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

Cornelius Gati, Dominik Oberthuer, Oleksandr Yefanov, Richard D. Bunker, Francesco Stellato, Elaine Chiu, Shin Mei Yeh, Andrew Aquila, Shibom Basu, Richard Bean, Kenneth R. Beyerlein, Sabine Botha, Sébastien Boutet, Daniel P. DePonte, R. Bruce Doak, Raimund Fromme, Lorenzo Galli, Ingo Grotjohann, Daniel R. James, Christopher Kupitz & 17 others Lukas Lomb, Marc Messerschmidt, Karol Nass, Kimberly Rendek, Robert L. Shoeman, Dingjie Wang, Uwe Weierstall, Thomas A. White, Garth J. Williams, Nadia Zatsepin, Petra Fromme, John Spence, Kenneth N. Goldie, Johannes A. Jehle, Peter Metcalf, Anton Barty, Henry N. Chapman

Research output: Contribution to journalArticle

25 Citations (Scopus)

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. 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 μm3 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 μm3 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.

Original languageEnglish (US)
Pages (from-to)2247-2252
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume114
Issue number9
DOIs
StatePublished - Feb 28 2017

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Granulovirus
Lasers
X-Rays
Electrons
Radiation
Synchrotrons
X Ray Crystallography
Cell Size
Proteins
granulin precursor protein
Light
Temperature

Keywords

  • Bioimaging
  • Nanocrystals
  • SFX
  • Structural biology
  • XFEL

ASJC Scopus subject areas

  • General

Cite this

Atomic structure of granulin determined from native nanocrystalline granulovirus using an X-ray free-electron laser. / Gati, Cornelius; Oberthuer, Dominik; Yefanov, Oleksandr; Bunker, Richard D.; Stellato, Francesco; Chiu, Elaine; Yeh, Shin Mei; Aquila, Andrew; Basu, Shibom; Bean, Richard; Beyerlein, Kenneth R.; Botha, Sabine; Boutet, Sébastien; DePonte, Daniel P.; Doak, R. Bruce; Fromme, Raimund; Galli, Lorenzo; Grotjohann, Ingo; James, Daniel R.; Kupitz, Christopher; Lomb, Lukas; Messerschmidt, Marc; Nass, Karol; Rendek, Kimberly; Shoeman, Robert L.; Wang, Dingjie; Weierstall, Uwe; White, Thomas A.; Williams, Garth J.; Zatsepin, Nadia; Fromme, Petra; Spence, John; Goldie, Kenneth N.; Jehle, Johannes A.; Metcalf, Peter; Barty, Anton; Chapman, Henry N.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 114, No. 9, 28.02.2017, p. 2247-2252.

Research output: Contribution to journalArticle

Gati, C, Oberthuer, D, Yefanov, O, Bunker, RD, Stellato, F, Chiu, E, Yeh, SM, Aquila, A, Basu, S, Bean, R, Beyerlein, KR, Botha, S, Boutet, S, DePonte, DP, Doak, RB, Fromme, R, Galli, L, Grotjohann, I, James, DR, Kupitz, C, Lomb, L, Messerschmidt, M, Nass, K, Rendek, K, Shoeman, RL, Wang, D, Weierstall, U, White, TA, Williams, GJ, Zatsepin, N, Fromme, P, Spence, J, Goldie, KN, Jehle, JA, Metcalf, P, Barty, A & Chapman, HN 2017, 'Atomic structure of granulin determined from native nanocrystalline granulovirus using an X-ray free-electron laser' Proceedings of the National Academy of Sciences of the United States of America, vol. 114, no. 9, pp. 2247-2252. https://doi.org/10.1073/pnas.1609243114
Gati, Cornelius ; Oberthuer, Dominik ; Yefanov, Oleksandr ; Bunker, Richard D. ; Stellato, Francesco ; Chiu, Elaine ; Yeh, Shin Mei ; Aquila, Andrew ; Basu, Shibom ; Bean, Richard ; Beyerlein, Kenneth R. ; Botha, Sabine ; Boutet, Sébastien ; DePonte, Daniel P. ; Doak, R. Bruce ; Fromme, Raimund ; Galli, Lorenzo ; Grotjohann, Ingo ; James, Daniel R. ; Kupitz, Christopher ; Lomb, Lukas ; Messerschmidt, Marc ; Nass, Karol ; Rendek, Kimberly ; Shoeman, Robert L. ; Wang, Dingjie ; Weierstall, Uwe ; White, Thomas A. ; Williams, Garth J. ; Zatsepin, Nadia ; Fromme, Petra ; Spence, John ; Goldie, Kenneth N. ; Jehle, Johannes A. ; Metcalf, Peter ; Barty, Anton ; Chapman, Henry N. / Atomic structure of granulin determined from native nanocrystalline granulovirus using an X-ray free-electron laser. In: Proceedings of the National Academy of Sciences of the United States of America. 2017 ; Vol. 114, No. 9. pp. 2247-2252.
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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. 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 μm3 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 {\AA} resolution structure of native nanocrystalline granulovirus occlusion bodies (OBs) that are less than 0.016 μm3 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.",
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AU - Gati, Cornelius

AU - Oberthuer, Dominik

AU - Yefanov, Oleksandr

AU - Bunker, Richard D.

AU - Stellato, Francesco

AU - Chiu, Elaine

AU - Yeh, Shin Mei

AU - Aquila, Andrew

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AU - James, Daniel R.

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AU - Shoeman, Robert L.

AU - Wang, Dingjie

AU - Weierstall, Uwe

AU - White, Thomas A.

AU - Williams, Garth J.

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AU - Spence, John

AU - Goldie, Kenneth N.

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N2 - 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 μm3 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 μm3 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.

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