Serial Femtosecond Crystallography (SFX) of Ground State Bacteriorhodopsin Crystallized from Bicelles in Complex with Iodine-labeled Detergent HAD13a Determined Using 7-keV X-ray Free Electron Laser (XFEL) at SACLA

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.166 

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Membrane protein structure determination by SAD, SIR, or SIRAS phasing in serial femtosecond crystallography using an iododetergent

Nakane, T.Hanashima, S.Suzuki, M.Saiki, H.Hayashi, T.Kakinouchi, K.Sugiyama, S.Kawatake, S.Matsuoka, S.Matsumori, N.Nango, E.Kobayashi, J.Shimamura, T.Kimura, K.Mori, C.Kunishima, N.Sugahara, M.Takakyu, Y.Inoue, S.Masuda, T.Hosaka, T.Tono, K.Joti, Y.Kameshima, T.Hatsui, T.Yabashi, M.Inoue, T.Nureki, O.Iwata, S.Murata, M.Mizohata, E.

(2016) Proc Natl Acad Sci U S A 113: 13039-13044

  • DOI: https://doi.org/10.1073/pnas.1602531113
  • Primary Citation of Related Structures:  
    5B34, 5B35

  • PubMed Abstract: 

    The 3D structure determination of biological macromolecules by X-ray crystallography suffers from a phase problem: to perform Fourier transformation to calculate real space density maps, both intensities and phases of structure factors are necessary; however, measured diffraction patterns give only intensities. Although serial femtosecond crystallography (SFX) using X-ray free electron lasers (XFELs) has been steadily developed since 2009, experimental phasing still remains challenging. Here, using 7.0-keV (1.771 Å) X-ray pulses from the SPring-8 Angstrom Compact Free Electron Laser (SACLA), iodine single-wavelength anomalous diffraction (SAD), single isomorphous replacement (SIR), and single isomorphous replacement with anomalous scattering (SIRAS) phasing were performed in an SFX regime for a model membrane protein bacteriorhodopsin (bR). The crystals grown in bicelles were derivatized with an iodine-labeled detergent heavy-atom additive 13a (HAD13a), which contains the magic triangle, I3C head group with three iodine atoms. The alkyl tail was essential for binding of the detergent to the surface of bR. Strong anomalous and isomorphous difference signals from HAD13a enabled successful phasing using reflections up to 2.1-Å resolution from only 3,000 and 4,000 indexed images from native and derivative crystals, respectively. When more images were merged, structure solution was possible with data truncated at 3.3-Å resolution, which is the lowest resolution among the reported cases of SFX phasing. Moreover, preliminary SFX experiment showed that HAD13a successfully derivatized the G protein-coupled A2a adenosine receptor crystallized in lipidic cubic phases. These results pave the way for de novo structure determination of membrane proteins, which often diffract poorly, even with the brightest XFEL beams.

  • Organizational Affiliation

    Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bacteriorhodopsin249Halobacterium salinarumMutation(s): 0 
Membrane Entity: Yes 
Find proteins for P02945 (Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1))
Explore P02945 
Go to UniProtKB:  P02945
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02945
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 4QL

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
2,4,6-tris(iodanyl)-5-(octanoylamino)benzene-1,3-dicarboxylic acid
C16 H18 I3 N O5
Query on RET

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C20 H28 O
Query on R16

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C16 H34
Query on D12

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G [auth A],
P [auth A],
Q [auth A],
R [auth A]
C12 H26
Query on D10

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H [auth A],
I [auth A],
K [auth A]
C10 H22
Query on DD9

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O [auth A],
S [auth A]
C9 H20
Query on OCT

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E [auth A],
F [auth A]
C8 H18
Query on HP6

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L [auth A],
M [auth A],
N [auth A]
C7 H16
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.2α = 90
b = 103β = 90
c = 128.7γ = 90
Software Package:
Software NamePurpose
Cheetahdata extraction
CrystFELdata processing

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
X-ray Free-Electron Laser Priority Strategy Program (MEXT)Japan--
Japanese Society of Technology ERATOJapan--

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-09
    Type: Initial release
  • Version 1.1: 2016-11-16
    Changes: Database references
  • Version 1.2: 2016-11-30
    Changes: Database references
  • Version 1.3: 2018-01-24
    Changes: Data collection, Database references
  • Version 1.4: 2023-09-06
    Changes: Data collection, Database references