5B35

Serial Femtosecond Crystallography (SFX) of Ground State Bacteriorhodopsin Crystallized from Bicelles Determined Using 7-keV X-ray Free Electron Laser (XFEL) at SACLA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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

  • 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; ...

    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 Applied Chemistry, Graduate School of Engineering, Osaka University, Osaka 565-0871, Japan; murata@chem.sci.osaka-u.ac.jp mizohata@chem.eng.osaka-u.ac.jp.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BacteriorhodopsinA249Halobacterium salinarumMutation(s): 0 
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Bacterial, Algal, and viral Rhodopsins
Protein: 
Bacteriorhodopsin (BR) native
Find proteins for B0R5N9 (Halobacterium salinarum (strain ATCC 29341 / DSM 671 / R1))
Explore B0R5N9 
Go to UniProtKB:  B0R5N9
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4QM
Query on 4QM

Download CCD File 
A
(3R,5S,7R,8R,9S,10S,12S,13R,14S,17R)-10,13-dimethyl-17-[(2R)-pentan-2-yl]-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthrene-3,7,12-triol
C24 H42 O3
PFZUIDNKXWIWBG-YHEMGIGTSA-N
 Ligand Interaction
RET
Query on RET

Download CCD File 
A
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
R16
Query on R16

Download CCD File 
A
HEXADECANE
C16 H34
DCAYPVUWAIABOU-UHFFFAOYSA-N
 Ligand Interaction
D12
Query on D12

Download CCD File 
A
DODECANE
C12 H26
SNRUBQQJIBEYMU-UHFFFAOYSA-N
 Ligand Interaction
D10
Query on D10

Download CCD File 
A
DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
 Ligand Interaction
DD9
Query on DD9

Download CCD File 
A
nonane
C9 H20
BKIMMITUMNQMOS-UHFFFAOYSA-N
 Ligand Interaction
OCT
Query on OCT

Download CCD File 
A
N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
 Ligand Interaction
HP6
Query on HP6

Download CCD File 
A
HEPTANE
C7 H16
IMNFDUFMRHMDMM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.169 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.2α = 90
b = 103β = 90
c = 128.7γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Cheetahdata extraction
CrystFELdata processing
SHELXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
X-ray Free-Electron Laser Priority Strategy Program (MEXT)JapanSACLA-SFX Project
Japanese Society of Technology ERATOJapanMurata Lipid Active Structure Project

Revision History 

  • 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