8CL9

Tubulin-DARPin D1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.0 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin alpha-1B chain437Bos taurusMutation(s): 0 
EC: 3.6.5
UniProt
Find proteins for P81947 (Bos taurus)
Explore P81947 
Go to UniProtKB:  P81947
Entity Groups  
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UniProt GroupP81947
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin beta-2B chain431Bos taurusMutation(s): 0 
UniProt
Find proteins for Q6B856 (Bos taurus)
Explore Q6B856 
Go to UniProtKB:  Q6B856
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UniProt GroupQ6B856
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN) D1C [auth F]155synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.47α = 90
b = 91.19β = 96.43
c = 82.7γ = 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 GTPClick 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