We are pleased to announce the 6th annual SIBYLS bioSAXS workshop:

                          "Frontiers in biological SAXS"

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Date: October 5 - 7, 2015

Location: Advanced Light Source (ALS) at Lawrence Berkeley National Laboratory, Berkeley, CA

Description: This two-day workshop will provide software tutorial sessions for biological SAXS studies and hands-on training in experimental techniques. Participants will also receive updates on current developments of software for analyzing SAXS for structural biology:

  • FoXS - MES
  • SSM
  • SAXS shape modeling

A half day will be dedicated for data processing by workshop participants.

Our keynote speaker will be Robert Rambo, the Principal Beamline Scientist for the solution state SAXS beamline B21 at the Diamond Light Source. Among his many accomplishments, Dr. Rambo is the author of ScAtter, a java-based program for bioSAXS and creator of BioIsis.net.

Other distinguished speakers include John J. Tanner from the University of Missouri-Columbia and Chris Brosey from Washington University in St. Louis. Check back for more to come.

Enrollment is limited to 30 participants. 

Organizers: Michal Hammel, Greg Hura

Inquires: Kathryn Burnett

Registration: Registration is now open. To attend “Frontiers in biological SAXS” you need to REGISTER for the 2015 Advanced Light Source User Meeting. When you register, you should indicate that you plan to attend “Frontiers in biological SAXS”.


Tuesday, October 6 (room TBD)

12:00 Lunch, ALS Patio and exhibitor tent

1:00 Welcoming remarks (Michal Hammel and Greg Hura)

1:10 Greg Hura : Updates on mail-in, new detector, High Throughput SAXS

2:00 Rob Rambo, Diamond Light Source

3:00 Coffee Break

3:10 Michal Hammel : SAXS modeling, SAXS profile computation using FOX, Calculating shape

4:00 Break

4:10 - Jack Tanner, University of Missouri-Columbia

4:30 - Chris Brosey, Washington University, St. Louis

5:00 - ALS Awards dinner

Wednesday, October 7 (room TBD):

9:00 Welcome back (Michal Hammel and Greg Hura)

9:10 Carrie Partch, University of California, San Diego

9:30 TBD

9:50 Dina Schneidman, Universtiy of California, San Francisco

10:30 Coffee Break

10:45 Rob Rambo, Diamond Light Source

12:00 Lunch, ALS Patio and Exhibitor tent

1:00 Practical session with mentors (Greg Hura, Michal Hammel, Dina Schneidman, Rob Rambo)

5:00 End of Workshop

The facilities and staff at the SIBYLS beamline contributed to this recent structural study of a human antibody that is able to neutralize Marburg and Ebola viruses.


The filoviruses, including Marburg and Ebola, express a single glycoprotein on their surface, termed GP, which is responsible for attachment and entry of target cells. Filovirus GPs differ by up to 70% in protein sequence, and no antibodies are yet described that cross-react among them. Here, we present the 3.6 Å crystal structure of Marburg virus GP in complex with a cross-reactive antibody from a human survivor, and a lower resolution structure of the antibody bound to Ebola virus GP. The antibody, MR78, recognizes a GP1 epitope conserved across the filovirus family, which likely represents the binding site of their NPC1 receptor. Indeed, MR78 blocks binding of the essential NPC1 domain C. These structures and additional small-angle X-ray scattering of mucin-containing MARV and EBOV GPs suggest why such antibodies were not previously elicited in studies of Ebola virus, and provide critical templates for development of immunotherapeutics and inhibitors of entry.

Hashiguchi T, Fusco ML, Bornholdt ZA, Lee JE, Flyak AI, Matsuoka R, Kohda D, Yanagi Y, Hammel M, Crowe JE, Saphire EO. “Structural basis for marburg virus neutralization by a cross-reactive human antibody.” Cell 2015 Feb 26 ;160(5):904-12 link

SAXS and MX data collected at SIBYLS enabled insights into protein flexibility in one of the proteins involved in Lou Gerigh’s disease. The results were recently published in PNAS and have been highlighted by Today At Berkeley Lab and and Daily Cal.

Protein framework alterations in heritable Cu, Zn superoxide dismutase (SOD) mutants cause misassembly and aggregation in cells affected by the motor neuron disease ALS. However, the mechanistic relationship between superoxide dismutase 1 (SOD1) mutations and human disease is controversial, with many hypotheses postulated for the propensity of specific SOD mutants to cause ALS. Here, we experimentally identify distinguishing attributes of ALS mutant SOD proteins that correlate with clinical severity by applying solution biophysical techniques to six ALS mutants at human SOD hotspot glycine 93. A small-angle X-ray scattering (SAXS) assay and other structural methods assessed aggregation propensity by defining the size and shape of fibrillar SOD aggregates after mild biochemical perturbations. Inductively coupled plasma MS quantified metal ion binding stoichiometry, and pulsed dipolar ESR spectroscopy evaluated the Cu2+ binding site and defined cross-dimer copper-copper distance distributions. Importantly, we find that copper deficiency in these mutants promotes aggregation in a manner strikingly consistent with their clinical severities. G93 mutants seem to properly incorporate metal ions under physiological conditions when assisted by the cop- per chaperone but release copper under destabilizing conditions more readily than the WT enzyme. Altered intradimer flexibility in ALS mutants may cause differential metal retention and promote distinct aggregation trends observed for mutant proteins in vitro and in ALS patients. Combined biophysical and structural results test and link copper retention to the framework destabilization hypothesis as a unifying general mechanism for both SOD aggregation and ALS disease progression, with implications for disease severity and therapeutic intervention strategies.


Pratt AJ, Shin DS, Merz GE, Rambo RP, Lancaster WA, Dyer KN, Borbat PP, Poole FL, Adams MW, Freed JH, Crane BR, Tainer JA, Getzoff ED. “Aggregation propensities of superoxide dismutase G93 hotspot mutants mirror ALS clinical phenotypes.” Proc. Natl. Acad. Sci. U.S.A. 2014 Oct 14 link

For posterity. justin-ishida-runaround.jpg

Recently in Science:


Structure determination of gold nanoparticles (AuNPs) is necessary for understanding their physical and chemical properties, but only one AuNP larger than 1 nanometer in diameter [a 102-gold atom NP (Au102NP)] has been solved to atomic resolution. Whereas the Au102NP structure was determined by x-ray crystallography, other large AuNPs have proved refractory to this approach. Here, we report the structure determination of a Au68NP at atomic resolution by aberration-corrected transmission electron microscopy, performed with the use of a minimal electron dose, an approach that should prove applicable to metal NPs in general. The structure of the Au68NP was supported by small-angle x-ray scattering and by comparison of observed infrared absorption spectra with calculations by density functional theory.

read about it here:

Azubel M, Koivisto J, Malola S, Bushnell D, Hura GL, Koh AL, Tsunoyama H, Tsukuda T, Pettersson M, Häkkinen H, Kornberg RD. “Nanoparticle imaging. Electron microscopy of gold nanoparticles at atomic resolution.” Science 2014 Aug 22 ;345(6199):909-12 link

We are pleased to announce the 5th annual SIBYLS bioSAXS workshop “Frontiers in biological SAXS”


Date: October 7-8, 2014 Location: Advance Light Source (ALS) at Lawrence Berkeley National Laboratory , Berkeley, CA

Small angle scattering (SAS) is experiencing a dramatic increase in popularity within the structural biology community. The availability of synchrotron radiation, low-noise detectors, powerful computing hardware, and better algoritms, has made the technique accessible to a much larger audience than ever before. At the same time, biologists are investigating ever more complex systems that pose increasing challenges to conventional crystallography. The latest advances in SAXS studies on biological systems will be reported and discussed in 2 days workshop by invited experts with focus on following four topics (see program). 1) Advances in Synchrotron Scattering technique 2) Dynamic & Flexible Structures in Biomolecules 3) Membrane Protein Scattering 4) Complementary Methods in Crystals and in Solution

The two-day workshop will provide training on experimental techniques and software tutorial sessions primarily for biological SAXS studies. Participants will also receive updates on current development of software dedicated to analyze SAXS for structural biology. Half day of the workshop will be dedicated for data processing by workshop participants. Enrollment is limited to 30 participants. 

Organizers: Michal Hammel, Greg Hura

Inquires: Jane Tanamachi

Registration: To attend “Frontiers in biological SAXS” you need register for the 2014 Advanced Light Source Users’ Meeting. ALS user meeting will be held at Berkeley Lab beginning Monday, October 6. “Frontiers in biological SAXS” will begin Thuesday October 7th and continue through Wednesday October 8th. When you registering, you must indicate “Frontiers in biological SAXS”

Tuesday, October 7th LBNL Building 2 , room 100B

11:30 Lunch at the ALS patio

12:30 Welcoming Remarks Michal Hammel and Greg Hura “Frontiers in biological SAXS”

12:45 Lois Pollack, Cornell Univesity

13:15 Edward Snell, Hauptman-Woodward Institute

13:45 Lokesh Gakhar, University of Iowa

14:15 Coffee Break

14:30 Greg Hura, LBNL

15:00 Dina Schneidman, University California, San Francisco “SAXS based modelling of proteins with long disordered fragments”

15:30 Sherry Wang, National Cheng Kung University, Taiwan “Molecular architecture and stepwise assembly of IL-33 signaling complex”

16:00 Michal Hammel LBNL “A molecular switch in nucleoid compaction dictates bacterial pathogenicity”

16:30 TBD

17:00 TBD

Wednesday, October 8th LBNL Building 2 , room 100B

9:00 Michal Hammel, LBNL “Data reduction and processing tutorial”

10:30 Coffee Break

10:45 Greg Hura “Data reduction and processing tutorial”

12:00 Lunch Break at the ALS patio

13:00 - till late Practical session with Mentors (Greg Hura, Michal Hammel, Dina Schneidman, Sherry Wang)

A new publication is available that describes practical aspects of collecting High-throughput SAXS data at the SIBYLS beamline, with a focus on challenging low concentration samples. Additional practical advice is laid out with respect to interpreting the resulting data.

Dyer KN, Hammel M, Rambo RP, Tsutakawa SE, Rodic I, Classen S, Tainer JA, Hura GL. “High-throughput SAXS for the characterization of biomolecules in solution: a practical approach.” Methods Mol. Biol. 2014;1091:245-58. link

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