Namdinator - Automatic Molecular Dynamics flexible fitting of structural models into cryo-EM and crystallography experimental maps

Kidmose, Rune T.; Juhl, Jonathan; Nissen, Poul; Boesen, Thomas; Karlsen, Jesper Lykkegaard; Pedersen, Bjørn Panyella

doi:10.1101/501197

Cited by 116 publications

(142 citation statements)

References 15 publications

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“…The molecular model of SWI/SNF Body module was then refined using Namdinator 69 (Extended Data Table 2). To obtain the model for the full complex, we rigid-body fitted the Body, the Arp module (PDB ID 4I6M) 33 and the ATPase-nucleosome bound with ADP-BeF x (PDB ID 5Z3V) 15 into the map of the full complexes in Coot.…”

Section: Methodsmentioning

confidence: 99%

Cryo-electron microscopy structure of a nucleosome-bound SWI/SNF chromatin remodeling complex

Han¹,

Aa²,

Malik³

et al. 2019

Preprint

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13The multi-subunit chromatin remodeling complex SWI/SNF 1-3 is highly conserved from 14 yeast to humans and plays critical roles in various cellular processes including 15 transcription and DNA damage repair 4,5 . It uses the energy from ATP hydrolysis to 16 remodel chromatin structure by sliding and evicting the histone octamer 6-10 , creating 17 DNA regions that become accessible to other essential protein complexes. However, 18 our mechanistic understanding of the chromatin remodeling activity is largely hindered 19 by the lack of a high-resolution structure of any complex from this family. Here we report 20 the first structure of SWI/SNF from the yeast S. cerevisiae bound to a nucleosome at 21 near atomic resolution determined by cryo-electron microscopy (cryo-EM). In the 22 remodels the +1 nucleosome to generate nucleosome-depleted regions during gene 35 activation [11][12][13] . 36 Main 37To gain insight into the molecular mechanisms of how SWI/SNF remodels chromatin, 38we purified endogenous SWI/SNF from S. cerevisiae, assembled the SWI/SNF-39 nucleosome complex in vitro (Extended Data Fig. 1) and determined its structure using 40 single particle cryo-EM. The complex was assembled in the presence of the non-41 hydrolysable ATP analog ADP-BeFx and was determined to sub-nanometer resolution 42 (Extended Data Fig. 2). We observed that the nucleosome is clamped between two 43 regions of the SWI/SNF complex ( Fig.

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Section: Methodsmentioning

confidence: 99%

Cryo-electron microscopy structure of a nucleosome-bound SWI/SNF chromatin remodeling complex

Han¹,

Aa²,

Malik³

et al. 2019

Preprint

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“…These models were docked into the cryo-EM map using the Fit in Map command in USCF Chimera (Pettersen et al, 2004). These models were refined against the map using Namdinator (Kidmose et al, 2020) and…”

Section: Model Building and Validationmentioning

confidence: 99%

A Structure-Based Mechanism for DNA Entry into the Cohesin Ring

Higashi

Eickhoff²,

Simões³

et al. 2020

Preprint

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Despite key roles in sister chromatid cohesion and chromosome organization, the mechanism by which cohesin rings are loaded onto DNA is still unknown. Here, we combine biophysical approaches and cryo-EM to visualize a cohesin loading intermediate in which DNA is locked between two gates that lead into the cohesin ring.Building on this structural framework, we design biochemical experiments to establish the order of events during cohesin loading. In an initial step, DNA traverses an Nterminal kleisin gate that is first opened upon ATP binding and then closed as the cohesin loader locks the DNA against a shut ATPase gate. ATP hydrolysis leads to ATPase gate opening to complete DNA entry. Whether DNA loading is successful, or rather results in loop extrusion, might be dictated by a conserved kleisin N-terminal tail that guides the DNA through the kleisin gate. Our results establish the molecular basis for cohesin loading onto DNA.

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“…The model refined against the map with voxel/pixel size of 1.111 maintained the best geometry and was used for further model building and refinement. The model was adjusted, and sequence of protein and DNA components matched to the biological sample manually in Coot 68 and refined using phenix.real_space_refine (Nightly build version 1.10pre-2091) 69 and Namdinator 70,71 . Additional restraints describing protein secondary structure, DNA base pairing and stacking were used in Phenix.…”

Section: Methodsmentioning

confidence: 99%

Retroviral integration into nucleosomes through DNA looping and sliding along the histone octamer

Wilson

Renault

Maskell

et al. 2019

Preprint

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24Retroviral integrase can efficiently utilise nucleosomes for insertion of the reverse-25 transcribed viral DNA. In face of the structural constraints imposed by the nucleosomal 26 structure, integrase gains access to the scissile phosphodiester bonds by lifting DNA off the 27 histone octamer at the site of integration. To clarify the mechanism of DNA looping by 28 integrase, we determined a 3.9 Å resolution structure of the prototype foamy virus intasome 29 engaged with a nucleosome core particle. The structural data along with complementary 30 single-molecule Förster resonance energy transfer measurements reveal twisting and sliding 31 of the nucleosomal DNA arm proximal to the integration site. Sliding the nucleosomal DNA 32 by approximately two base pairs along the histone octamer accommodates the necessary 33 DNA lifting from the histone H2A-H2B subunits to allow engagement with the intasome. 34Thus, retroviral integration into nucleosomes involves the looping-and-sliding mechanism for 35 nucleosomal DNA repositioning, bearing unexpected similarities with chromatin remodelers. 36 37 38 42 function, a multimer of IN assembles on viral DNA (vDNA) ends forming a highly stable 43 nucleoprotein complex, known as the intasome 2-4 . In its first catalytic step, IN resects 3' ends 44 of the vDNA downstream of the invariant CA dinucleotides (3'-processing reaction). It then 45 utilises the freshly released 3'-hydroxyl groups as nucleophiles to attack a pair of 46 phosphodiester bonds on opposing strands of chromosomal DNA, cleaving host DNA and 47 simultaneously joining it to 3' vDNA ends (strand transfer reaction) 5,6 .48 Many important questions pertaining to the nature of the host-virus transactions on 49 chromatin remain unanswered. In particular, it is unclear what role chromatin structure plays 50 in the integration process. Strikingly, although only a fraction of the nucleosomal DNA 51 surface is exposed within the nucleosome core particle (NCP) 7-9 , nucleosomal DNA packing 52 does not impede and rather stimulates integration 10-15 . Because retroviral INs have long 53 been known to prefer bent or distorted DNA targets, DNA bending as it wraps around the 54 histone octamer was thought to facilitate integration into NCPs 12,13 . However, recent 55 structural data revealed that retroviral intasomes require target DNA to adopt a considerably 56 sharper deformation than the smooth bend observed on NCPs 15-19 .57 Intasome structures from several retroviral genera have been determined by X-ray 58 crystallography and cryo-EM 4,17-20 . Despite considerable variability, all intasomes were 59 found to contain the structurally conserved intasomal core assembly minimally comprising 60 four IN subunits synapsing a pair of vDNA ends. Depending on the retroviral species, the 61 core assembly can be decorated by a number of additional IN subunits. The nucleoprotein 62 complex from the prototype foamy virus (PFV) contains only a tetramer of IN, making this 63 well-characterised intasome an ideal model to study the basic mech...

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Namdinator - Automatic Molecular Dynamics flexible fitting of structural models into cryo-EM and crystallography experimental maps

Cited by 116 publications

References 15 publications

Cryo-electron microscopy structure of a nucleosome-bound SWI/SNF chromatin remodeling complex

Cryo-electron microscopy structure of a nucleosome-bound SWI/SNF chromatin remodeling complex

A Structure-Based Mechanism for DNA Entry into the Cohesin Ring

Retroviral integration into nucleosomes through DNA looping and sliding along the histone octamer

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