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Yorodumi- PDB-7tbm: Composite structure of the dilated human nuclear pore complex (NP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tbm | |||||||||||||||
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Title | Composite structure of the dilated human nuclear pore complex (NPC) generated with a 37A in situ cryo-ET map of CD4+ T cell NPC | |||||||||||||||
Components |
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Keywords | TRANSPORT PROTEIN / nuclear pore complex / nucleocytoplasmic transport / alpha-helical solenoid / nuclear pore | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 37 Å | |||||||||||||||
Authors | Bley, C.J. / Nie, S. / Mobbs, G.W. / Petrovic, S. / Gres, A.T. / Liu, X. / Mukherjee, S. / Harvey, S. / Huber, F.M. / Lin, D.H. ...Bley, C.J. / Nie, S. / Mobbs, G.W. / Petrovic, S. / Gres, A.T. / Liu, X. / Mukherjee, S. / Harvey, S. / Huber, F.M. / Lin, D.H. / Brown, B. / Tang, A.W. / Rundlet, E.J. / Correia, A.R. / Chen, S. / Regmi, S.G. / Stevens, T.A. / Jette, C.A. / Dasso, M. / Patke, A. / Palazzo, A.F. / Kossiakoff, A.A. / Hoelz, A. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Cell / Year: 2021 Title: Cone-shaped HIV-1 capsids are transported through intact nuclear pores. Authors: Vojtech Zila / Erica Margiotta / Beata Turoňová / Thorsten G Müller / Christian E Zimmerli / Simone Mattei / Matteo Allegretti / Kathleen Börner / Jona Rada / Barbara Müller / Marina ...Authors: Vojtech Zila / Erica Margiotta / Beata Turoňová / Thorsten G Müller / Christian E Zimmerli / Simone Mattei / Matteo Allegretti / Kathleen Börner / Jona Rada / Barbara Müller / Marina Lusic / Hans-Georg Kräusslich / Martin Beck / Abstract: Human immunodeficiency virus (HIV-1) remains a major health threat. Viral capsid uncoating and nuclear import of the viral genome are critical for productive infection. The size of the HIV-1 capsid ...Human immunodeficiency virus (HIV-1) remains a major health threat. Viral capsid uncoating and nuclear import of the viral genome are critical for productive infection. The size of the HIV-1 capsid is generally believed to exceed the diameter of the nuclear pore complex (NPC), indicating that capsid uncoating has to occur prior to nuclear import. Here, we combined correlative light and electron microscopy with subtomogram averaging to capture the structural status of reverse transcription-competent HIV-1 complexes in infected T cells. We demonstrated that the diameter of the NPC in cellulo is sufficient for the import of apparently intact, cone-shaped capsids. Subsequent to nuclear import, we detected disrupted and empty capsid fragments, indicating that uncoating of the replication complex occurs by breaking the capsid open, and not by disassembly into individual subunits. Our data directly visualize a key step in HIV-1 replication and enhance our mechanistic understanding of the viral life cycle. | |||||||||||||||
History |
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Remark 0 | THIS ENTRY 7TBM REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN EMD-11967, DETERMINED BY E. ...THIS ENTRY 7TBM REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN EMD-11967, DETERMINED BY E.Margiotta,M.Beck |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tbm.cif.gz | 9.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7tbm.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7tbm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tb/7tbm ftp://data.pdbj.org/pub/pdb/validation_reports/tb/7tbm | HTTPS FTP |
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-Related structure data
Related structure data | 7mniC 7mnjC 7mnkC 7mnlC 7mnmC 7mnnC 7mnoC 7mnpC 7mnqC 7mnrC 7mnsC 7mntC 7mnuC 7mnvC 7mnwC 7mnxC 7mnyC 7mnzC 7mo0C 7mo1C 7mo2C 7mo3C 7mo4C 7mo5C 7tblC M: map data used to model this data C: citing same article (ref.) |
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-Links
-Assembly
Deposited unit |
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1 |
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-Components
+Protein , 31 types, 99 molecules A1A3A2A4A5A6D1D2D3D4D5D6D7F1F2G1G2I1I2I3I4I5J1J2J3J4J5M1M2M3...
-Protein/peptide , 10 types, 38 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) Homo sapiens (human) #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) Homo sapiens (human) #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) Homo sapiens (human) #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) Homo sapiens (human) #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) Homo sapiens (human) #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) Homo sapiens (human) #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) Homo sapiens (human) #37: Protein/peptide | | Mass: 4416.920 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Crystal structure of Xenopus laevis NUP62 CCS2 ortholog component of the channel nucleoporin heterotrimer (CNT; NUP62-NUP54-NUP58) structure (PDB ID 5C3L). To remain faithful to ...Details: Crystal structure of Xenopus laevis NUP62 CCS2 ortholog component of the channel nucleoporin heterotrimer (CNT; NUP62-NUP54-NUP58) structure (PDB ID 5C3L). 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) Homo sapiens (human) #39: Protein/peptide | | Mass: 3337.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Poly-alanine model of the NUP214 CCS2 based on the Xenopus laevis and Chaetomium thermophilum channel nucleoporin heterotrimer (CNT; NUP62-NUP54-NUP58) crystal structures (PDB ID 5C3L and 5CWS). Source: (natural) Homo sapiens (human) #41: Protein/peptide | | Mass: 1720.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Poly-alanine model of the NUP88 CCS2 based on the Xenopus laevis and Chaetomium thermophilum channel nucleoporin heterotrimer (CNT; NUP62-NUP54-NUP58) crystal structures (PDB ID 5C3L and 5CWS). Source: (natural) Homo sapiens (human) |
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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: CELL / 3D reconstruction method: subtomogram averaging |
-Sample preparation
Component | Name: Nuclear pore complex from human CD4+ T cells.Nuclear pore Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4500 nm / Nominal defocus min: 2000 nm |
Image recording | Electron dose: 4 e/Å2 / Avg electron dose per subtomogram: 140 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 792 / Symmetry type: POINT |
EM volume selection | Num. of tomograms: 99 / Num. of volumes extracted: 792 |
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. |