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Staff at EMBL

Dr. Vladimir Rybin

Senior Officer - Biophysical Support
Protein Expression and Purification Core Facility

EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

E-mail: send a mail

Biophysical Support


Publications

Total: 55 publication(s)

2014

Bojar D, Martinez J, Santiago J, Rybin V, Bayliss R, Hothorn M. (2014)
Crystal structures of the phosphorylated BRI1 kinase domain and implications for brassinosteroid signal initiation.
Plant J. 78(1):31-43. doi:10.1111/tpj.12445
Europe PMC | doi


2013

Hondele M, Stuwe T, Hassler M, Halbach F, Bowman A, Zhang ET, Nijmeijer B, Kotthoff C, Rybin V, Amlacher S, Hurt E, Ladurner AG. (2013)
Structural basis of histone H2A-H2B recognition by the essential chaperone FACT
Nature 499(7456):111-114. doi:10.1038/nature12242
Europe PMC | doi

Taylor NM, Glatt S, Hennrich ML, von Scheven G, Grötsch H, Fernández-Tornero C, Rybin V, Gavin AC, Kolb P, Müller CW. (2013)
Structural and functional characterization of a phosphatase domain within yeast general transcription factor IIIC
J. Biol. Chem. 288(21):15110-15120. doi:10.1074/jbc.m112.427856
Europe PMC | doi

Jankevicius G, Hassler M, Golia B, Rybin V, Zacharias M, Timinszky G, Ladurner AG. (2013)
A family of macrodomain proteins reverses cellular mono-ADP-ribosylation
Nat. Struct. Mol. Biol. 20(4):508-514. doi:10.1038/nsmb.2523
Europe PMC | doi


2012

Zanier K, ould M'hamed ould Sidi A, Boulade-Ladame C, Rybin V, Chappelle A, Atkinson A, Kieffer B, Travé G. (2012)
Solution structure analysis of the HPV16 E6 oncoprotein reveals a self-association mechanism required for E6-mediated degradation of p53
Structure 20(4):604-617. doi:10.1016/j.str.2012.02.001
Europe PMC | doi

van Noort V, Seebacher J, Bader S, Mohammed S, Vonkova I, Betts MJ, Kühner S, Kumar R, Maier T, O'Flaherty M, Rybin V, Schmeisky A, Yus E, Stülke J, Serrano L, Russell RB, Heck AJ, Bork P, Gavin AC. (2012)
Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium
Mol. Syst. Biol. 8:571. doi:10.1038/msb.2012.4
Europe PMC | doi


2011

Duszczyk MM, Wutz A, Rybin V, Sattler M. (2011)
The Xist RNA A-repeat comprises a novel AUCG tetraloop fold and a platform for multimerization
RNA 17(11):1973-1982. doi:10.1261/rna.2747411
Europe PMC | doi

Nowak AJ, Alfieri C, Stirnimann CU, Rybin V, Baudin F, Ly-Hartig N, Lindner D, Müller CW. (2011)
Chromatin-modifying complex component Nurf55/p55 associates with histones H3 and H4 and polycomb repressive complex 2 subunit Su(z)12 through partially overlapping binding sites
J. Biol. Chem. 286(26):23388-23396. doi:10.1074/jbc.m110.207407
Europe PMC | doi

Mackereth CD, Madl T, Bonnal S, Simon B, Zanier K, Gasch A, Rybin V, Valcárcel J, Sattler M. (2011)
Multi-domain conformational selection underlies pre-mRNA splicing regulation by U2AF
Nature 475(7356):408-411. doi:10.1038/nature10171
Europe PMC | doi

Langer K, Dian C, Rybin V, Müller CW, Petosa C. (2011)
Insights into the function of the CRM1 cofactor RanBP3 from the structure of its Ran-binding domain
PLoS ONE 6(2):e17011. doi:10.1371/journal.pone.0017011
Europe PMC | doi


2010

Gallego O, Betts MJ, Gvozdenovic-Jeremic J, Maeda K, Matetzki C, Aguilar-Gurrieri C, Beltran-Alvarez P, Bonn S, Fernández-Tornero C, Jensen LJ, Kuhn M, Trott J, Rybin V, Müller CW, Bork P, Kaksonen M, Russell RB, Gavin AC. (2010)
A systematic screen for protein-lipid interactions in Saccharomyces cerevisiae
Mol. Syst. Biol. 6:430. doi:10.1038/msb.2010.87
Europe PMC | doi

Hothorn M, Van den Ende W, Lammens W, Rybin V, Scheffzek K. (2010)
Structural insights into the pH-controlled targeting of plant cell-wall invertase by a specific inhibitor protein
Proc. Natl. Acad. Sci. U.S.A. 107(40):17427-17432. doi:10.1073/pnas.1004481107
Europe PMC | doi

Wirtz M, Birke H, Heeg C, Müller C, Hosp F, Throm C, König S, Feldman-Salit A, Rippe K, Petersen G, Wade RC, Rybin V, Scheffzek K, Hell R. (2010)
Structure and function of the hetero-oligomeric cysteine synthase complex in plants
J. Biol. Chem. 285(43):32810-32817. doi:10.1074/jbc.m110.157446
Europe PMC | doi

Schallus T, Fehér K, Sternberg U, Rybin V, Muhle-Goll C. (2010)
Analysis of the specific interactions between the lectin domain of malectin and diglucosides
Glycobiology 20(8):1010-1020. doi:10.1093/glycob/cwq059
Europe PMC | doi

Stankiewicz M, Nikolay R, Rybin V, Mayer MP. (2010)
CHIP participates in protein triage decisions by preferentially ubiquitinating Hsp70-bound substrates
FEBS J. 277(16):3353-3367. doi:10.1111/j.1742-4658.2010.07737.x
Europe PMC | doi

Eder M, Knackmuss S, Le Gall F, Reusch U, Rybin V, Little M, Haberkorn U, Mier W, Eisenhut M. (2010)
68Ga-labelled recombinant antibody variants for immuno-PET imaging of solid tumours
Eur. J. Nucl. Med. Mol. Imaging 37(7):1397-1407. doi:10.1007/s00259-010-1392-6
Europe PMC | doi

Krzic U, Rybin V, Leonard KR, Linke WA, Bullard B. (2010)
Regulation of oscillatory contraction in insect flight muscle by troponin
J. Mol. Biol. 397(1):110-118. doi:10.1016/j.jmb.2010.01.039
Europe PMC | doi

Zanier K, Ruhlmann C, Melin F, Masson M, Ould M'hamed Ould Sidi A, Bernard X, Fischer B, Brino L, Ristriani T, Rybin V, Baltzinger M, Vande Pol S, Hellwig P, Schultz P, Travé G. (2010)
E6 proteins from diverse papillomaviruses self-associate both in vitro and in vivo
J. Mol. Biol. 396(1):90-104. doi:10.1016/j.jmb.2009.11.022
Europe PMC | doi


2009

Kühner S, van Noort V, Betts MJ, Leo-Macias A, Batisse C, Rode M, Yamada T, Maier T, Bader S, Beltran-Alvarez P, Castaño-Diez D, Chen WH, Devos D, Güell M, Norambuena T, Racke I, Rybin V, Schmidt A, Yus E, Aebersold R, Herrmann R, Böttcher B, Frangakis AS, Russell RB, Serrano L, Bork P, Gavin AC. (2009)
Proteome organization in a genome-reduced bacterium
Science 326(5957):1235-1240. doi:10.1126/science.1176343
Europe PMC | doi

Van Doorslaer K, Sidi AO, Zanier K, Rybin V, Deryckère F, Rector A, Burk RD, Lienau EK, van Ranst M, Travé G. (2009)
Identification of unusual E6 and E7 proteins within avian papillomaviruses: cellular localization, biophysical characterization, and phylogenetic analysis
J. Virol. 83(17):8759-8770. doi:10.1128/jvi.01777-08
Europe PMC | doi

Grimm C, Matos R, Ly-Hartig N, Steuerwald U, Lindner D, Rybin V, Müller J, Müller CW. (2009)
Molecular recognition of histone lysine methylation by the Polycomb group repressor dSfmbt
EMBO J. 28(13):1965-1977. doi:10.1038/emboj.2009.147
Europe PMC | doi

Hothorn M, Neumann H, Lenherr ED, Wehner M, Rybin V, Hassa PO, Uttenweiler A, Reinhardt M, Schmidt A, Seiler J, Ladurner AG, Herrmann C, Scheffzek K, Mayer A. (2009)
Catalytic core of a membrane-associated eukaryotic polyphosphate polymerase
Science 324(5926):513-516. doi:10.1126/science.1168120
Europe PMC | doi

Kuehnel MP, Rybin V, Anand PK, Anes E, Griffiths G. (2009)
Lipids regulate P2X7-receptor-dependent actin assembly by phagosomes via ADP translocation and ATP synthesis in the phagosome lumen
J. Cell. Sci. 122(Pt 4):499-504. doi:10.1242/jcs.034199
Europe PMC | doi

Corsini L, Hothorn M, Stier G, Rybin V, Scheffzek K, Gibson TJ, Sattler M. (2009)
Dimerization and protein binding specificity of the U2AF homology motif of the splicing factor Puf60
J. Biol. Chem. 284(1):630-639. doi:10.1074/jbc.m805395200
Europe PMC | doi


2008

Stuwe T, Hothorn M, Lejeune E, Rybin V, Bortfeld M, Scheffzek K, Ladurner AG. (2008)
The FACT Spt16 "peptidase" domain is a histone H3-H4 binding module
Proc. Natl. Acad. Sci. U.S.A. 105(26):8884-8889. doi:10.1073/pnas.0712293105
Europe PMC | doi

Gromes R, Hothorn M, Lenherr ED, Rybin V, Scheffzek K, Rausch T. (2008)
The redox switch of gamma-glutamylcysteine ligase via a reversible monomer-dimer transition is a mechanism unique to plants
Plant J. 54(6):1063-1075. doi:10.1111/j.1365-313x.2008.03477.x
Europe PMC | doi

Fiedler M, Sánchez-Barrena MJ, Nekrasov M, Mieszczanek J, Rybin V, Müller J, Evans P, Bienz M. (2008)
Decoding of methylated histone H3 tail by the Pygo-BCL9 Wnt signaling complex
Mol. Cell 30(4):507-518. doi:10.1016/j.molcel.2008.03.011
Europe PMC | doi

Koyama S, Hata S, Witt CC, Ono Y, Lerche S, Ojima K, Chiba T, Doi N, Kitamura F, Tanaka K, Abe K, Witt SH, Rybin V, Gasch A, Franz T, Labeit S, Sorimachi H. (2008)
Muscle RING-finger protein-1 (MuRF1) as a connector of muscle energy metabolism and protein synthesis
J. Mol. Biol. 376(5):1224-1236. doi:10.1016/j.jmb.2007.11.049
Europe PMC | doi

Denayer E, Parret A, Chmara M, Schubbert S, Vogels A, Devriendt K, Frijns JP, Rybin V, de Ravel TJ, Shannon K, Cools J, Scheffzek K, Legius E. (2008)
Mutation analysis in Costello syndrome: functional and structural characterization of the HRAS p.Lys117Arg mutation
Hum. Mutat. 29(2):232-239. doi:10.1002/humu.20616
Europe PMC | doi


2007

Grimm C, de Ayala Alonso AG, Rybin V, Steuerwald U, Ly-Hartig N, Fischle W, Müller J, Müller CW. (2007)
Structural and functional analyses of methyl-lysine binding by the malignant brain tumour repeat protein Sex comb on midleg
EMBO Rep. 8(11):1031-1037. doi:10.1038/sj.embor.7401085
Europe PMC | doi

Sjekloća L, Pudas R, Sjöblom B, Konarev P, Carugo O, Rybin V, Kiema TR, Svergun D, Ylänne J, Djinović Carugo K. (2007)
Crystal structure of human filamin C domain 23 and small angle scattering model for filamin C 23-24 dimer
J. Mol. Biol. 368(4):1011-1023. doi:10.1016/j.jmb.2007.02.018
Europe PMC | doi

Oddone A, Lorentzen E, Basquin J, Gasch A, Rybin V, Conti E, Sattler M. (2007)
Structural and biochemical characterization of the yeast exosome component Rrp40
EMBO Rep. 8(1):63-69. doi:10.1038/sj.embor.7400856
Europe PMC | doi


2006

Kalamidas SA, Kuehnel MP, Peyron P, Rybin V, Rauch S, Kotoulas OB, Houslay M, Hemmings BA, Gutierrez MG, Anes E, Griffiths G. (2006)
cAMP synthesis and degradation by phagosomes regulate actin assembly and fusion events: consequences for mycobacteria
J. Cell. Sci. 119(Pt 17):3686-3694. doi:10.1242/jcs.03091
Europe PMC | doi

Boyault C, Gilquin B, Zhang Y, Rybin V, Garman E, Meyer-Klaucke W, Matthias P, Müller CW, Khochbin S. (2006)
HDAC6-p97/VCP controlled polyubiquitin chain turnover
EMBO J. 25(14):3357-3366. doi:10.1038/sj.emboj.7601210
Europe PMC | doi

Pastore C, Adinolfi S, Huynen MA, Rybin V, Martin S, Mayer M, Bukau B, Pastore A. (2006)
YfhJ, a molecular adaptor in iron-sulfur cluster formation or a frataxin-like protein?
Structure 14(5):857-867. doi:10.1016/j.str.2006.02.010
Europe PMC | doi

Gareus R, Di Nardo A, Rybin V, Witke W. (2006)
Mouse profilin 2 regulates endocytosis and competes with SH3 ligand binding to dynamin 1
J. Biol. Chem. 281(5):2803-2811. doi:10.1074/jbc.m503528200
Europe PMC | doi


2005

Odintsov SG, Sabała I, Bourenkov G, Rybin V, Bochtler M. (2005)
Substrate access to the active sites in aminopeptidase T, a representative of a new metallopeptidase clan
J. Mol. Biol. 354(2):403-412. doi:10.1016/j.jmb.2005.09.042
Europe PMC | doi

Odintsov SG, Sabała I, Bourenkov G, Rybin V, Bochtler M. (2005)
Staphylococcus aureus aminopeptidase S is a founding member of a new peptidase clan
J. Biol. Chem. 280(30):27792-27799. doi:10.1074/jbc.m502023200
Europe PMC | doi


2002

Reina J, Lacroix E, Hobson SD, Fernandez-Ballester G, Rybin V, Schwab MS, Serrano L, Gonzalez C. (2002)
Computer-aided design of a PDZ domain to recognize new target sequences
Nat. Struct. Biol. 9(8):621-627. doi:10.1038/nsb815
Europe PMC | doi

Grandi P, Rybin V, Bassler J, Petfalski E, Strauss D, Marzioch M, Schäfer T, Kuster B, Tschochner H, Tollervey D, Gavin AC, Hurt E. (2002)
90S pre-ribosomes include the 35S pre-rRNA, the U3 snoRNP, and 40S subunit processing factors but predominantly lack 60S synthesis factors
Mol. Cell 10(1):105-115. doi:10.1016/s1097-2765(02)00579-8
Europe PMC | doi

Defacque H, Bos E, Garvalov B, Barret C, Roy C, Mangeat P, Shin HW, Rybin V, Griffiths G. (2002)
Phosphoinositides regulate membrane-dependent actin assembly by latex bead phagosomes
Mol. Biol. Cell 13(4):1190-1202. doi:10.1091/mbc.01-06-0314
Europe PMC | doi

Gavin AC, Bösche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon AM, Cruciat CM, Remor M, Höfert C, Schelder M, Brajenovic M, Ruffner H, Merino A, Klein K, Hudak M, Dickson D, Rudi T, Gnau V, Bauch A, Bastuck S, Huhse B, Leutwein C, Heurtier MA, Copley RR, Edelmann A, Querfurth E, Rybin V, Drewes G, Raida M, Bouwmeester T, Bork P, Seraphin B, Kuster B, Neubauer G, Superti-Furga G. (2002)
Functional organization of the yeast proteome by systematic analysis of protein complexes
Nature 415(6868):141-147. doi:10.1038/415141a
Europe PMC | doi


2001

Lippé R, Miaczynska M, Rybin V, Runge A, Zerial M. (2001)
Functional synergy between Rab5 effector Rabaptin-5 and exchange factor Rabex-5 when physically associated in a complex
Mol. Biol. Cell 12(7):2219-2228. doi:10.1091/mbc.12.7.2219
Europe PMC | doi

Esters H, Alexandrov K, Iakovenko A, Ivanova T, Thomä N, Rybin V, Zerial M, Scheidig AJ, Goody RS. (2001)
Vps9, Rabex-5 and DSS4: proteins with weak but distinct nucleotide-exchange activities for Rab proteins
J. Mol. Biol. 310(1):141-156. doi:10.1006/jmbi.2001.4735
Europe PMC | doi

Van de Putte T, Zwijsen A, Lonnoy O, Rybin V, Cozijnsen M, Francis A, Baekelandt V, Kozak CA, Zerial M, Huylebroeck D. (2001)
Mice with a homozygous gene trap vector insertion in mgcRacGAP die during pre-implantation development
Mech. Dev. 102(1-2):33-44. doi:10.1016/s0925-4773(01)00279-9
Europe PMC | doi

Jahraus A, Egeberg M, Hinner B, Habermann A, Sackman E, Pralle A, Faulstich H, Rybin V, Defacque H, Griffiths G. (2001)
ATP-dependent membrane assembly of F-actin facilitates membrane fusion
Mol. Biol. Cell 12(1):155-170. doi:10.1091/mbc.12.1.155
Europe PMC | doi


2000

Lanzetti L, Rybin V, Malabarba MG, Christoforidis S, Scita G, Zerial M, Di Fiore PP. (2000)
The Eps8 protein coordinates EGF receptor signalling through Rac and trafficking through Rab5
Nature 408(6810):374-377. doi:10.1038/35042605
Europe PMC | doi

McCarthy AA, Haebel PW, Törrönen A, Rybin V, Baker EN, Metcalf P. (2000)
Crystal structure of the protein disulfide bond isomerase, DsbC, from Escherichia coli
Nat. Struct. Biol. 7(3):196-199. doi:10.1038/73295
Europe PMC | doi


1999

McBride HM, Rybin V, Murphy C, Giner A, Teasdale R, Zerial M. (1999)
Oligomeric complexes link Rab5 effectors with NSF and drive membrane fusion via interactions between EEA1 and syntaxin 13
Cell 98(3):377-386. doi:10.1016/s0092-8674(00)81966-2
Europe PMC | doi


1998

Vitale G, Rybin V, Christoforidis S, Thornqvist P, McCaffrey M, Stenmark H, Zerial M. (1998)
Distinct Rab-binding domains mediate the interaction of Rabaptin-5 with GTP-bound Rab4 and Rab5
EMBO J. 17(7):1941-1951. doi:10.1093/emboj/17.7.1941
Europe PMC | doi

Gournier H, Stenmark H, Rybin V, Lippé R, Zerial M. (1998)
Two distinct effectors of the small GTPase Rab5 cooperate in endocytic membrane fusion
EMBO J. 17(7):1930-1940. doi:10.1093/emboj/17.7.1930
Europe PMC | doi


1997

Horiuchi H, Lippé R, McBride HM, Rubino M, Woodman P, Stenmark H, Rybin V, Wilm M, Ashman K, Mann M, Zerial M. (1997)
A novel Rab5 GDP/GTP exchange factor complexed to Rabaptin-5 links nucleotide exchange to effector recruitment and function
Cell 90(6):1149-1159. doi:10.1016/s0092-8674(00)80380-3
Europe PMC | doi


1996

Murphy C, Saffrich R, Grummt M, Gournier H, Rybin V, Rubino M, Auvinen P, Lütcke A, Parton RG, Zerial M. (1996)
Endosome dynamics regulated by a Rho protein
Nature 384(6608):427-432. doi:10.1038/384427a0
Europe PMC | doi

Rybin V, Zapun A, Törrönen A, Raina S, Missiakas D, Creighton TE, Metcalf P. (1996)
Crystallization of DsbC, the disulfide bond isomerase of Escherichia coli
Acta Crystallogr. D Biol. Crystallogr. 52(Pt 6):1219-1221. doi:10.1107/s0907444996008967
Europe PMC | doi

Rybin V, Ullrich O, Rubino M, Alexandrov K, Simon I, Seabra MC, Goody R, Zerial M. (1996)
GTPase activity of Rab5 acts as a timer for endocytic membrane fusion
Nature 383(6597):266-269. doi:10.1038/383266a0
Europe PMC | doi