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Newsletter No. 391
February 4, 2019

ACA News, IUCr Newsletter, IUCr Meetings List

ACA 2019, FEBS 2019, Protein Society 2019

JANUARY 2018 PUBLICATIONS BY MEMBERS OF THE GROUP  

1: Lo YH, Sobhany M, Hsu AL, Ford BL, Krahn JM, Borgnia MJ, Stanley RE. Cryo-EM
structure of the essential ribosome assembly AAA-ATPase Rix7
. Nat Commun. 2019
Jan 31;10(1):513. doi: 10.1038/s41467-019-08373-0. PubMed PMID: 30705282.

2: Gao Y, Cui Y, Fox T, Lin S, Wang H, de Val N, Zhou ZH, Yang W. Structures and
operating principles of the replisome.
Science. 2019 Jan 24. pii: eaav7003. doi:
10.1126/science.aav7003. [Epub ahead of print] PubMed PMID: 30679383.

3: Ruszkowski M, Dauter Z. Comment on Wang's paper on the covalent Cys-X-Lys
bridges
. Protein Sci. 2019 Jan 21. doi: 10.1002/pro.3576. [Epub ahead of print]
PubMed PMID: 30666728.

4: Chen X, Ebelle DL, Wright BJ, Sridharan V, Hooper E, Walters KJ. Structure of
hRpn10 Bound to UBQLN2 UBL Illustrates Basis for Complementarity between Shuttle
Factors and Substrates at the Proteasome
. J Mol Biol. 2019 Jan 18. pii:
S0022-2836(19)30030-0. doi: 10.1016/j.jmb.2019.01.021. [Epub ahead of print]
PubMed PMID: 30664872.

5: Smith MR, Shock DD, Beard WA, Greenberg MM, Freudenthal BD, Wilson SH. A
guardian residue hinders insertion of a Fapy•dGTP analog by modulating the
open-closed DNA polymerase transition
. Nucleic Acids Res. 2019 Jan 16. doi:
10.1093/nar/gkz002. [Epub ahead of print] PubMed PMID: 30649431.

6: Li M, Srp J, Gustchina A,
Dauter Z, Mares M, Wlodawer A. Crystal structures of
the complex of a kallikrein inhibitor from Bauhinia bauhinioides with trypsin and
modeling of kallikrein complexes
. Acta Crystallogr D Struct Biol. 2019 Jan
1;75(Pt 1):56-69. doi: 10.1107/S2059798318016492. Epub 2019 Jan 7. PubMed PMID:
30644845; PubMed Central PMCID: PMC6333282.

7: Hogan M, Bahta M, Tsuji K, Nguyen TX, Cherry S, Lountos GT, Tropea JE, Zhao
BM, Zhao XZ, Waugh DS, Burke TR Jr, Ulrich RG. Targeting Protein-Protein
Interactions of Tyrosine Phosphatases with Microarrayed Fragment Libraries
Displayed on Phosphopeptide Substrate Scaffolds
. ACS Comb Sci. 2019 Jan 31. doi:
10.1021/acscombsci.8b00122. [Epub ahead of print] PubMed PMID: 30629404.

8: Bofill-De Ros X, Kasprzak WK, Bhandari Y, Fan L, Cavanaugh Q, Jiang M, Dai L,
Yang A, Shao TJ, Shapiro BA, Wang YX, Gu S. Structural Differences between
Pri-miRNA Paralogs Promote Alternative Drosha Cleavage and Expand Target
Repertoires
. Cell Rep. 2019 Jan 8;26(2):447-459.e4. doi:
10.1016/j.celrep.2018.12.054. PubMed PMID: 30625327.

9: Thornton AM, Lu J, Korty PE, Kim YC, Martens C, Sun PD, Shevach EM. Helios(+)
and Helios(-) Treg subpopulations are phenotypically and functionally distinct
and express dissimilar TCR repertoires
. Eur J Immunol. 2019 Jan 8. doi:
10.1002/eji.201847935. [Epub ahead of print] PubMed PMID: 30620397.

10: Lai YT, Wang T, O'Dell S, Louder MK, Schön A, Cheung CSF, Chuang GY, Druz A,
Lin B, McKee K, Peng D, Yang Y, Zhang B, Herschhorn A, Sodroski J, Bailer RT,
Doria-Rose NA, Mascola JR, Langley DR,
Kwong PD. Lattice engineering enables
definition of molecular features allowing for potent small-molecule inhibition of
HIV-1 entry
. Nat Commun. 2019 Jan 3;10(1):47. doi: 10.1038/s41467-018-07851-1.
PubMed PMID: 30604750; PubMed Central PMCID: PMC6318274.

11: Yost SA, Whidby J, Khan AG, Wang Y,
Marcotrigiano J. Overcoming Challenges of
Hepatitis C Virus Envelope Glycoprotein Production in Mammalian Cells
. Methods
Mol Biol. 2019;1911:305-316. doi: 10.1007/978-1-4939-8976-8_21. PubMed PMID:
30593635.



For timely listing, please send a heads-up E-mail to the Editor upon publication.
TIPS, TRICKS, METHODS New Detergent-Free System for Membrane                                                                         Protein Structural Biology

Detergent-Free Membrane Protein System |  In a newly published paper in PNAS, a team led by Dr. Youzhong Guo of VCU's School of Pharmacy used a new detergent-free method that allowed them to examine the membrane of an Escherichia coli cell, with lipids still in place, providing the clearest view ever of cell membrane that yields unexpected structure. 

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)