Coarse-grain Models of HIV-1 Nucleoids

These are PDB-format files that may be read by most molecular<br> graphics programs. The script JSmol.script will create a customized<br> view with appropriate radii, using JSmol. The PDB format is modified<br> in the following ways:<br> --coordinates are in nanometers<br> --RNA strands have atom name "P" and residue name "RNA"<br> --integrase subunits have atom name "CA" and residue name "IN"<br> --nucleocapsid subunits have atom name "N", and residue names<br> "NCO" for experimentally-observed positions and<br> "NCR" for randomly-placed positions Each file contains 25 instances of the nucleoid model.<br> Each model includes 2 gRNA strands, 2000 nucleocapsid subunits, and 140/0 integrase subunits.<br> Nine models are included in this release, exploring two types of variables:<br> 1) Three types of starting models: <br> "selfavoidingGag" assumes that the RNA forms a non-overlapping random walk on<br> the lattice of gag proteins in the immature virion<br> "overlappingGag" assumes a similar random walk, but the RNA strands may overlap<br> "random" assumes that RNA is released from gag and randomly fills the interior of<br> the virion before condensation <br> 2) Three assumptions about integrase interaction:<br> 35 integrase tetramers, 70 integrase dimers, and no integrase More information is available at:<br> http://ccsb.scripps.edu/latticenucleoid/HIVnucleoid本数据集包含PDB（Protein Data Bank）格式文件，可被绝大多数分子可视化程序读取。配套脚本JSmol.script可借助JSmol生成带有适配半径的自定义视图。该PDB格式经过如下修改： -- 坐标单位为纳米 -- RNA链的原子名称为"P"，残基名称为"RNA" -- 整合酶亚基的原子名称为"CA"，残基名称为"IN" -- 核衣壳亚基的原子名称为"N"，其中实验观测到的位点对应的残基名称为"NCO"，随机放置的位点对应的残基名称为"NCR" 每个文件包含25个类核模型实例。每个模型包含2条gRNA（guide RNA）链、2000个核衣壳亚基以及140/0个整合酶亚基。本发布版本共包含9个模型，用于探究两类变量： 1) 三类初始模型： "selfavoidingGag"模型假设RNA在未成熟病毒体的gag蛋白晶格上进行无重叠随机游走 "overlappingGag"模型采用类似的随机游走假设，但允许RNA链发生重叠 "random"模型假设RNA从gag蛋白上释放后，在浓缩前随机填充病毒体内部空间 2) 三种整合酶相互作用假设： 分别为35个整合酶四聚体、70个整合酶二聚体，以及无整合酶的情况 更多信息可访问：http://ccsb.scripps.edu/latticenucleoid/HIVnucleoid