5G3X

Structure of recombinant granulovirus polyhedrin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.153 

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This is version 2.0 of the entry. See complete history


Literature

Atomic structure of granulin determined from native nanocrystalline granulovirus using an X-ray free-electron laser.

Gati, C.Oberthuer, D.Yefanov, O.Bunker, R.D.Stellato, F.Chiu, E.Yeh, S.M.Aquila, A.Basu, S.Bean, R.Beyerlein, K.R.Botha, S.Boutet, S.DePonte, D.P.Doak, R.B.Fromme, R.Galli, L.Grotjohann, I.James, D.R.Kupitz, C.Lomb, L.Messerschmidt, M.Nass, K.Rendek, K.Shoeman, R.L.Wang, D.Weierstall, U.White, T.A.Williams, G.J.Zatsepin, N.A.Fromme, P.Spence, J.C.Goldie, K.N.Jehle, J.A.Metcalf, P.Barty, A.Chapman, H.N.

(2017) Proc Natl Acad Sci U S A 114: 2247-2252

  • DOI: 10.1073/pnas.1609243114
  • Primary Citation of Related Structures:  
    5G0Z, 5G3X

  • PubMed Abstract: 
  • To understand how molecules function in biological systems, new methods are required to obtain atomic resolution structures from biological material under physiological conditions. Intense femtosecond-duration pulses from X-ray free-electron lasers (XFELs) can outrun most damage processes, vastly increasing the tolerable dose before the specimen is destroyed ...

    To understand how molecules function in biological systems, new methods are required to obtain atomic resolution structures from biological material under physiological conditions. Intense femtosecond-duration pulses from X-ray free-electron lasers (XFELs) can outrun most damage processes, vastly increasing the tolerable dose before the specimen is destroyed. This in turn allows structure determination from crystals much smaller and more radiation sensitive than previously considered possible, allowing data collection from room temperature structures and avoiding structural changes due to cooling. Regardless, high-resolution structures obtained from XFEL data mostly use crystals far larger than 1 μm 3 in volume, whereas the X-ray beam is often attenuated to protect the detector from damage caused by intense Bragg spots. Here, we describe the 2 Å resolution structure of native nanocrystalline granulovirus occlusion bodies (OBs) that are less than 0.016 μm 3 in volume using the full power of the Linac Coherent Light Source (LCLS) and a dose up to 1.3 GGy per crystal. The crystalline shell of granulovirus OBs consists, on average, of about 9,000 unit cells, representing the smallest protein crystals to yield a high-resolution structure by X-ray crystallography to date. The XFEL structure shows little to no evidence of radiation damage and is more complete than a model determined using synchrotron data from recombinantly produced, much larger, cryocooled granulovirus granulin microcrystals. Our measurements suggest that it should be possible, under ideal experimental conditions, to obtain data from protein crystals with only 100 unit cells in volume using currently available XFELs and suggest that single-molecule imaging of individual biomolecules could almost be within reach.


    Organizational Affiliation

    Center for Ultrafast Imaging, University of Hamburg, Hamburg 20355, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GRANULOVIRUS POLYHEDRINA248Cydia pomonella granulovirusMutation(s): 0 
UniProt
Find proteins for P87577 (Cydia pomonella granulosis virus (isolate Mexico/1963))
Explore P87577 
Go to UniProtKB:  P87577
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.153 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.058α = 90
b = 102.058β = 90
c = 102.058γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-22
    Type: Initial release
  • Version 1.1: 2017-03-01
    Changes: Database references
  • Version 1.2: 2017-03-15
    Changes: Database references
  • Version 2.0: 2019-10-23
    Changes: Atomic model, Data collection, Other