I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[1228]
Abstract: Lentiviruses are widespread in a variety of vertebrates, often associated with chronic disease states. However, until the recent discovery of the prehistoric endogenous lentiviruses in rabbits (RELIK) and lemurs (PSIV), it was thought that lentiviruses had no capacity for germline integration and were only spread horizontally in an exogenous fashion. The existence of RELIK and PSIV refuted these ideas, revealing lentiviruses to be present in a range of mammals, capable of germline integration, and far more ancient than previously thought. Using Gag sequences reconstructed from the remnants of these prehistoric lentiviruses, we have produced chimeric lentiviruses capable of infecting nondividing cells and determined structures of capsid domains from PSIV and RELIK. We show that the structures from these diverse viruses are highly similar, containing features found in modern-day lentiviruses, including a functional cyclophilin-binding loop. Together, these data provide evidence for an ancient capsid-cyclophilin interaction preserved throughout lentiviral evolution.
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Sep 2010
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I02-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
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Clinton K. Y.
Lau
,
Louise
Turner
,
Jakob S.
Jespersen
,
Edward D.
Lowe
,
Bent
Petersen
,
Christian W.
Wang
,
Jens E. V.
Petersen
,
John
Lusingu
,
Thor G.
Theander
,
Thomas
Lavstsen
,
Matthew K.
Higgins
Open Access
Abstract: The PfEMP1 family of surface proteins is central for Plasmodium falciparum virulence and must retain the ability to bind to host receptors while also diversifying to aid immune evasion. The interaction between CIDRα1 domains of PfEMP1 and endothelial protein C receptor (EPCR) is associated with severe childhood malaria. We combine crystal structures of CIDRα1:EPCR complexes with analysis of 885 CIDRα1 sequences, showing that the EPCR-binding surfaces of CIDRα1 domains are conserved in shape and bonding potential, despite dramatic sequence diversity. Additionally, these domains mimic features of the natural EPCR ligand and can block this ligand interaction. Using peptides corresponding to the EPCR-binding region, antibodies can be purified from individuals in malaria-endemic regions that block EPCR binding of diverse CIDRα1 variants. This highlights the extent to which such a surface protein family can diversify while maintaining ligand-binding capacity and identifies features that should be mimicked in immunogens to prevent EPCR binding.
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Jan 2015
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I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[9826]
Open Access
Abstract: The SAMHD1 triphosphohydrolase inhibits HIV-1 infection of myeloid and resting T cells by depleting dNTPs. To overcome SAMHD1, HIV-2 and some SIVs encode either of two lineages of the accessory protein Vpx that bind the SAMHD1 N or C terminus and redirect the host cullin-4 ubiquitin ligase to target SAMHD1 for proteasomal degradation. We present the ternary complex of Vpx from SIV that infects mandrills (SIVmnd-2) with the cullin-4 substrate receptor, DCAF1, and N-terminal and SAM domains from mandrill SAMHD1. The structure reveals details of Vpx lineage-specific targeting of SAMHD1 N-terminal “degron” sequences. Comparison with Vpx from SIV that infects sooty mangabeys (SIVsmm) complexed with SAMHD1-DCAF1 identifies molecular determinants directing Vpx lineages to N- or C-terminal SAMHD1 sequences. Inspection of the Vpx-DCAF1 interface also reveals conservation of Vpx with the evolutionally related HIV-1/SIV accessory protein Vpr. These data suggest a unified model for how Vpx and Vpr exploit DCAF1 to promote viral replication.
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Apr 2015
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I04-1-Macromolecular Crystallography (fixed wavelength)
I04-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
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Kristof
Moonens
,
Pär
Gideonsson
,
Suresh
Subedi
,
Jeanna
Bugaytsova
,
Ema
Romaõ
,
Melissa
Mendez
,
Jenny
Nordén
,
Mahsa
Fallah
,
Lena
Rakhimova
,
Anna
Shevtsova
,
Martina
Lahmann
,
Gaetano
Castaldo
,
Kristoffer
Brännström
,
Fanny
Coppens
,
Alvin W
Lo
,
Tor
Ny
,
Jay v
Solnick
,
Guy
Vandenbussche
,
Stefan
Oscarson
,
Lennart
Hammarström
,
Anna
Arnqvist
,
Douglas e
Berg
,
Serge
Muyldermans
,
Thomas
Borén
,
Han
Remaut
Diamond Proposal Number(s):
[9426]
Abstract: The Helicobacter pylori adhesin BabA binds mucosal ABO/Le(b) blood group (bg) carbohydrates. BabA facilitates bacterial attachment to gastric surfaces, increasing strain virulence and forming a recognized risk factor for peptic ulcers and gastric cancer. High sequence variation causes BabA functional diversity, but the underlying structural-molecular determinants are unknown. We generated X-ray structures of representative BabA isoforms that reveal a polymorphic, three-pronged Le(b) binding site. Two diversity loops, DL1 and DL2, provide adaptive control to binding affinity, notably ABO versus O bg preference. H. pylori strains can switch bg preference with single DL1 amino acid substitutions, and can coexpress functionally divergent BabA isoforms. The anchor point for receptor binding is the embrace of an ABO fucose residue by a disulfide-clasped loop, which is inactivated by reduction. Treatment with the redox-active pharmaceutic N-acetylcysteine lowers gastric mucosal neutrophil infiltration in H. pylori-infected Le(b)-expressing mice, providing perspectives on possible H. pylori eradication therapies.
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Jan 2016
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I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[7351, 12718]
Abstract: Uropathogenic E. coli (UPEC) is the dominant cause of urinary tract infections, clinically described as cystitis. UPEC express CUP pili, which are extracellular fibers tipped with adhesins that bind mucosal surfaces of the urinary tract. Here we identify the role of the F9/Yde/Fml pilus for UPEC persistence in the inflamed urothelium. The Fml adhesin FmlH binds galactose β1-3 N-acetylgalactosamine found in core-1 and -2 O-glycans. Deletion of fmlH had no effect on UPEC virulence in an acute mouse model of cystitis. However, FmlH provided a fitness advantage during chronic cystitis, which is manifested as persistent bacteriuria, high bladder bacterial burdens, and chronic inflammation. In situ binding confirmed that FmlH bound avidly to the inflamed, but not the naive bladder. In accordance with its pathogenic profile, vaccination with FmlH significantly protected mice from chronic cystitis. Thus, UPEC employ separate CUP pili to adapt to the rapidly changing niche during bladder infection.
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Oct 2016
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I02-Macromolecular Crystallography
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Frank
Lennartz
,
Yvonne
Adams
,
Anja
Bengtsson
,
Rebecca W.
Olsen
,
Louise
Turner
,
Nicaise T.
Ndam
,
Gertrude
Ecklu-Mensah
,
Azizath
Moussiliou
,
Michael F.
Ofori
,
Benoit
Gamain
,
John P.
Lusingu
,
Jens E. V.
Petersen
,
Christian W.
Wang
,
Sofia
Nunes-Silva
,
Jakob S.
Jespersen
,
Clinton K. Y.
Lau
,
Thor G.
Theander
,
Thomas
Lavstsen
,
Lars
Hviid
,
Matthew K.
Higgins
,
Anja T. R.
Jensen
Open Access
Abstract: Cerebral malaria is a deadly outcome of infection by Plasmodium falciparum, occurring when parasite-infected erythrocytes accumulate in the brain. These erythrocytes display parasite proteins of the PfEMP1 family that bind various endothelial receptors. Despite the importance of cerebral malaria, a binding phenotype linked to its symptoms has not been identified. Here, we used structural biology to determine how a group of PfEMP1 proteins interacts with intercellular adhesion molecule 1 (ICAM-1), allowing us to predict binders from a specific sequence motif alone. Analysis of multiple Plasmodium falciparum genomes showed that ICAM-1-binding PfEMP1s also interact with endothelial protein C receptor (EPCR), allowing infected erythrocytes to synergistically bind both receptors. Expression of these PfEMP1s, predicted to bind both ICAM-1 and EPCR, is associated with increased risk of developing cerebral malaria. This study therefore reveals an important PfEMP1-binding phenotype that could be targeted as part of a strategy to prevent cerebral malaria.
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Mar 2017
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I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
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M. Fleur
Sernee
,
Julie E.
Ralton
,
Tracy L.
Nero
,
Lukasz F.
Sobala
,
Joachim
Kloehn
,
Marcel A.
Vieira-Lara
,
Simon A.
Cobbold
,
Lauren
Stanton
,
Douglas E. V.
Pires
,
Eric
Hanssen
,
Alexandra
Males
,
Tom
Ward
,
Laurence M.
Bastidas
,
Phillip L.
Van Der Peet
,
Michael W.
Parker
,
David B.
Ascher
,
Spencer J.
Williams
,
Gideon J.
Davies
,
Malcolm J.
Mcconville
Diamond Proposal Number(s):
[13587, 18598]
Open Access
Abstract: Parasitic protists belonging to the genus Leishmania synthesize the non-canonical carbohydrate reserve, mannogen, which is composed of β-1,2-mannan oligosaccharides. Here, we identify a class of dual-activity mannosyltransferase/phosphorylases (MTPs) that catalyze both the sugar nucleotide-dependent biosynthesis and phosphorolytic turnover of mannogen. Structural and phylogenic analysis shows that while the MTPs are structurally related to bacterial mannan phosphorylases, they constitute a distinct family of glycosyltransferases (GT108) that have likely been acquired by horizontal gene transfer from gram-positive bacteria. The seven MTPs catalyze the constitutive synthesis and turnover of mannogen. This metabolic rheostat protects obligate intracellular parasite stages from nutrient excess, and is essential for thermotolerance and parasite infectivity in the mammalian host. Our results suggest that the acquisition and expansion of the MTP family in Leishmania increased the metabolic flexibility of these protists and contributed to their capacity to colonize new host niches.
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Sep 2019
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I03-Macromolecular Crystallography
Krios I-Titan Krios I at Diamond
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Jiandong
Huo
,
Yuguang
Zhao
,
Jingshan
Ren
,
Daming
Zhou
,
Helen M. E.
Duyvesteyn
,
Helen M.
Ginn
,
Loic
Carrique
,
Tomas
Malinauskas
,
Reinis R.
Ruza
,
Pranav N. M.
Shah
,
Tiong Kit
Tan
,
Pramila
Rijal
,
Naomi
Coombes
,
Kevin R.
Bewley
,
Julia A.
Tree
,
Julika
Radecke
,
Neil
Paterson
,
Piyasa
Supasa
,
Juthathip
Mongkolsapaya
,
Gavin R.
Screaton
,
Miles
Carroll
,
Alain
Townsend
,
Elizabeth E.
Fry
,
Raymond J.
Owens
,
David I.
Stuart
Diamond Proposal Number(s):
[19946, 26983]
Open Access
Abstract: There are as yet no licenced therapeutics for the COVID-19 pandemic. The causal coronavirus (SARS-CoV-2) binds host cells via a trimeric Spike whose receptor binding domain (RBD) recognises angiotensin-converting enzyme 2 (ACE2), initiating conformational changes that drive membrane fusion. We find that the monoclonal antibody CR3022 binds the RBD tightly, neutralising SARS-CoV-2 and report the crystal structure at 2.4 Å of the Fab/RBD complex. Some crystals are suitable for screening for entry-blocking inhibitors. The highly conserved, structure-stabilising, CR3022 epitope is inaccessible in the prefusion Spike, suggesting that CR3022 binding facilitates conversion to the fusion-incompetent post-fusion state. Cryo-EM analysis confirms that incubation of Spike with CR3022 Fab leads to destruction of the prefusion trimer. Presentation of this cryptic epitope in an RBD-based vaccine might advantageously focus immune responses. Binders at this epitope may be useful therapeutically, possibly in synergy with an antibody blocking receptor attachment.
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Jun 2020
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I02-Macromolecular Crystallography
I03-Macromolecular Crystallography
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Sander
Herfst
,
Jie
Zhang
,
Mathilde
Richard
,
Ryan
Mcbride
,
Pascal
Lexmond
,
Theo M.
Bestebroer
,
Monique I. J.
Spronken
,
Dennis
De Meulder
,
Judith M.
Van Den Brand
,
Miruna E.
Rosu
,
Stephen R.
Martin
,
Steven J.
Gamblin
,
Xiaoli
Xiong
,
Wenjie
Peng
,
Rogier
Bodewes
,
Erhard
Van Der Vries
,
Albert D. M. E.
Osterhaus
,
James C.
Paulson
,
John J.
Skehel
,
Ron A. M.
Fouchier
Diamond Proposal Number(s):
[9826, 13775]
Abstract: In 2014, an outbreak of avian A/H10N7 influenza virus occurred among seals along North-European coastal waters, significantly impacting seal populations. Here, we examine the cross-species transmission and mammalian adaptation of this influenza A virus, revealing changes in the hemagglutinin surface protein that increase stability and receptor binding. The seal A/H10N7 virus was aerosol or respiratory droplet transmissible between ferrets. Compared with avian H10 hemagglutinin, seal H10 hemagglutinin showed stronger binding to the human-type sialic acid receptor, with preferential binding to α2,6-linked sialic acids on long extended branches. In X-ray structures, changes in the 220-loop of the receptor-binding pocket caused similar interactions with human receptor as seen for pandemic strains. Two substitutions made seal H10 hemagglutinin more stable than avian H10 hemagglutinin and similar to human hemagglutinin. Consequently, identification of avian-origin influenza viruses across mammals appears critical to detect influenza A viruses posing a major threat to humans and other mammals.
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Oct 2020
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I03-Macromolecular Crystallography
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Chang
Liu
,
Daming
Zhou
,
Rungtiwa
Nutalai
,
Helen M. E.
Duyvesteyn
,
Aekkachai
Tuekprakhon
,
Helen M.
Ginn
,
Wanwisa
Dejnirattisai
,
Piyada
Supasa
,
Alexander J.
Mentzer
,
Beibei
Wang
,
James Brett
Case
,
Yuguang
Zhao
,
Donal T.
Skelly
,
Rita E.
Chen
,
Sile Ann
Johnson
,
Thomas G.
Ritter
,
Chris
Mason
,
Tariq
Malik
,
Nigel
Temperton
,
Neil G.
Paterson
,
Mark A.
Williams
,
David R.
Hall
,
Daniel K.
Clare
,
Andrew
Howe
,
Philip J. R.
Goulder
,
Elizabeth E.
Fry
,
Michael S.
Diamond
,
Juthathip
Mongkolsapaya
,
Jingshan
Ren
,
David I.
Stuart
,
Gavin R.
Screaton
Diamond Proposal Number(s):
[27009]
Open Access
Abstract: Alpha-B.1.1.7, Beta-B.1.351, Gamma-P.1 and Delta-B.1.617.2 variants of SARS-CoV-2 express multiple mutations in the spike protein (S). These may alter the antigenic structure of S, causing escape from natural or vaccine-induced immunity. Beta is particularly difficult to neutralize using serum induced by early pandemic SARS-CoV-2 strains and is most antigenically separated from Delta. To understand this, we generated 674 mAbs from Beta infected individuals and performed a detailed structure-function analysis of the 27 most potent mAbs: one binding the spike N-terminal domain (NTD), the rest the receptor binding domain (RBD). Two of these RBD-binding mAbs recognise a neutralizing epitope conserved between SARS-CoV-1 and -2, whilst 18 target mutated residues in Beta: K417N, E484K, and N501Y. There is a major response to N501Y including a public IgVH4-39 sequence, with E484K and K417N also targeted. Recognition of these key residues underscores why serum from Beta cases poorly neutralizes early pandemic and Delta viruses.
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Nov 2021
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