8CL7

Krokinobacter eikastus rhodopsin 2 (KR2) in dark state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted RETClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

A multi-reservoir extruder for time-resolved serial protein crystallography and compound screening at X-ray free-electron lasers.

Wranik, M.Kepa, M.W.Beale, E.V.James, D.Bertrand, Q.Weinert, T.Furrer, A.Glover, H.Gashi, D.Carrillo, M.Kondo, Y.Stipp, R.T.Khusainov, G.Nass, K.Ozerov, D.Cirelli, C.Johnson, P.J.M.Dworkowski, F.Beale, J.H.Stubbs, S.Zamofing, T.Schneider, M.Krauskopf, K.Gao, L.Thorn-Seshold, O.Bostedt, C.Bacellar, C.Steinmetz, M.O.Milne, C.Standfuss, J.

(2023) Nat Commun 14: 7956-7956

  • DOI: https://doi.org/10.1038/s41467-023-43523-5
  • Primary Citation of Related Structures:  
    8CL5, 8CL6, 8CL7, 8CL8, 8CL9, 8CLB, 8CLC, 8CLD, 8CLE, 8CLF, 8CLG, 8CLH

  • PubMed Abstract: 

    Serial crystallography at X-ray free-electron lasers (XFELs) permits the determination of radiation-damage free static as well as time-resolved protein structures at room temperature. Efficient sample delivery is a key factor for such experiments. Here, we describe a multi-reservoir, high viscosity extruder as a step towards automation of sample delivery at XFELs. Compared to a standard single extruder, sample exchange time was halved and the workload of users was greatly reduced. In-built temperature control of samples facilitated optimal extrusion and supported sample stability. After commissioning the device with lysozyme crystals, we collected time-resolved data using crystals of a membrane-bound, light-driven sodium pump. Static data were also collected from the soluble protein tubulin that was soaked with a series of small molecule drugs. Using these data, we identify low occupancy (as little as 30%) ligands using a minimal amount of data from a serial crystallography experiment, a result that could be exploited for structure-based drug design.


  • Organizational Affiliation

    Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen-PSI, Villigen, 5232, Switzerland. maximilian.wranik@psi.ch.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium pumping rhodopsin265Dokdonia eikastaMutation(s): 0 
Gene Names: NaR
Membrane Entity: Yes 
UniProt
Find proteins for N0DKS8 (Dokdonia eikasta)
Explore N0DKS8 
Go to UniProtKB:  N0DKS8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupN0DKS8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RET (Subject of Investigation/LOI)
Query on RET

Download Ideal Coordinates CCD File 
B [auth A]RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
LFA
Query on LFA

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
EICOSANE
C20 H42
CBFCDTFDPHXCNY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.46α = 90
b = 84.89β = 90
c = 234.95γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted RETClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland31003A_179351
Swiss National Science FoundationSwitzerland310030_207462
Swiss National Science FoundationSwitzerland310030_192566

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-13
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Structure summary