Cryo-Electron Microscopy(Cryo-EM)images are characterized by the low signal-to-noise ratio,low contrast,serious background noise,more impurities,less data,difficult data labeling,simpler image semantics,and relatively...Cryo-Electron Microscopy(Cryo-EM)images are characterized by the low signal-to-noise ratio,low contrast,serious background noise,more impurities,less data,difficult data labeling,simpler image semantics,and relatively fixed structure,while U-Net obtains low resolution when downsampling rate information to complete object category recognition,obtains highresolution information during upsampling to complete precise segmentation and positioning,fills in the underlying information through skip connection to improve the accuracy of image segmentation,and has advantages in biological image processing like Cryo-EM image.This article proposes A U-Net based residual intensive neural network(Urdnet),which combines point-level and pixel-level tags,used to accurately and automatically locate particles from cryo-electron microscopy images,and solve the bottleneck that cryo-EM Single-particle biologicalmacromolecule reconstruction requires tens of thousands of automatically picked particles.The 80S ribosome,HCN1 channel and TcdA1 toxin subunits,and other public protein datasets have been trained and tested on Urdnet.The experimental results show that Urdnet could reach the same excellent particle picking performances as the mainstream methods of RELION,DeepPicker,and acquire the 3Dstructure of picked particleswith higher resolution.展开更多
The single particle reconstruction technique has become particularly important in the structure analysis of biomacromolecules. The problem of reconstructing a picture from identical samples polluted by colored noises ...The single particle reconstruction technique has become particularly important in the structure analysis of biomacromolecules. The problem of reconstructing a picture from identical samples polluted by colored noises is studied, and the alignment error in the correlation computation of single particle reconstruction technique is analyzed systematically. The concept of systematic error is introduced, and the explicit form of the systematic error is given under the weak noise approximation. The influence of the systematic error on the reconstructed picture is discussed also, and an analytical formula for correcting the distortion in the picture reconstruction is obtained.展开更多
SecA is the essential component of the signal-peptide dependent translocation pathway in Escherichia coil （E.coh）. The structure and function of SecA must be known to understand the molecular mechanism of preprotein...SecA is the essential component of the signal-peptide dependent translocation pathway in Escherichia coil （E.coh）. The structure and function of SecA must be known to understand the molecular mechanism of preprotein translocation. The high flexibility of SecA causes a dynamic conformational heterogeneity which presents a barrier to the growth of crystals of high diffraction quality. Electron microscopy was used to resolve the macromolecular structure of SecA in solution by negative staining and single particle analysis at a resolution of 2.9 nm. The structure of E. coil SecA is similar to the dimeric form of Bacillus subtilis SecA and is 10 nm × 10 nm × 5 nm in size.展开更多
基金supported by Key Projects of the Ministry of Science and Technology of the People’s Republic of China(2018AAA0102301)the Open Research Fund of Hunan Provincial Key Laboratory of Network Investigational Technology,Grant No.2018WLZC001.
文摘Cryo-Electron Microscopy(Cryo-EM)images are characterized by the low signal-to-noise ratio,low contrast,serious background noise,more impurities,less data,difficult data labeling,simpler image semantics,and relatively fixed structure,while U-Net obtains low resolution when downsampling rate information to complete object category recognition,obtains highresolution information during upsampling to complete precise segmentation and positioning,fills in the underlying information through skip connection to improve the accuracy of image segmentation,and has advantages in biological image processing like Cryo-EM image.This article proposes A U-Net based residual intensive neural network(Urdnet),which combines point-level and pixel-level tags,used to accurately and automatically locate particles from cryo-electron microscopy images,and solve the bottleneck that cryo-EM Single-particle biologicalmacromolecule reconstruction requires tens of thousands of automatically picked particles.The 80S ribosome,HCN1 channel and TcdA1 toxin subunits,and other public protein datasets have been trained and tested on Urdnet.The experimental results show that Urdnet could reach the same excellent particle picking performances as the mainstream methods of RELION,DeepPicker,and acquire the 3Dstructure of picked particleswith higher resolution.
基金Project supported by the National Natural Science Foundation of China (Grant No. 39570204).
文摘The single particle reconstruction technique has become particularly important in the structure analysis of biomacromolecules. The problem of reconstructing a picture from identical samples polluted by colored noises is studied, and the alignment error in the correlation computation of single particle reconstruction technique is analyzed systematically. The concept of systematic error is introduced, and the explicit form of the systematic error is given under the weak noise approximation. The influence of the systematic error on the reconstructed picture is discussed also, and an analytical formula for correcting the distortion in the picture reconstruction is obtained.
基金Supported by the National Natural Science Foundation of China (Nos. 30170196 and 30330160)
文摘SecA is the essential component of the signal-peptide dependent translocation pathway in Escherichia coil （E.coh）. The structure and function of SecA must be known to understand the molecular mechanism of preprotein translocation. The high flexibility of SecA causes a dynamic conformational heterogeneity which presents a barrier to the growth of crystals of high diffraction quality. Electron microscopy was used to resolve the macromolecular structure of SecA in solution by negative staining and single particle analysis at a resolution of 2.9 nm. The structure of E. coil SecA is similar to the dimeric form of Bacillus subtilis SecA and is 10 nm × 10 nm × 5 nm in size.
