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Newsletter No. 388
December 3, 2018

ACA News, IUCr Newsletter, IUCr Meetings List

ACA 2019, FEBS 2019, Protein Society 2019

NOVEMBER 2018 PUBLICATIONS BY MEMBERS OF THE GROUP  

1: Lu J, Mold C, Du Clos TW, Sun PD. Pentraxins and Fc Receptor-Mediated Immune
Responses
. Front Immunol. 2018 Nov 13;9:2607. doi: 10.3389/fimmu.2018.02607.
eCollection 2018. Review. PubMed PMID: 30483265; PubMed Central PMCID:
PMC6243083.

2: Rana MS, Wang X, Banerjee A. An Improved Strategy for Fluorescent Tagging of
Membrane Proteins for Overexpression and Purification in Mammalian Cells
.
Biochemistry. 2018 Nov 27. doi: 10.1021/acs.biochem.8b01070. [Epub ahead of
print] PubMed PMID: 30481009.

3: Prasad R, Horton JK, Dai DP,
Wilson SH. Repair pathway for PARP-1 DNA-protein
crosslinks
. DNA Repair (Amst). 2018 Nov 12. pii: S1568-7864(18)30151-4. doi:
10.1016/j.dnarep.2018.11.004. [Epub ahead of print] PubMed PMID: 30466837.

4: Olson MA, Lee MS, Kissner TL, Alam S,
Waugh DS, Saikh KU. Author Correction:
Discovery of small molecule inhibitors of MyD88-dependent signaling pathways
using a computational screen.
Sci Rep. 2018 Nov 19;8(1):17074. doi:
10.1038/s41598-018-35538-6. PubMed PMID: 30451949; PubMed Central PMCID:
PMC6242992.

5: Khera T, Behrendt P, Bankwitz D, Brown RJP, Todt D, Doepke M, Ghafoor Khan A,
Schulze K, Law J, Logan M, Hockman D, Wong JAJ, Dold L, Gonzalez-Motos V,
Spengler U, Viejo-Borbolla A, Ströh L, Krey T, Tarr AW, Steinmann E, Manns MP,
Klein F, Guzman CA, Marcotrigiano J, Houghton M, Pietschmann T. Functional and
immunogenic characterization of diverse HCV glycoprotein E2 variants
. J Hepatol.
2018 Nov 12. pii: S0168-8278(18)32527-3. doi: 10.1016/j.jhep.2018.11.003. [Epub
ahead of print] PubMed PMID: 30439392.

6: Feng H, Zhou BR, Bai Y. Binding Affinity and Function of the Extremely
Disordered Protein Complex Containing Human Linker Histone H1.0 and Its Chaperone
ProTα
. Biochemistry. 2018 Nov 19. doi: 10.1021/acs.biochem.8b01075. [Epub ahead
of print] PubMed PMID: 30430826.

7: Diesterbeck US, Gittis AG, Garboczi DN, Moss B. The 2.1 Å structure of protein
F9 and its comparison to L1, two components of the conserved poxvirus
entry-fusion complex
. Sci Rep. 2018 Nov 14;8(1):16807. doi:
10.1038/s41598-018-34244-7. PubMed PMID: 30429486; PubMed Central PMCID:
PMC6235832.

8: Chen Z, Diaz G, Pollicino T, Zhao H, Engle RE, Schuck P, Shen CH, Zamboni F,
Long Z, Kabat J, De Battista D, Bock KW, Moore IN, Wollenberg K, Soto C,
Govindarajan S,
Kwong PD, Kleiner DE, Purcell RH, Farci P. Role of humoral
immunity against hepatitis B virus core antigen in the pathogenesis of acute
liver failure
. Proc Natl Acad Sci U S A. 2018 Nov 27;115(48):E11369-E11378. doi:
10.1073/pnas.1809028115. Epub 2018 Nov 12. PubMed PMID: 30420516.

9: Stewart-Jones GBE, Chuang GY, Xu K, Zhou T, Acharya P, Tsybovsky Y, Ou L,
Zhang B, Fernandez-Rodriguez B, Gilardi V, Silacci-Fregni C, Beltramello M, Baxa
U, Druz A, Kong WP, Thomas PV, Yang Y, Foulds KE, Todd JP, Wei H, Salazar AM,
Scorpio DG, Carragher B, Potter CS, Corti D, Mascola JR, Lanzavecchia A,
Kwong PD. Structure-based design of a quadrivalent fusion glycoprotein vaccine for
human parainfluenza virus types 1-4
. Proc Natl Acad Sci U S A. 2018 Nov
27;115(48):12265-12270. doi: 10.1073/pnas.1811980115. Epub 2018 Nov 12. PubMed
PMID: 30420505.

10: Borst AJ, Weidle CE, Gray MD, Frenz B, Snijder J, Joyce MG, Georgiev IS,
Stewart-Jones GB,
Kwong PD, McGuire AT, DiMaio F, Stamatatos L, Pancera M,
Veesler D. Germline VRC01 antibody recognition of a modified clade C HIV-1
envelope trimer and a glycosylated HIV-1 gp120 core
. Elife. 2018 Nov 7;7. pii:
e37688. doi: 10.7554/eLife.37688. PubMed PMID: 30403372; PubMed Central PMCID:
PMC6237438.

11:
Thapar R, Bacolla A, Oyeniran C, Brickner JR, Chinnam NB, Mosammaparast N,
Tainer JA. RNA Modifications: Reversal Mechanisms and Cancer. Biochemistry. 2018
Nov 7. doi: 10.1021/acs.biochem.8b00949. [Epub ahead of print] PubMed PMID:
30346748.

12: Hickman AB, Voth AR, Ewis H, Li X, Craig NL, Dyda F. Structural insights into
the mechanism of double strand break formation by Hermes, a hAT family eukaryotic
DNA transposase.
Nucleic Acids Res. 2018 Nov 2;46(19):10286-10301. doi:
10.1093/nar/gky838. PubMed PMID: 30239795; PubMed Central PMCID: PMC6212770.



For timely listing, please send a heads-up E-mail to the Editor upon publication.
TIPS, TRICKS, METHODS FSEARCH: cryo-EM Map Replacement

FSEARCH: cryo-EM Map Replacement |  Recently, a  hybrid method that integrates X-ray crystallography with cryo-EM for structure determination is presented by Lingxiao Zeng, Wei Ding, and Quan Hao in the IUCrJ (5:382-389, 2018). The starting point is a cryo-EM map  and the end point is a high-resolution crystal structure. The workflow of the method and four case study examples can be seen here.

A new MR-SAD algorithm | 
Recently, a  new MR-SAD algorithm was  reported  by Pavol Skubak, Navray Pannu, and co-workers in the IUCrJ (5:166-171, 2018), for automatic building of protein models from low-resolution X-ray diffraction data and a poor starting model. According to the authors, their algorithm uses a multivariate function to simultatnerously exploit informatino from both the initial partial model and low-resolution SAD data. Details of the algorithm and its application to six challenging structure determinations can be seen here.

ARCHIVE: Introduction, Pre-crystallization, Crystallization, Post-crystallization, Derivatization, Cryoprotection, Diffraction, Symmetry, Structure Solution, Structure Refinement, Structure Analysis & Presentation, Biophysical Methods.

TOPIC DISCUSSIONTable 1

A perspective article "Against Method: Table 1--Cui Bono?" was  recently published in Structure by Bernhard Rupp, pointing out that "Information contained in 'Table 1' is insufficient to evaluate or repeat the experiment, is redundant with information extractable from deposited diffraction data, and includes data items whose meaning is under increased scrutiny in the crystallographic community," and suggesting that "Direct and consistent extraction and analysis of data quality metrics from preferably unmerged intensity data with graphical presentation of reciprocal space features, including impact on map and model features, should replace 'Table 1'."

Do you agree with Bernhard? Please share your opinion and ideas with fellow crystallographers.

Dr. Lothar Esser: Commentary on “Against Method: Table 1 – Cui Bono?” B. Rupp Structure 26 (2018) 919-923. In his perspective Hofkristallrat Rupp argues essentially that ‘Table 1’ should be ‘relegated to the depths of supplementary material where it will be […] rightfully forgotten.’ Table 1 in brief refers to a tabulated summary of direct crystallographic data like cell dimensions and symmetry as well as derived characterizations of the presented molecular structure like root mean square deviations of bond lengths and angles from standard values. It is suggested that this information is neither useful to reproduce the experiment (presumably diffraction experiment), nor does it help to evaluate the quality of the final structure model and is in fact redundant because all values can be retrieve from databases easily. Table 1 could however be maintained if outmoded and woefully inadequate statistical values be replaced by 21st century quality indicators like CC* and enhanced graphic depictions of reciprocal space. This kind of unmitigated assault on Table 1 is not quite new and is to be understood in the broader context of an ongoing process of improving quality control and giving editors and reviewers meaningful tools to correctly evaluate a given new structure in the absence of having all data available for full-fledged inspections. All this introspection is meant to benefit the structural biologist whose work critically depends on having exact knowledge of the structure down to side chain rotamers, ligand positions and hydration of catalytic or other sites of interest. Being in this field for a while, I have yet to meet one of those beneficiaries – someone who works with structural data but does not know how to evaluate its quality.  In conclusion, Table 1 would benefit, as everything else from a critical review and update to 21st century standards. The reader can only draw one conclusion equally applicable to my comments and Prof. Rupp’s perspective in response to the self-imposed question ‘Cui bono’: No one.


Dr. Mariusz Jackolski: "Dr. Xinhua Ji has encouraged discussion on the somewhat controversial proposition of Dr. Bernhard Rupp to get rid of Table 1 from published crystallographic papers.  As much as I sympathize with Bernhard's crusade to wed "post modern relativism" from exact science, I am not sure that his aim at Table 1 is well advised.  I am afraid that his proposition could have the opposite effect, i.e., could accelerate the demise of something that is perhaps not perfect but certainly very useful; in the end Table 1 would be replaced by just nothing.  Bernhard is giving strong arguments to the opponents of any kind of Table 1 information in experimental papers.  If we want to maintain high standard in crystallographic literature, we should work out a concrete (improved) alternative to Table 1 and start using it in practice."

 

Dr. Peter D. Sun: “I do not agree with the author of the perspective article in Structure.  I think one has to ask who reads Table 1 and how useful it is in a crystallographic structure publication.  Without giving too much thought, I think  Table 1 is very useful to most non-crystallographic trained but structurally tuned readers—which probably makes up the majority of the scientists who are interested in crystal structures.  Majority of them do care about resolution and a few also care about R-factors.  Table 1 serves primarily the purpose of announcing the birth of a “new” structure with certain attributes to allow general public to assess the quality and compare the current on with any other structures they know of.   In the past, crystallographic community have relied on Table 1 to evaluate a structure for its correctness.  It is true that the information in the table is insufficient to repeat the experiment and in many cases indifferent to minor errors in structures.  However, in this day and age and with the exception of few, most of crystallographers read structural publications for new scientific insights and structural information, not with a purpose to validate and repeat the published structures.  This is mostly due to the software development in our field. 

Secondly, I would caution to use highly specialized statistics for data quality representation.  Even though such representation, such as unmerged intensity data with graphical presentation of reciprocal space features, may indeed reflect more accurately the state of a refined model, they are less comprehensive to our audience, and thus less useful.  In fact, it is not clear how many crystallographers understand the errors and their propagation in our models. 

In anycase, my point is a structural publication is best regarded as an illustration to a new consumer product.  It is for the interest of general audience.  For a few specialized experts, then again, there is PDB. 

I do however, think it benefits the community to shorten the Table 1, so that the critical information can be easily discerned in main text not through supplemental as most of Table 1’s are.”

ARCHIVE: Test-set-and-R-free, Twinning, Low Resolution Crystallography, PHASER, HKL2000, Parallel Expression, NCS, Missing Atoms, Trends in CrystallographyAbsorption Correction, Data for Refinement and PublicationValidation.

LECTURES AND TUTORIALS CRYSTALLOGRAPHY


DR. ZBIGNIEW DAUTER'S LECTURES AT THE NIH (2005)
 

Part 1: "How to read international tables?"

Part 2: "Data collection strategy" and "Twinning"

           "Phasing methods - a general introduction to all methods"

Part 3: "SAD phasing, Quick halide soaking, and Radiation damage 

            with possible use of it for phasing"


RIGAKU WEBINAR SERIES (2009 - PRESENT)

LOW RESOLUTION PHASING AND REFINEMENT (2011)

CRYSTALLOGRAPHY: SEEING THINGS IN A DIFFERENT LIGHT (2013)

CRYSTALLOGRAPHY: FOR ASPIRING CRYSTALLOGRAPHERS (2013)

 STRUCTURE FACTOR TUTORIAL (2014)

DATA COLLECTION FOR STRUCTURE DETERMENATION (2014)

ACHESYM: AN ALGORITHM AND SERVER FOR STANDARDIZED PLACEMENT OF MACROMOLECULAR MODELS IN THE UNIT CELL (2014)

A GLIMPSE OF STRUCTURAL BIOLOGY THROUGH X-RAY CRYSTALLOGRAPHY (2014)

CRYSTAL CLEAR (2014)

NATIVE SAD IS MATURING (2015)

LITERATURE ON CRYSTALLOGRAPHY THEORY AND METHODS (2017)

PROTEIN CRYSTALLOGRAPHY Methods and Protocols (2017)

 LINKS - Suggestions?

Databases: BMCDDisProt, ExPASy, HAD, HIC-Up, Metal Sites, NDBPDB, PDBe
,
                 Protein Geometry, Scattering

Programs: CCP4, COOT, DSSR, HKLPHENIX, PyMOL, SOLVE, XDS


Servers: ACHESYM,
Anisotropy, CheckMyMetal, Crystal, C6, Dali, DSSR, ESPript
              Grade, PDBePISA, Phyre, MolProbity, Protein, Robetta Fragment, HHpred,
 
            RestraintLib,


Facilities: 
APS SER-CAT, APS SAXS Capabilities

 
Copyright © NIH X-Ray Diffraction Group                       Maintained by Dr. Xinhua Ji
on the NIH-NCI-CCR-MCL server (http://mcl1.ncifcrf.gov)