Newsletter 516 (June 17, 2024) NIH X-ray Diffraction SIG
May
2024 PUBLICATIONS BY MEMBERS OF THE GROUP
1: Zhan J, Zeher A, Huang R, Tang
WK, Jenkins LM, Xia D.
Nat Commun. 2024 May
31;15(1):4655. doi: 10.1038/s41467-024-49029-y.
PMID: 38821922; PMCID: PMC11143374.
2: Zhang B, Chuang GY, Biju A, Biner D, Cheng J, Wang Y,
Bao S, Chao CW, Lei H, Liu T, Nazzari AF, Yang Y,
Zhou T, Chen SJ, Chen X, Kong WP, Ou L, Parchment DK, Sarfo EK, SiMa H, Todd JP, Wang S, Woodward RA, Cheng C, Rawi R, Mascola JR, Kwong
PD.
Cholesterol reduction by
immunization with a PCSK9 mimic.
Cell Rep. 2024 May 30;43(6):114285. doi:
10.1016/j.celrep.2024.114285. Epub ahead of
print.
PMID: 38819987.
3: Jia M, Zhao H, Morano NC, Lu
H, Lui YM, Du H, Becker JE, Yuen KY, Ho DD, Kwong
PD, Shapiro L, To KK, Wu X.
Human neutralizing
antibodies target a conserved lateral patch on H7N9 hemagglutinin head.
Nat Commun. 2024 May
27;15(1):4505. doi: 10.1038/s41467-024-48758-4.
PMID: 38802413; PMCID:PMC11130183.
4: Wang S, Chan KW, Wei D, Ma X, Liu S, Hu G, Park S, Pan
R, Gu Y, Nazzari AF, Olia AS, Xu K, Lin BC, Louder
MK, McKee K, Doria-Rose NA, Montefiori D, Seaman MS,
Zhou T, Kwong
PD, Arthos J, Kong XP, Lu S.
Nat Commun. 2024 May
21;15(1):4301. doi: 10.1038/s41467-024-48514-8.
PMID: 38773089; PMCID: PMC11109196.
5: Diarra S, Ghosh S, Cissé L,
Coulibaly T, Yalcouyé A, Harmison
G, Diallo S, Diallo SH, Coulibaly O, Schindler A, Cissé
CAK, Maiga AB, Bamba S, Samassekou
O, Khokha MK, Mis EK, Lakhani SA, Donovan FX,
Jacobson S, Blackstone C, Guinto CO, Landouré
G, Bonifacino JS,
Fischbeck KH, Grunseich C.
AP2A2 mutation and
defective endocytosis in a Malian family with hereditary spastic paraplegia.
Neurobiol Dis.
2024 May 19;198:106537. doi:
10.1016/j.nbd.2024.106537. Epub ahead of print.
PMID: 38772452.
6: Chinnam NB, Thapar
R, Arvai AS, Sarker AH, Soll JM,
Paul T, Syed A, Rosenberg DJ, Hammel M, Bacolla A, Katsonis P, Asthana A, Tsai MS, Ivanov I, Lichtarge O, Silverman RH, Mosammaparast
N, Tsutakawa SE, Tainer
JA.
J Biol Chem. 2024 May 13:107368. doi:
10.1016/j.jbc.2024.107368. Epub ahead of print.
PMID: 38750793.
7: Kumar P, Tomita T, Gerken TA,
Ballard CJ, Lee YS, Weiss LM, Samara
NL.
Nat Commun. 2024 May
6;15(1):3792. doi: 10.1038/s41467-024-48253-w.
PMID: 38710711; PMCID: PMC11074326.
8: Xu J, Zhou T, McKee K, Zhang B, Liu C, Nazzari AF, Pegu A, Shen CH,
Becker JE, Bender MF, Chan P, Changela A, Chaudhary
R, Chen X, Einav T, Kwon YD, Lin BC, Louder MK,
Merriam JS, Morano NC, O'Dell S, Olia AS, Rawi R, Roark RS, Stephens T, Teng IT, Tourtellott-Fogt
E, Wang S, Yang ES, Shapiro L, Tsybovsky Y,
Doria-Rose NA, Casellas R, Kwong
PD.
Ultrapotent Broadly
Neutralizing Human-llama Bispecific Antibodies against HIV-1.
Adv Sci (Weinh). 2024 May 5:e2309268.doi: 10.1002/advs.202309268. Epub
ahead of print.
PMID: 38704686.
9: Osei-Amponsa V, Magidson
V, Walters
KJ.
STAR Protoc. 2024 May
2;5(2):103060. doi: 10.1016/j.xpro.2024.103060. Epub ahead of print.
PMID: 38700979; PMCID: PMC11078693.
10: Jiang J, Natarajan K, Margulies
DH.
Chaperone-mediated MHC-I
peptide exchange in antigen presentation.
IUCrJ. 2024
May 1;11(Pt 3):287-298. doi:
10.1107/S2052252524002768.
PMID: 38656309; PMCID: PMC11067752.
11: De Pace R, Maroofian R, Paimboeuf A, Zamani M, Zaki MS, Sadeghian
S, Azizimalamiri R, Galehdari
H, Zeighami J, Williamson CD, Fleming E, Zhou D,
Gannon JL, Thiffault I, Roze E, Suri M, Zifarelli G, Bauer P, Houlden H,
Severino M, Patten SA, Farrow E, Bonifacino JS.
Brain. 2024 May 3;147(5):1751-1767. doi:
10.1093/brain/awad427.
PMID: 38128568; PMCID: PMC11068110.
For timely listing, please send a heads-up E-mail to
the Editor upon
publication.
METHODS – Integrative
Structural Biology
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.
READINGS & TUTORIALS – Macromolecular Crystallography
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,