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

• 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 |           

• Jakobi AJ, Wilmanns M, Sachse C.
  Model-based local density sharpening of cryo-EM maps.
  eLife 6: e27131 (2017) | 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) ^#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

• 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) | doi |          

       Highlighted in Nature News and Views
       Featured in EMBL News

• 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

Full publication list

orcid.org/0000-0002-7761-2027

2020 2019 2018 2017 2016 2015 2014 2013 2012 2011 2008

Preprints

• Jakobi AJ, Huber ST, Mortensen SA, Schultz SW, Palara A, Kuhm T, Shrestha BK, Lamark T, Hagen WJH, Wilmanns M, Johansen T, Brech A, Sachse C.
  Structural basis of p62/SQSTM1 helical filaments, their presence in p62 bodies and role of cargo recognition in the cell
  bioRxiv 671792 (2019) | pdf | doi |  

• Jakobi AJ, Wilmanns M, Sachse C.
  Iterative model-based density improvement yields better atomic structures from cryo-EM maps
  bioRxiv 121913 (2017) | pdf | doi |  

Peer-reviewed articles

2020

• 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, in press (2020) | pdf | doi |    

• 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 |           

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.
  FEBS J 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 |  

• 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 |