcitation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A versatile approach to high-density microcrystals in lipidic cubic phase for room-temperature serial crystallography.

Birch, J.Kwan, T.O.C.Judge, P.J.Axford, D.Aller, P.Butryn, A.Reis, R.I.Bada Juarez, J.F.Vinals, J.Owen, R.L.Nango, E.Tanaka, R.Tono, K.Joti, Y.Tanaka, T.Owada, S.Sugahara, M.Iwata, S.Orville, A.M.Watts, A.Moraes, I.

(2023) J Appl Crystallogr 56: 1361-1370

  • DOI: https://doi.org/10.1107/S1600576723006428
  • Primary Citation of Related Structures:  
    7ZY3, 8A2O, 8A2P

  • PubMed Abstract: 

    Serial crystallography has emerged as an important tool for structural studies of integral membrane proteins. The ability to collect data from micrometre-sized weakly diffracting crystals at room temperature with minimal radiation damage has opened many new opportunities in time-resolved studies and drug discovery. However, the production of integral membrane protein microcrystals in lipidic cubic phase at the desired crystal density and quantity is challenging. This paper introduces VIALS (versatile approach to high-density microcrystals in lipidic cubic phase for serial crystallography), a simple, fast and efficient method for preparing hundreds of microlitres of high-density microcrystals suitable for serial X-ray diffraction experiments at both synchrotron and free-electron laser sources. The method is also of great benefit for rational structure-based drug design as it facilitates in situ crystal soaking and rapid determination of many co-crystal structures. Using the VIALS approach, room-temperature structures are reported of (i) the archaerhodopsin-3 protein in its dark-adapted state and 110 ns photocycle intermediate, determined to 2.2 and 1.7 Å, respectively, and (ii) the human A 2A adenosine receptor in complex with two different ligands determined to a resolution of 3.5 Å.


  • Organizational Affiliation

    Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Archaerhodopsin-3252Halorubrum sodomenseMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P96787 (Halorubrum sodomense)
Explore P96787 
Go to UniProtKB:  P96787
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP96787
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RET (Subject of Investigation/LOI)
Query on RET

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B [auth A]RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
PLM
Query on PLM

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E [auth A],
F [auth A]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
R16
Query on R16

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D [auth A]HEXADECANE
C16 H34
DCAYPVUWAIABOU-UHFFFAOYSA-N
DD9
Query on DD9

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C [auth A]nonane
C9 H20
BKIMMITUMNQMOS-UHFFFAOYSA-N
CA
Query on CA

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G [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

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J [auth A],
K [auth A],
L [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

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I [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

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H [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA
A
L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.2α = 90
b = 48.3β = 90
c = 104.7γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
DIALSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government--
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/N006011/1
Wellcome TrustUnited Kingdom202892/Z/16/Z

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-14
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Database references
  • Version 1.2: 2024-02-07
    Changes: Refinement description