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Deriving and refining atomic models in crystallography and cryo-EM: the latest Phenix tools to facilitate structure analysis.

Klaholz BP.

Acta Crystallogr D Struct Biol. 2019 Oct 1;75(Pt 10):878-881. doi: 10.1107/S2059798319013391. Epub 2019 Oct 1. No abstract available.


CENP-A nucleosome clusters form rosette-like structures around HJURP during G1.

Andronov L, Ouararhni K, Stoll I, Klaholz BP, Hamiche A.

Nat Commun. 2019 Sep 30;10(1):4436. doi: 10.1038/s41467-019-12383-3.


Publisher Correction: N6-Methyladenosine methyltransferase ZCCHC4 mediates ribosomal RNA methylation.

Ma H, Wang X, Cai J, Dai Q, Natchiar SK, Lv R, Chen K, Lu Z, Chen H, Shi YG, Lan F, Fan J, Klaholz BP, Pan T, Shi Y, He C.

Nat Chem Biol. 2019 May;15(5):549. doi: 10.1038/s41589-019-0233-6.


N6-Methyladenosine methyltransferase ZCCHC4 mediates ribosomal RNA methylation.

Ma H, Wang X, Cai J, Dai Q, Natchiar SK, Lv R, Chen K, Lu Z, Chen H, Shi YG, Lan F, Fan J, Klaholz BP, Pan T, Shi Y, He C.

Nat Chem Biol. 2019 Jan;15(1):88-94. doi: 10.1038/s41589-018-0184-3. Epub 2018 Dec 10. Erratum in: Nat Chem Biol. 2019 Feb 8;:.


Visualizing the Role of 2'-OH rRNA Methylations in the Human Ribosome Structure.

Natchiar SK, Myasnikov AG, Hazemann I, Klaholz BP.

Biomolecules. 2018 Oct 25;8(4). pii: E125. doi: 10.3390/biom8040125. Review.


Tetracyclines Modify Translation by Targeting Key Human rRNA Substructures.

Mortison JD, Schenone M, Myers JA, Zhang Z, Chen L, Ciarlo C, Comer E, Natchiar SK, Carr SA, Klaholz BP, Myers AG.

Cell Chem Biol. 2018 Dec 20;25(12):1506-1518.e13. doi: 10.1016/j.chembiol.2018.09.010. Epub 2018 Oct 11.


New tools for the analysis and validation of cryo-EM maps and atomic models.

Afonine PV, Klaholz BP, Moriarty NW, Poon BK, Sobolev OV, Terwilliger TC, Adams PD, Urzhumtsev A.

Acta Crystallogr D Struct Biol. 2018 Sep 1;74(Pt 9):814-840. doi: 10.1107/S2059798318009324. Epub 2018 Sep 3.


3DClusterViSu: 3D clustering analysis of super-resolution microscopy data by 3D Voronoi tessellations.

Andronov L, Michalon J, Ouararhni K, Orlov I, Hamiche A, Vonesch JL, Klaholz BP.

Bioinformatics. 2018 Sep 1;34(17):3004-3012. doi: 10.1093/bioinformatics/bty200.


Structure-function analyses unravel distinct effects of allosteric inhibitors of HIV-1 integrase on viral maturation and integration.

Bonnard D, Le Rouzic E, Eiler S, Amadori C, Orlov I, Bruneau JM, Brias J, Barbion J, Chevreuil F, Spehner D, Chasset S, Ledoussal B, Moreau F, Saïb A, Klaholz BP, Emiliani S, Ruff M, Zamborlini A, Benarous R.

J Biol Chem. 2018 Apr 20;293(16):6172-6186. doi: 10.1074/jbc.M117.816793. Epub 2018 Mar 5.


Volta phase plate data collection facilitates image processing and cryo-EM structure determination.

von Loeffelholz O, Papai G, Danev R, Myasnikov AG, Natchiar SK, Hazemann I, Ménétret JF, Klaholz BP.

J Struct Biol. 2018 Jun;202(3):191-199. doi: 10.1016/j.jsb.2018.01.003. Epub 2018 Jan 11.


Structural features of the salivary gland hypertrophy virus of the tsetse fly revealed by cryo-electron microscopy and tomography.

Orlov I, Drillien R, Spehner D, Bergoin M, Abd-Alla AMM, Klaholz BP.

Virology. 2018 Jan 15;514:165-169. doi: 10.1016/j.virol.2017.11.016. Epub 2017 Nov 27.


Visualization of chemical modifications in the human 80S ribosome structure.

Natchiar SK, Myasnikov AG, Kratzat H, Hazemann I, Klaholz BP.

Nature. 2017 Nov 23;551(7681):472-477. doi: 10.1038/nature24482. Epub 2017 Nov 15.


The HIV-1 integrase-LEDGF allosteric inhibitor MUT-A: resistance profile, impairment of virus maturation and infectivity but without influence on RNA packaging or virus immunoreactivity.

Amadori C, van der Velden YU, Bonnard D, Orlov I, van Bel N, Le Rouzic E, Miralles L, Brias J, Chevreuil F, Spehner D, Chasset S, Ledoussal B, Mayr L, Moreau F, García F, Gatell J, Zamborlini A, Emiliani S, Ruff M, Klaholz BP, Moog C, Berkhout B, Plana M, Benarous R.

Retrovirology. 2017 Nov 9;14(1):50. doi: 10.1186/s12977-017-0373-2.


Focused classification and refinement in high-resolution cryo-EM structural analysis of ribosome complexes.

von Loeffelholz O, Natchiar SK, Djabeur N, Myasnikov AG, Kratzat H, Ménétret JF, Hazemann I, Klaholz BP.

Curr Opin Struct Biol. 2017 Oct;46:140-148. doi: 10.1016/ Epub 2017 Aug 29. Review.


The Ribosome Holds the RNA Polymerase on Track in Bacteria.

Klaholz BP.

Trends Biochem Sci. 2017 Sep;42(9):686-689. doi: 10.1016/j.tibs.2017.07.003. Epub 2017 Aug 8.


Importance of the Sequence-Directed DNA Shape for Specific Binding Site Recognition by the Estrogen-Related Receptor.

Mohideen-Abdul K, Tazibt K, Bourguet M, Hazemann I, Lebars I, Takacs M, Cianférani S, Klaholz BP, Moras D, Billas IML.

Front Endocrinol (Lausanne). 2017 Jun 20;8:140. doi: 10.3389/fendo.2017.00140. eCollection 2017.


Cryo-EM study of start codon selection during archaeal translation initiation.

Coureux PD, Lazennec-Schurdevin C, Monestier A, Larquet E, Cladière L, Klaholz BP, Schmitt E, Mechulam Y.

Nat Commun. 2016 Nov 7;7:13366. doi: 10.1038/ncomms13366.


The integrative role of cryo electron microscopy in molecular and cellular structural biology.

Orlov I, Myasnikov AG, Andronov L, Natchiar SK, Khatter H, Beinsteiner B, Ménétret JF, Hazemann I, Mohideen K, Tazibt K, Tabaroni R, Kratzat H, Djabeur N, Bruxelles T, Raivoniaina F, Pompeo LD, Torchy M, Billas I, Urzhumtsev A, Klaholz BP.

Biol Cell. 2017 Feb;109(2):81-93. doi: 10.1111/boc.201600042. Epub 2016 Nov 25. Review.


Structure-function insights reveal the human ribosome as a cancer target for antibiotics.

Myasnikov AG, Kundhavai Natchiar S, Nebout M, Hazemann I, Imbert V, Khatter H, Peyron JF, Klaholz BP.

Nat Commun. 2016 Sep 26;7:12856. doi: 10.1038/ncomms12856.


Ribosomal 18S rRNA base pairs with mRNA during eukaryotic translation initiation.

Martin F, Ménétret JF, Simonetti A, Myasnikov AG, Vicens Q, Prongidi-Fix L, Natchiar SK, Klaholz BP, Eriani G.

Nat Commun. 2016 Aug 24;7:12622. doi: 10.1038/ncomms12622.


SharpViSu: integrated analysis and segmentation of super-resolution microscopy data.

Andronov L, Lutz Y, Vonesch JL, Klaholz BP.

Bioinformatics. 2016 Jul 15;32(14):2239-41. doi: 10.1093/bioinformatics/btw123. Epub 2016 Mar 18.


ClusterViSu, a method for clustering of protein complexes by Voronoi tessellation in super-resolution microscopy.

Andronov L, Orlov I, Lutz Y, Vonesch JL, Klaholz BP.

Sci Rep. 2016 Apr 12;6:24084. doi: 10.1038/srep24084.


Protein Delivery System Containing a Nickel-Immobilized Polymer for Multimerization of Affinity-Purified His-Tagged Proteins Enhances Cytosolic Transfer.

Postupalenko V, Desplancq D, Orlov I, Arntz Y, Spehner D, Mely Y, Klaholz BP, Schultz P, Weiss E, Zuber G.

Angew Chem Int Ed Engl. 2015 Sep 1;54(36):10583-6. doi: 10.1002/anie.201505437. Epub 2015 Jul 31.


IBiSS, a versatile and interactive tool for integrated sequence and 3D structure analysis of large macromolecular complexes.

Beinsteiner B, Michalon J, Klaholz BP.

Bioinformatics. 2015 Oct 15;31(20):3339-44. doi: 10.1093/bioinformatics/btv347. Epub 2015 Jun 19.


Structure of the human 80S ribosome.

Khatter H, Myasnikov AG, Natchiar SK, Klaholz BP.

Nature. 2015 Apr 30;520(7549):640-5. doi: 10.1038/nature14427. Epub 2015 Apr 22.


Structure-function relationships in nuclear receptors: the facts.

Moras D, Billas IM, Rochel N, Klaholz BP.

Trends Biochem Sci. 2015 Jun;40(6):287-90. doi: 10.1016/j.tibs.2015.03.009. Epub 2015 Apr 19. No abstract available.


Structure and function insights into the NuRD chromatin remodeling complex.

Torchy MP, Hamiche A, Klaholz BP.

Cell Mol Life Sci. 2015 Jul;72(13):2491-507. doi: 10.1007/s00018-015-1880-8. Epub 2015 Mar 22. Review.


Structural insight into the mechanism of stabilization of the 7SK small nuclear RNA by LARP7.

Uchikawa E, Natchiar KS, Han X, Proux F, Roblin P, Zhang E, Durand A, Klaholz BP, Dock-Bregeon AC.

Nucleic Acids Res. 2015 Mar 31;43(6):3373-88. doi: 10.1093/nar/gkv173. Epub 2015 Mar 9.


Conformation transitions of eukaryotic polyribosomes during multi-round translation.

Afonina ZA, Myasnikov AG, Shirokov VA, Klaholz BP, Spirin AS.

Nucleic Acids Res. 2015 Jan;43(1):618-28. doi: 10.1093/nar/gku1270. Epub 2014 Dec 17.


The molecular structure of the left-handed supra-molecular helix of eukaryotic polyribosomes.

Myasnikov AG, Afonina ZA, Ménétret JF, Shirokov VA, Spirin AS, Klaholz BP.

Nat Commun. 2014 Nov 7;5:5294. doi: 10.1038/ncomms6294.


Formation of circular polyribosomes on eukaryotic mRNA without cap-structure and poly(A)-tail: a cryo electron tomography study.

Afonina ZA, Myasnikov AG, Shirokov VA, Klaholz BP, Spirin AS.

Nucleic Acids Res. 2014 Aug;42(14):9461-9. doi: 10.1093/nar/gku599. Epub 2014 Jul 12.


The palindromic DNA-bound USP/EcR nuclear receptor adopts an asymmetric organization with allosteric domain positioning.

Maletta M, Orlov I, Roblin P, Beck Y, Moras D, Billas IM, Klaholz BP.

Nat Commun. 2014 Jun 19;5:4139. doi: 10.1038/ncomms5139.


Cryo-electron microscopy structure of lactococcal siphophage 1358 virion.

Spinelli S, Bebeacua C, Orlov I, Tremblay D, Klaholz BP, Moineau S, Cambillau C.

J Virol. 2014 Aug;88(16):8900-10. doi: 10.1128/JVI.01040-14. Epub 2014 May 28.


Purification, characterization and crystallization of the human 80S ribosome.

Khatter H, Myasnikov AG, Mastio L, Billas IM, Birck C, Stella S, Klaholz BP.

Nucleic Acids Res. 2014 Apr;42(6):e49. doi: 10.1093/nar/gkt1404. Epub 2014 Jan 21.


Escherichia coli ribosomal protein S1 unfolds structured mRNAs onto the ribosome for active translation initiation.

Duval M, Korepanov A, Fuchsbauer O, Fechter P, Haller A, Fabbretti A, Choulier L, Micura R, Klaholz BP, Romby P, Springer M, Marzi S.

PLoS Biol. 2013 Dec;11(12):e1001731. doi: 10.1371/journal.pbio.1001731. Epub 2013 Dec 10.


Initiation factor 2 crystal structure reveals a different domain organization from eukaryotic initiation factor 5B and mechanism among translational GTPases.

Eiler D, Lin J, Simonetti A, Klaholz BP, Steitz TA.

Proc Natl Acad Sci U S A. 2013 Sep 24;110(39):15662-7. doi: 10.1073/pnas.1309360110. Epub 2013 Sep 12.


Involvement of protein IF2 N domain in ribosomal subunit joining revealed from architecture and function of the full-length initiation factor.

Simonetti A, Marzi S, Billas IM, Tsai A, Fabbretti A, Myasnikov AG, Roblin P, Vaiana AC, Hazemann I, Eiler D, Steitz TA, Puglisi JD, Gualerzi CO, Klaholz BP.

Proc Natl Acad Sci U S A. 2013 Sep 24;110(39):15656-61. doi: 10.1073/pnas.1309578110. Epub 2013 Sep 12.


Topology of mRNA chain in isolated eukaryotic double-row polyribosomes.

Afonina ZhA, Myasnikov AG, Khabibullina NF, Belorusova AY, Menetret JF, Vasiliev VD, Klaholz BP, Shirokov VA, Spirin AS.

Biochemistry (Mosc). 2013 May;78(5):445-54. doi: 10.1134/S0006297913050027.


Structure of the protein core of translation initiation factor 2 in apo, GTP-bound and GDP-bound forms.

Simonetti A, Marzi S, Fabbretti A, Hazemann I, Jenner L, Urzhumtsev A, Gualerzi CO, Klaholz BP.

Acta Crystallogr D Biol Crystallogr. 2013 Jun;69(Pt 6):925-33. doi: 10.1107/S0907444913006422. Epub 2013 Apr 23.


Single particle and molecular assembly analysis of polyribosomes by single- and double-tilt cryo electron tomography.

Myasnikov AG, Afonina ZA, Klaholz BP.

Ultramicroscopy. 2013 Mar;126:33-9. doi: 10.1016/j.ultramic.2012.12.009. Epub 2012 Dec 20.


Rapid purification of ribosomal particles assembled on histone H4 mRNA: a new method based on mRNA-DNA chimaeras.

Prongidi-Fix L, Schaeffer L, Simonetti A, Barends S, Ménétret JF, Klaholz BP, Eriani G, Martin F.

Biochem J. 2013 Feb 1;449(3):719-28. doi: 10.1042/BJ20121211.


Structure of the full human RXR/VDR nuclear receptor heterodimer complex with its DR3 target DNA.

Orlov I, Rochel N, Moras D, Klaholz BP.

EMBO J. 2012 Jan 18;31(2):291-300. doi: 10.1038/emboj.2011.445. Epub 2011 Dec 16.


Molecular recognition and catalysis in translation termination complexes.

Klaholz BP.

Trends Biochem Sci. 2011 May;36(5):282-92. doi: 10.1016/j.tibs.2011.02.001. Epub 2011 Mar 17. Review.


Let's see how tmRNA rescues a stuck ribosome.

Klaholz BP.

EMBO J. 2010 Nov 17;29(22):3747-9. doi: 10.1038/emboj.2010.269. Epub 2010 Nov 17.


Structure-function insights into prokaryotic and eukaryotic translation initiation.

Myasnikov AG, Simonetti A, Marzi S, Klaholz BP.

Curr Opin Struct Biol. 2009 Jun;19(3):300-9. doi: 10.1016/ Epub 2009 Jun 1. Review.


A structural view of translation initiation in bacteria.

Simonetti A, Marzi S, Jenner L, Myasnikov A, Romby P, Yusupova G, Klaholz BP, Yusupov M.

Cell Mol Life Sci. 2009 Feb;66(3):423-36. doi: 10.1007/s00018-008-8416-4. Review.


Structure of the 30S translation initiation complex.

Simonetti A, Marzi S, Myasnikov AG, Fabbretti A, Yusupov M, Gualerzi CO, Klaholz BP.

Nature. 2008 Sep 18;455(7211):416-20. doi: 10.1038/nature07192. Epub 2008 Aug 31.


[Twisting of mRNA reversibly blocks its translation by the ribosome].

Marzi S, Romby P, Klaholz BP.

Med Sci (Paris). 2007 Oct;23(10):881-3. French. No abstract available.


Structured mRNAs regulate translation initiation by binding to the platform of the ribosome.

Marzi S, Myasnikov AG, Serganov A, Ehresmann C, Romby P, Yusupov M, Klaholz BP.

Cell. 2007 Sep 21;130(6):1019-31.


Conformational transition of initiation factor 2 from the GTP- to GDP-bound state visualized on the ribosome.

Myasnikov AG, Marzi S, Simonetti A, Giuliodori AM, Gualerzi CO, Yusupova G, Yusupov M, Klaholz BP.

Nat Struct Mol Biol. 2005 Dec;12(12):1145-9. Epub 2005 Nov 13.


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