Publications
( ) Open Access articles are available for download as PDF.
( ) For papers behind paywall, PDF versions prior to copy-editing can be made available on request.
Selected publications
- Huber ST, Terwiel D, Evers WH, Maresca D, Jakobi AJ
Cryo-EM structure of gas vesicles for buoyancy-controlled motility
Cell 186:975-986 (2023) | pdf | doi |
Associated data:
Highlighted in: Nature Structural & Molecular Biology – News & Views
Featured in: TNW News
-
Bharadwaj A and Jakobi AJ
Electron scattering properties of biological macromolecules and their use in cryo-EM map sharpening
Faraday Discussions 240:168-183 (2022) | pdf | doi |
Associated data: -
Huber ST, Sarajlic E, Huijjink R, Weis F, Evers WH, Jakobi AJ
Nanofluidic chips for cryo-EM structure determination from picoliter sample volumes
eLife 11:e72629 (2022) | pdf | doi |
Associated data: -
Jakobi AJ, Huber ST, Mortensen SA, Schultz SW, Palara A, Kuhm T, Shrestha BK, Lamark T, Johansen T, Brech A, Sachse C. Structural basis of p62/SQSTM1 helical filaments and their role in cellular cargo uptake
Nature Communications 11: 440 (2020) | pdf | doi |
Associated data: -
Jakobi AJ, Wilmanns M, Sachse C.
Model-based local density sharpening of cryo-EM maps.
eLife 6: e27131 (2017) | pdf | doi |
Associated data: -
Jakobi AJ#*, Passon DM, Knoops K, Stellato F, White TA, Seine T, Messerschmidt M, Chapman HN, Wilmanns M#.
In cellulo X-ray Diffraction of Native Alcohol Oxidase Crystals in Yeast Cells by Serial Femtosecond Crystallography
IUCrJ 3: 88-95 (2016) #corresponding author, *equal contribution | pdf | doi |
Highlighted in IUCrJ Editorial Notes, DESY Photon Science Highlights
Featured in: DESY News, Femto, Research in Germany, CUI, chemie.de
Full publication list
2023 2022 2021 2020 2019 2018 2017 2016 2015 2014 2013 2012 2011 2008
Preprints
-
Kuhm TI, de Agrela Pinto C, Gross L, Huber ST, Taisne CM, Giannopolou EA, Pardon E, Steyaert J, Tans SJ, Jakobi AJ Structural basis of membrane targeting and coatomer assembly by human GBP1 bioRxiv 534355 (2023) | [ pdf ][pp06] | doi | Associated data:
-
Skoupý R, Boltje DB, Slouf M, Mrázová K, Láznička T, Taisne CM, Krzyzanek V, Hoogenboom JP, Jakobi AJ
Robust local thickness estimation of sub-micrometer specimen by 4D-STEM
ChemRxiv wsx83 (2023)
| pdf | doi | Associated data: -
Wang W, Jakobi AJ, Wu Y-L, Ries J, Stallinga S, Rieger B
Particle fusion of Single Molecule Localization Microscopy data reveals structure of Nup96 in Nuclear Pore Complex
bioRxiv 510818 (2022) | pdf | doi |
Associated data: -
Ramlal K, Burt A, Martín Garrido N, Palmer CM#, Jakobi AJ#, Aylett CHS#
Direct information estimation from cryo-EM movies with CARYON
bioRxiv 398891 (2020) | pdf | doi |
Published articles
2023
- Huber ST, Terwiel D, Evers WH, Maresca D, Jakobi AJ
Cryo-EM structure of gas vesicles for buoyancy-controlled motility
Cell 186:975-986 (2023) | pdf | doi |
Associated data:
Highlighted in NSMB News & views
2022
-
Maan R$, Reese L$, Volkov VA$, King MR, van der Sluis E, Andrea N, Evers WH, Jakobi AJ, Dogterom M
Multivalent interactions facilitate motor-dependent protein accumulation at growing microtubule plus ends
Nature Cell Biol 25:68-78 (2022) | pdf | doi |
Associated data: -
Boltje DB#, Hoogenboom JP#, Jakobi AJ, Jensen GJ, Jonker CTH, Kaag MJ, Koster AJ, Last MGF, de Agrela Pinto C, Plitzko JM, Raunser S, Tacke S, Wang Z, van der Wee EB, Wepf R, ten Hoedt S.
A cryogenic, coincident fluorescence, electron, and ion beam microscope
eLife 11:e82891 (2022) | pdf | doi |
Associated data: -
Bharadwaj A and Jakobi AJ
Electron scattering properties of biological macromolecules and their use in cryo-EM map sharpening
Faraday Discussions 240:168-183 (2022) | pdf | doi |
Associated data: -
Bakker SE, Bergeron J, Bharadwaj A, Bhella D, Bullough P, Chau P-L, Frank RAW, Jakobi AJ, Joseph AP, Kühlbrandt W, Lahiri I, Menday R, Muench SP, Nakasone M, Nerukh D, Paris G, Russo CJ, Saibil HR, Scheres SHW, Sherawat V, Shah AR, Thorn A, Vilas JL, Zanetti G.
Map/model validation and machine learning in EM
Faraday Discussions 240:229-242 (2022) | pdf | doi | -
Huber ST, Sarajlic E, Huijjink R, Weis F, Evers WH, Jakobi AJ
Nanofluidic chips for cryo-EM structure determination from picoliter sample volumes
eLife 11:e72629 (2022) | pdf | doi |
Associated data:
2021
- Klionsky D, Abdel-Aziz AK, Abdelfatah S, Abdoli A, Abel S, …, Jakobi AJ et al.
Guidelines for the use and interpretation of assays for monitoring autophagy
Autophagy 27: 1-240 (2021) | pdf | doi |
2020
-
Jakobi AJ
Seeing with electrons
Europhysics News 51: 20-23 (2020) | pdf | doi | -
Joseph AP , Jakobi AJ, Burnley T, Patwardhan A, Topf M, Wynn M.
Comparing Cryo-EM Reconstructions and Validating Atomic Model Fit using Difference Maps
J Chem Inf Model 60: 2552–2560 (2020) | pdf | doi |
Associated code: -
Jakobi AJ, Huber ST, Mortensen SA, Schultz SW, Palara A, Kuhm T, Shrestha BK, Lamark T, Johansen T, Brech A, Sachse C. Structural basis of p62/SQSTM1 helical filaments and their role in cellular cargo uptake
Nature Communications 11: 440 (2020) | pdf | doi |
Associated data:
2019
- Koiwai K, Tsukimoto J, Higashi T, Mafune F, Miyajima K, Nakane T, Matsugaki N, Jakobi AJ, Sugahara M, Tanaka T, Tono K, Joti Y, Yabashi M, Nureki O, Mizohata E, Nakatsu T, Nango E, Iwata S, Chavas LMG, Senda T, Itoh K, Yumoto F.
Improvement of production and isolation of human neuraminidase-1 in cellulo crystals
ACS Appl. Bio Mater. 2: 4941-4952 (2019) | pdf | doi |
2018
- Beckers M, Jakobi AJ, Sachse C.
Thresholding of cryo-EM density maps by false discovery rate control
IUCrJ 6: 1-16 (2018) | pdf | doi |
Highlighted in IUCrJ Editorial Notes
2017
-
Jakobi AJ, Wilmanns M, Sachse C.
Model-based local density sharpening of cryo-EM maps.
eLife 6: e27131 (2017) | pdf | doi |
Highlighted in IUCrJ Editorial Notes -
Sadian Y, Tafur L, Kosinski J, Jakobi AJ, Wetzel R, Buczak K, Hagen WJH, Beck M, Sachse C, Mueller CW.
Molecular architecture of a minimal yeast Pol I pre-initiation complex.
EMBO J 36: 2698-2709 (2017) | pdf | doi |
2016
-
Tafur L, Sadian Y, Hoffmann NA, Jakobi AJ Wetzel R, Hagen WJH, Sachse C, Muller CW
Molecular structures of transcribing RNA polymerase I.
Molecular Cell 64: 1135-1143 (2016) | pdf | doi | -
Schur FKM, Obr M, Wan W, Jakobi AJ, Sachse C, Krausslich HG, Briggs JAG
An atomic model of the HIV-1 capsid-SP1 layer reveals structures regulating assembly and maturation
Science 353: 506-508 (2016) | pdf | doi | -
Ohashi Y, Soler N, Garcia Ortegon M, Zhang L, Kirsten M, Perisic O, Masson, GR, Burke J, Jakobi AJ, Apostolakis AA, Johnson CM, Ohashi M, Ktistakis NT, Sachse C, Williams RL.
Characterization of Atg38 and NRBF2, a fifth subunit of the autophagic Vps34 complex.
Autophagy 12: 2129-2144 (2016) | pdf | doi | -
Bertipaglia C#, Jakobi AJ, Tarafder AK, Bykov YS, Picco A, Kukulski W, Kosinski J, Hagen WJH, Wilmanns M, Kaksonen M, Briggs JAG, Sachse C. #equal contribution
Higher-order assemblies of oligomeric cargo receptor complexes form the membrane scaffold of the Cvt vesicle.
EMBO Rep. 17: 1044-1060 (2016) | pdf | doi | Featured in EMBOpress Collection on Autophagy -
Hoffmann NA, Jakobi AJ, Vorlander MK, Sachse C, Muller CW.
Transcribing RNA polymerase III observed by electron cryo-microscopy.
FEBS J 283: 2811-19 (2016) | pdf | doi | -
Jakobi AJ#*, Passon DM, Knoops K, Stellato F, White TA, Seine T, Messerschmidt M, Chapman HN, Wilmanns M#
In cellulo X-ray Diffraction of Native Alcohol Oxidase Crystals in Yeast Cells by Serial Femtosecond Crystallography.
IUCrJ 3: 88-95 (2016) | pdf | doi | #corresponding author, *equal contribution
2015
-
Hoffmann NA, Jakobi AJ, Morcillo-Moreno M, Glatt S, Sachse C, Mueller CW
Molecular structures of unbound and transcribing RNA polymerase III.
Nature 528: 231-236 (2015) | pdf | doi | -
Skruzny M, Desfosses A, Prinz S, Dodonova S, Uetrecht C, Gieras A, Jakobi AJ, Abella M, Hagen WJH, Schulz J, Meijers R, Rybin V, Briggs JAG, Sachse C, Kaksonen M.
An organized co-assembly of clathrin adaptors is essential for endocytosis.
Developmental Cell 33: 150-162 (2015) | pdf | doi | -
Ehebauer MT, Jakobi AJ, Noens EE, Laubitz D, Cichocki B, Marrakchi H, Laneelle MA, Daffe M, Sachse C, Dziembowski A, Sauer U, Wilmanns M
Characterization of the mycobacterial Acyl-CoA carboxylase holo complexes reveals their functional expansion into amino acid catabolism.
PLoS Pathogens 33: 150-162 (2015) | pdf | doi -
Fromm SA, Bharat T, Jakobi AJ, Hagen W, Sachse C
Seeing Tobacco Mosaic Virus through direct electron detectors.
J Struct Biol 189: 87-97 (2015) | pdf | doi |
2014
- Volokhina E, Jakobi AJ, Urbanus RT, Huizinga EG, Sluiter H, Dineke Westra D, van Heerde W, van de Kar N, van den Heuvel L
Novel Sequence Variation affects GPIba in Post-diarrheal Hemolytic Uremic Syndrome.
J Nephrol Therapeutic S11: 007 (2014) | pdf | doi |
2013
- Popovic M, Jakobi AJ, Rensen-de Leeuw M, Rehmann H
The guanine nucleotide exchange factor Rlf interacts with SH3 domain-containing proteins via a binding site with a preselected conformation.
J Struct Biol 183: 312-319 (2013) | pdf | doi |
2012
- Jakobi AJ, Mashaghi A, Tans S, Huizinga EG
Calcium modulates force sensing by the von Willebrand Factor A2 domain
Nature Communications 2: e385 (2011) | pdf | doi |
Featured in: Chemisch Weekblad C2W, NWO, AMOLF, NU.nl
-
Jakobi AJ, Huizinga EG
A rapid cloning method employing orthogonal end protection.
PLoS One e37617 (2012) | pdf | doi | -
Jose RA, Voet A, Broos K, Jakobi AJ, Bruylants G, Egle B, Zhang KY, De Maeyer M, Deckmyn H, De Borggraeve WM
An integrated fragment based screening approach for the discovery of small molecule modulators of the VWF-GPIb interaction.
Chem Commun 48: 11349-11351 (2012) | pdf | doi |
2011
- Jakobi AJ, Lutz M
Structure of Ammonium 2-aminopyrazine-3-carboxylate.
Acta Cryst Section E: Crystallographic Communications 67: o984 (2011) | pdf | doi |
2008
- Jakobi AJ, Mauser H, Clark T
ParaFrag - a novel approach for surface-based similarity comparison of molecular fragments.
J Mol Model 14: 547-558 (2008) | pdf | doi |