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Newsletter No. 440
April 5, 2021

ACA News, IUCr Newsletter, IUCr Meetings List


MARCH 2021 PUBLICATIONS BY MEMBERS OF THE GROU


1: McIlwain BC, Erwin AL, Davis AR, Ben Koff B, Chang L, Bylund T, Chuang GY,
Kwong PD, Ohi MD, Lai YT, Stockbridge RB. N-terminal Transmembrane-Helix Epitope
Tag for X-ray Crystallography and Electron Microscopy of Small Membrane
Proteins
. J Mol Biol. 2021 Mar 5:166909. doi: 10.1016/j.jmb.2021.166909. Epub
ahead of print. PMID: 33676924.

2: Wlodawer A. Protein crystallography: alive and well. FEBS J. 2021 Mar 24.
doi: 10.1111/febs.15822. Epub ahead of print. PMID: 33759375.

3: Yi M, Negishi M, Lee SJ. Estrogen Sulfotransferase (SULT1E1): Its Molecular
Regulation, Polymorphisms, and Clinical Perspectives
. J Pers Med. 2021 Mar
11;11(3):194. doi: 10.3390/jpm11030194. PMID: 33799763.

4: Giddings LA, Lountos GT, Kim KW, Brockley M, Needle D, Cherry S, Tropea JE,
Waugh DS. Characterization of a broadly specific cadaverine N-hydroxylase
involved in desferrioxamine B biosynthesis in Streptomyces sviceus
. PLoS One.
2021 Mar 30;16(3):e0248385. doi: 10.1371/journal.pone.0248385. PMID: 33784308.

5: Naskręcki B, Dauter Z, Jaskolski M. Arithmetic proof of the multiplicity-
weighted Euler characteristic for symmetrically arranged space-filling
polyhedra
. Acta Crystallogr A Found Adv. 2021 Mar 1;77(Pt 2):126-129. doi:
10.1107/S2053273320016186. Epub 2021 Feb 4. PMID: 33646198.

6: Chen Y, Xu K, Piccoli L, Foglierini M, Tan J, Jin W, Gorman J, Tsybovsky Y,
Zhang B, Traore B, Silacci-Fregni C, Daubenberger C, Crompton PD, Geiger R,
Sallusto F,
Kwong PD, Lanzavecchia A. Structural basis of malaria RIFIN binding
by LILRB1-containing antibodies
. Nature. 2021 Mar 31. doi:
10.1038/s41586-021-03378-6. Epub ahead of print. PMID: 33790470.

7: Buch MHC, Newcomb WW, Winkler DC, Steven AC, Heymann JB. Cryo-Electron
Tomography of the Herpesvirus Procapsid Reveals Interactions of the Portal with
the Scaffold and a Shift on Maturation
. mBio. 2021 Mar 16;12(2):e03575-20. doi:
10.1128/mBio.03575-20. PMID: 33727359.

8: Lee SJ, Shizu R, Negishi M. Glucocorticoid receptor dimerization in the
cytoplasm might be essential for nuclear localization
. Biochem Biophys Res
Commun. 2021 Mar 24;553:154-159. doi: 10.1016/j.bbrc.2021.03.071. Epub ahead of
print. PMID: 33773137.

9: Wang P, Nair MS, Liu L, Iketani S, Luo Y, Guo Y, Wang M, Yu J, Zhang B, Kwong
PD
, Graham BS, Mascola JR, Chang JY, Yin MT, Sobieszczyk M, Kyratsous CA,
Shapiro L, Sheng Z, Huang Y, Ho DD. Antibody resistance of SARS-CoV-2 variants
B.1.351 and B.1.1.7
. Nature. 2021 Mar 8. doi: 10.1038/s41586-021-03398-2. Epub
ahead of print. PMID: 33684923.

10: Madan B, Zhang B, Xu K, Chao CW, O'Dell S, Wolfe JR, Chuang GY, Fahad AS,
Geng H, Kong R, Louder MK, Nguyen TD, Rawi R, Schön A, Sheng Z, Nimrania R, Wang
Y, Zhou T, Lin BC, Doria-Rose NA, Shapiro L,
Kwong PD, DeKosky BJ. Mutational
fitness landscapes reveal genetic and structural improvement pathways for a
vaccine-elicited HIV-1 broadly neutralizing antibody
. Proc Natl Acad Sci U S A.
2021 Mar 9;118(10):e2011653118. doi: 10.1073/pnas.2011653118. PMID: 33649208;
PMCID: PMC7958426.

11: Valarcher JF, Hägglund S, Näslund K, Jouneau L, Malmström E, Boulesteix O,
Pinard A, Leguéré D, Deslis A, Gauthier D, Dubuquoy C, Pietralunga V, Rémot A,
Falk A, Shevchenko G, Bergström Lind S, Von Brömssen C, Vargmar K, Zhang B,
Kwong PD, Rodriguez MJ, Garcia Duran M, Schwartz-Cornil I, Taylor G, Riffault S.
Single-Shot Vaccines against Bovine Respiratory Syncytial Virus (BRSV):
Comparative Evaluation of Long-Term Protection after Immunization in the
Presence of BRSV-Specific Maternal Antibodies
. Vaccines (Basel). 2021 Mar
9;9(3):236. doi: 10.3390/vaccines9030236. PMID: 33803302.

12: Mayer ML. Structural biology of kainate receptors. Neuropharmacology. 2021
Mar 30:108511. doi: 10.1016/j.neuropharm.2021.108511. Epub ahead of print. PMID:
33798545.

13: Zhou BR, Bai Y. Preparation of scFv stabilized chromatosomes for single-
particle cryo-EM structure determination
. STAR Protoc. 2021 Mar 20;2(2):100396.
doi: 10.1016/j.xpro.2021.100396. PMID: 33786462; PMCID: PMC7994535.

14: Cerutti G, Guo Y, Zhou T, Gorman J, Lee M, Rapp M, Reddem ER, Yu J, Bahna F,
Bimela J, Huang Y, Katsamba PS, Liu L, Nair MS, Rawi R, Olia AS, Wang P, Zhang
B, Chuang GY, Ho DD, Sheng Z,
Kwong PD, Shapiro L. Potent SARS-CoV-2
neutralizing antibodies directed against spike N-terminal domain target a single
supersite
. Cell Host Microbe. 2021 Mar 12:S1931-3128(21)00133-5. doi:
10.1016/j.chom.2021.03.005. Epub ahead of print. PMID: 33789084; PMCID:
PMC7953435.

15: Francica JR, Shi W, Chuang GY, Chen SJ, Da Silva Pereira L, Farney SK, Flynn
BJ, Ou L, Stephens T, Tsybovsky Y, Wang LT, Anderson A, Beck Z, Dillon M, Idris
AH, Hurlburt N, Liu T, Zhang B, Alving CR, Matyas GR, Pancera M, Mascola JR,
Kwong PD, Seder RA. Design of Alphavirus Virus-Like Particles Presenting
Circumsporozoite Junctional Epitopes That Elicit Protection against Malaria
.
Vaccines (Basel). 2021 Mar 18;9(3):272. doi: 10.3390/vaccines9030272. PMID:
33803622.

16: Ma B, Bai G, Nussinov R, Ding J,
Wang YX. Conformational Ensemble of
<i>Tte</i>AdoCbl Riboswitch Provides Stable Structural Elements for Conformation
Selection and Population Shift in Cobalamin Recognition
. J Phys Chem B. 2021 Mar
18;125(10):2589-2596. doi: 10.1021/acs.jpcb.1c00038. Epub 2021 Mar 8. PMID:
33683130.

17: Rapp M, Guo Y, Reddem ER, Yu J, Liu L, Wang P, Cerutti G, Katsamba P, Bimela
JS, Bahna FA, Mannepalli SM, Zhang B,
Kwong PD, Huang Y, Ho DD, Shapiro L, Sheng
Z. Modular basis for potent SARS-CoV-2 neutralization by a prevalent
VH1-2-derived antibody class
. Cell Rep. 2021 Mar 19:108950. doi:
10.1016/j.celrep.2021.108950. Epub ahead of print. PMID: 33794145; PMCID:
PMC7972811.

18: Silale A, Lea SM, Berks BC. The DNA transporter ComEC has metal-dependent
nuclease activity that is important for natural transformation
. Mol Microbiol.
2021 Mar 26. doi: 10.1111/mmi.14720. Epub ahead of print. PMID: 33772889.


For timely listing, please send a heads-up E-mail to the Editor upon publication.
METHODS - Evolving data standards for cryo-EM structures

The development of cryo-EM is directly reflected by the growth of cryo-EM strructure depositions contributed worldwide to public data archived. The archiving systems and underlying data standards supporting depostioin, annotation, release, and validation of cyro-EM stuctures and the associated metadata describing cryo-EM experiments have been developed over time to support this growth. Recently,  CL Lawson, HM Berman, and W Chiu outlined the history of these systems and described the process by which data standards had been developed. For details, please click the link.

Reliable cryo-EM resolution estimation
A modified Fourier shell correlation (FSC) moehodology is introduced by Pawel Penczek, which is aimed addressing two fundamental problems that mar the use of FSC: the strong influence of mask-induced artifacts on resolution estimation and the lack of assessment of FSC uncertaninties stemming from the inability to determine the asscociated number of degrees of freedom. For details, please click the link.

New approach for  structure determination from tiny crystals
Many crystals can't be grown into crystals large enough for their atomic arrangements to be deciphered. To tackle this challenge, scientists at the U.S. DOE's Brookhaven National Laboratory and colleagues at Columbia University have developed a new approach for solving protein structure from tiny crystal. For details, please click the link.

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

DISCUSSIONSWhat do you as a structural biologist think of the use of AI by DeepMind to predict protein folds?

Please find an analysis by Prof. John Helliwell and share your thoughts with the community.

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, Table 1.

READINGS AND TUTORIALS - Joachim Frank, Nobel Single-Partical Cryo-EM: Visualizing Biological Molecules in Their Native State


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"


LOW RESOLUTION PHASING AND REFINEMENT (2011)

 Data Collection Strategies (2013)

 STRUCTURE FACTOR TUTORIAL (2014)

DATA COLLECTION FOR STRUCTURE DETERMENATION (2014)

CRYSTAL CLEAR (2014)

LITERATURE ON CRYSTALLOGRAPHY THEORY AND METHODS (2017)

PROTEIN CRYSTALLOGRAPHY Methods and Protocols (2017)

 Understanding Biology Through Structure (2017)

 On the state of crystallography at the dawn of the electron microscopy revolution (2017)

 The Fascinating World of Crystallography (2018)

 Data science skills for referees: I biological X-ray crystallography  (2018)

Correcting the public record of biological crystallography (2019)

A Little Dictionary of Crystallography (2019)

Early history of cryo-cooling for macromolecular crystallography (2019)

Methods Comparison: XFEL vs microED (2020)

The data universe of structural biology (2020)

MicroED Methodology & Development (2020)

How to Speak, Lecture by Patrick Winston (2020)

Nobel Lecture of Jennifer Doudna (2020)

 LINKS - PDB SARS-CoV-2 Resources (Link)

Databases: DisProt, ExPASy, HAD, HIC-Up, NDBPDB, PDBe
, Protein Geometry
                  SARS-CoV-2 Related Structures, PDB SARS-CoV-2 Resources,


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


Servers: ACHESYM,
Anisotropy, C6@C3, DaliESPript, Grade, PDBePISA, Phyre2,
             MolProbity, RestraintLib,

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