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- PDB-7tbj: Composite structure of the human nuclear pore complex (NPC) symme... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7tbj | |||||||||||||||
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Title | Composite structure of the human nuclear pore complex (NPC) symmetric core generated with a 12A cryo-ET map of the purified HeLa cell NPC | |||||||||||||||
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![]() | TRANSPORT PROTEIN / nuclear pore complex / nucleocytoplasmic transport / alpha-helical solenoid / nuclear pore | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 23 Å | |||||||||||||||
![]() | Petrovic, S. / Samanta, D. / Perriches, T. / Bley, C.J. / Thierbach, K. / Brown, B. / Nie, S. / Mobbs, G.W. / Stevens, T.A. / Liu, X. ...Petrovic, S. / Samanta, D. / Perriches, T. / Bley, C.J. / Thierbach, K. / Brown, B. / Nie, S. / Mobbs, G.W. / Stevens, T.A. / Liu, X. / Tomaleri, G.P. / Schaus, L. / Hoelz, A. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: AI-based structure prediction empowers integrative structural analysis of human nuclear pores Authors: Mosalaganti, S. / Obarska-Kosinska, A. / Siggel, M. / Taniguchi, R. / Turonova, B. / Zimmerli, C.E. / Buczak, K. / Schmidt, F.H. / Margiotta, E. / Mackmull, M.-T. / Hagen, W.J.H. / Hummer, G. ...Authors: Mosalaganti, S. / Obarska-Kosinska, A. / Siggel, M. / Taniguchi, R. / Turonova, B. / Zimmerli, C.E. / Buczak, K. / Schmidt, F.H. / Margiotta, E. / Mackmull, M.-T. / Hagen, W.J.H. / Hummer, G. / Kosinski, J. / Beck, M. | |||||||||||||||
History |
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Remark 0 | THIS ENTRY 7TBJ REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN EMD-14322, DETERMINED BY S. ...THIS ENTRY 7TBJ REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN EMD-14322, DETERMINED BY S.Mosalaganti,A.Obarska-Kosinska,M.Siggel,R.Taniguchi,B.Turonova, C.E.Zimmerli,K.Buczak,F.H.Schmidt,E.Margiotta,M.T.Mackmull,W.J.H.Hagen,G.Hummer,J.Kosinski,M.Beck |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 8.3 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 3.6 MB | Display | |
Data in XML | ![]() | 1.2 MB | Display | |
Data in CIF | ![]() | 1.8 MB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7mvtC ![]() 7mvuC ![]() 7mvvC ![]() 7mvwC ![]() 7mvxC ![]() 7mvyC ![]() 7mvzC ![]() 7mw0C ![]() 7mw1C ![]() 7tbiC ![]() 7tbkC M: map data used to model this data C: citing same article ( |
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Links
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Assembly
Deposited unit | ![]()
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Components
+Protein , 23 types, 87 molecules A1A3A2A4A5A6D1D2D3D4D5D6D7F1F2G1G2I1I2I3I4I5J1J2J3J4J5M1M2M3...
-Protein/peptide , 7 types, 35 molecules B1B2B3B4B5B6C1C2C3C4C5C6E1E2E3E4E5E6E7H1H2K1K2K3K4K5L1L2L3L4...
#4: Protein/peptide | Mass: 1612.008 Da / Num. of mol.: 6 / Source method: isolated from a natural source Details: Crystal structure of the Chaetomium thermophilum NUP53 R3 ortholog component of the Nup170-Nup53 heterodimer structure (PDB ID 5HAX). To remain faithful to experimentally determined ...Details: Crystal structure of the Chaetomium thermophilum NUP53 R3 ortholog component of the Nup170-Nup53 heterodimer structure (PDB ID 5HAX). To remain faithful to experimentally determined structures, we opted to interpret the cryo-ET map of the Homo sapiens NPC with ortholog crystal structures. Source: (natural) ![]() #5: Protein/peptide | Mass: 2258.661 Da / Num. of mol.: 6 / Source method: isolated from a natural source Details: Crystal structure of the Chaetomium thermophilum NUP98 R3 ortholog component of the Nup170-Nup145N heterodimer structure (PDB ID 5HB0). To remain faithful to experimentally determined ...Details: Crystal structure of the Chaetomium thermophilum NUP98 R3 ortholog component of the Nup170-Nup145N heterodimer structure (PDB ID 5HB0). To remain faithful to experimentally determined structures, we opted to interpret the cryo-ET map of the Homo sapiens NPC with ortholog crystal structures. Source: (natural) ![]() #7: Protein/peptide | Mass: 903.057 Da / Num. of mol.: 7 / Source method: isolated from a natural source Details: Crystal structure of the Homo sapiens NUP53 R2 component of the NUP93-NUP53 heterodimer crystal structure (PDB ID 7MW1) used to interpret the cryo-ET map of the Homo sapiens NPC. Source: (natural) ![]() #10: Protein/peptide | Mass: 1348.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: Single particle cryo-EM structure of the Chaetomium thermophilum NUP98 R2 ortholog component of the Nup188-Nic96-Nup145N heterotrimer structure (PDB ID 7MVZ). To remain faithful to ...Details: Single particle cryo-EM structure of the Chaetomium thermophilum NUP98 R2 ortholog component of the Nup188-Nic96-Nup145N heterotrimer structure (PDB ID 7MVZ). To remain faithful to experimentally determined structures, we opted to interpret the cryo-ET map of the Homo sapiens NPC with ortholog single particle cryo-EM structures. Source: (natural) ![]() #13: Protein/peptide | Mass: 1062.345 Da / Num. of mol.: 5 / Source method: isolated from a natural source Details: Single particle cryo-EM structure of the Chaetomium thermophilum NUP98 R1 ortholog component of the Nup192-Nic96-Nup53-Nup145N heterotetramer structure (PDB ID 7MVV). To remain faithful to ...Details: Single particle cryo-EM structure of the Chaetomium thermophilum NUP98 R1 ortholog component of the Nup192-Nic96-Nup53-Nup145N heterotetramer structure (PDB ID 7MVV). To remain faithful to experimentally determined structures, we opted to interpret the cryo-ET map of the Homo sapiens NPC with ortholog single particle cryo-EM structures. Source: (natural) ![]() #14: Protein/peptide | Mass: 222.241 Da / Num. of mol.: 5 / Source method: isolated from a natural source Details: Single particle cryo-EM structure of the Chaetomium thermophilum NUP53 R1 ortholog component of the Nup192-Nic96-Nup53-Nup145N heterotetramer structure (PDB ID 7MVV). To remain faithful to ...Details: Single particle cryo-EM structure of the Chaetomium thermophilum NUP53 R1 ortholog component of the Nup192-Nic96-Nup53-Nup145N heterotetramer structure (PDB ID 7MVV). To remain faithful to experimentally determined structures, we opted to interpret the cryo-ET map of the Homo sapiens NPC with ortholog single particle cryo-EM structures. Source: (natural) ![]() #20: Protein/peptide | Mass: 4441.164 Da / Num. of mol.: 4 / Source method: isolated from a natural source Details: Crystal structure of the Chaetomium thermophilum NUP93 R1 ortholog component of the Nup49-Nup57-Nsp1-Nic96 heterotetramer structure (PDB ID 5CWS). To remain faithful to experimentally ...Details: Crystal structure of the Chaetomium thermophilum NUP93 R1 ortholog component of the Nup49-Nup57-Nsp1-Nic96 heterotetramer structure (PDB ID 5CWS). To remain faithful to experimentally determined structures, we opted to interpret the cryo-ET map of the Homo sapiens NPC with ortholog crystal structures. Source: (natural) ![]() |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging |
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Sample preparation
Component | Name: Nuclear pore complex from purified HeLa cell nuclear envelopes. Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 4000 nm / Nominal defocus min: 1900 nm |
Image recording | Electron dose: 4 e/Å2 / Avg electron dose per subtomogram: 110 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 23 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17368 / Symmetry type: POINT |
EM volume selection | Num. of tomograms: 170 / Num. of volumes extracted: 17368 |
Atomic model building | Details: Authors state that the clashes between nucleoporin structures result from docking nucleoporin structures from different species into low-resolution cryo-ET maps of intact NPCs without flexible fitting. |