Newsletter 519 (August 5, 2024) NIH X-ray Diffraction SIG
July
2024 PUBLICATIONS BY MEMBERS OF THE GROUP
1: Tugarinov V, Torricella F, Ying J, Clore GM.
J Biomol NMR. 2024 Jul 31. doi: 10.1007/s10858-024-00445-8. Epub
ahead of print.
PMID: 39083133.
2: Umuhire Juru
A, Ghirlando R, Zhang J.
Structural
basis of tRNA recognition by the widespread OB fold.
Nat Commun. 2024 Jul
29;15(1):6385. doi: 10.1038/s41467-024-50730-1.
PMID: 39075051; PMCID: PMC11286949.
3: Lee M, Lu M, Zhang B, Zhou T, Katte
R, Han Y, Rawi R, Kwong
PD.
bioRxiv
[Preprint]. 2024 Jul 17:2024.07.15.603531. doi:
10.1101/2024.07.15.603531.
PMID: 39071380; PMCID: PMC11275901.
4: Ongey EL, Banerjee A.
In
vitro reconstitution of transition metal transporters.
J Biol Chem. 2024 Jul 18:107589. doi:
10.1016/j.jbc.2024.107589. Epub ahead of print.
PMID: 39032653.
5: Sim MJW, Hanada KI, Stotz Z, Yu Z, Lu J, Brennan P, Quastel
M, Gillespie GM, Long EO, Yang JC, Sun PD.
Eur J
Immunol. 2024 Jul 18:e2451079. doi:
10.1002/eji.202451079. Epub ahead of print.
PMID: 39030753.
6: Zhang P, Gorman J, Tsybovsky
Y, Lu M, Liu Q, Gopan V, Singh M, Lin Y, Miao H, Seo Y, Kwon A, Olia AS, Chuang
GY, Geng H, Lai YT, Zhou T, Mascola
JR, Mothes W, Kwong
PD, Lusso P.
Cell Rep. 2024 Jul 18;43(8):114518. doi:
10.1016/j.celrep.2024.114518. Epub ahead of print.
PMID: 39028623.
7: Skeparnias I, Zhang J.
Structural
basis of NEAT1 lncRNA maturation and menRNA instability.
Nat Struct Mol Biol. 2024 Jul 18. doi:
10.1038/s41594-024-01361-z. Epub ahead of print.
PMID: 39026030.
8: Kumar JP, Kosek D, Durell SR, Miller Jenkins LM, Debnath S, Coussens NP, Hall MD, Appella DH,
Dyda
F, Mazur SJ, Appella E.
Crystal
structure and mechanistic studies of the PPM1D serine/threonine phosphatase
catalytic domain.
J Biol Chem. 2024 Jul 11;300(8):107561. doi:
10.1016/j.jbc.2024.107561. Epub ahead of print.
PMID: 39002674.
9: Tong AY, Tong EL, Hannani MA,
Shaffer SN, Santiago D, Ferré-D'Amaré AR, Passalacqua LFM, Abdelsayed MM.
RNA
thermometers are widespread upstream of ABC transporter genes in bacteria.
J Biol Chem. 2024 Jul 9;300(8):107547. doi:10.1016/j.jbc.2024.107547.
Epub ahead of print.
PMID: 38992441.
10: Walters KJ.
Virus-host
warfare by PROTACs.
Nat Rev Mol Cell Biol. 2024 Jul 9. doi:
10.1038/s41580-024-00761-9. Epub ahead of print.
PMID: 38982303.
11: Giarimoglou N, Kouvela A, Zhang J, Stamatopoulou V, Stathopoulos C.
Structural
idiosyncrasies of glycyl T-box riboswitches among pathogenic bacteria.
RNA. 2024 Jul 9:rna.080071.124. doi: 10.1261/rna.080071.124. Epub
ahead of print.
PMID: 38981655.
12: Dauter Z, Wlodawer A.
IUCrJ. 2024
Jul 1;11(Pt 4):643-644. doi:
10.1107/S2052252524005803.
PMID: 38958017; PMCID: PMC11220886.
13: Skeparnias I, Bou-Nader C, Anastasakis DG, Fan L, Wang YX, Hafner M, Zhang J.
Structural
basis of MALAT1 RNA maturation and mascRNA biogenesis.
Nat Struct Mol Biol. 2024 Jul 2. doi:
10.1038/s41594-024-01340-4. Epub ahead of print.
PMID: 38956168.
14: Lu X, Passalacqua LFM, Nodwell M, Kong KYS, Caballero-García G, Dolgosheina EV, Ferré-D'Amaré AR, Britton R, Unrau
PJ.
Nucleic Acids Res. 2024 Jul 1:gkae493.
doi: 10.1093/nar/gkae493. Epub ahead of print.
PMID: 38945550.
For timely listing, please send a heads-up E-mail to
the Editor upon publication.
METHODS – Sample
Preparation Tips
S. Yadav and K.R. Vinothkumar, “Factors
affecting macromolecule orientations in thin films formed in cryo-EM”
PMID: 38935342
S.E.J. Bowman et al., “Preparing
research samples for safe arrival at centers and facilities: recipes for
successful experiments” PMID: 38990054
METHODS – Integrative
Structural Biology
M. Bazayeva et al., “A
database overview of metal-coordination distances in metalloproteins”
PMID: 38682667
H. Zheng et al., “PinMyMetal: A hybrid learning system to accurately model metal
binding sites in macromolecules” PMID: 38463967.
M. Bochtler, “X-rays,
electrons, and neutrons as probes of atomic matter” PMID: 38412856.
METHODS – XFEL,
3D-printed liquid sheet jet technology
M. Trebbin, “Thinner
than a knife’s edge: 3D-printed liquid sheet jet technology for solution phase
XFEL experiments” PMID: 37910141.
METHODS – Micro-ED,
AlphaFold-Assisted
J.E. Miller et al., “AlphaFold-assisted
structure determination of a bacterial protein of unknown function using X-ray
and electron crystallography” PMID: 38451205
METHODS – Cryo-EM
C.L. Lawson et al., “Outcomes
of the EMDataResource Cryo-EM Ligand Modeling
Challenge” PMID: 38343795
B. Greber
et al., “High-resolution
cryo-EM of the human CDK-activating kinase for structure-based drug design” PMID: 38480681
G.J. Kleywegt,
“Community
recommendations on cryoEM data archiving and
validation” PMID: 38358351
M. Kschonsak et al., “Cryo-EM
reveals an unprecedented binding site for Nav1.7 inhibitors enabling rational
design of potent hybrid inhibitors” PMID: 36975198.
METHODS – SAXS
K. Lytje
and J.S. Pederson, “Validation
of electron-microscopy maps using solution small-angle X-ray scattering” PMID: 38935344.
METHODS – NMR
and Ligand Screening
M. Bütikofer
et al., “Rapid
Protein-Ligand Affinity Determination by Photoinduced Hyperpolarized NMR” PMID: 38957136.
READINGS & TUTORIALS – Macromolecular Crystallography
K.L. Shelley and E.F. Garman, “Identifying
and avoiding radiation damage in macromolecular crystallography”
PMID: 38700059
G. Khusainov et al., “The
time revolution in macromolecular crystallography” PMID: 38616866.
J.R. Helliwell et al., “The
evolution of raw data archiving and the growth of its importance in
crystallography” PMID: 38864497.
D.J. Haas, “Fifty years on: why macromolecular cryocrystallography
has been so successful” IUCr Newsletter (2023) 31(3).
W.A. Hendrickson, “Facing
the phase problem” PMID: 37668214.
READINGS & TUTORIALS – Cryo-EM
E. Nogales & J. Mahamid, “Bridging
structural and cell biology with cryo-electron microscopy” PMID: 38570716.
DATABASES – Structural
Biology
AlphaFold
DB, BioCyc, DisProt, ExPASy, HAD, HIC-Up, NDB, PDB, PDBe, PDB
SARS-CoV-2 Resources, SARS-CoV-2
Related Structures, RaMP-DB, virusMED,