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- PDB-7m6j: Human Septin Hexameric Complex SEPT2G/SEPT6/SEPT7 by Single Parti... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7m6j | ||||||||||||
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Title | Human Septin Hexameric Complex SEPT2G/SEPT6/SEPT7 by Single Particle Cryo-EM | ||||||||||||
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![]() | CELL CYCLE / Complex / SPA / Cytoskeleton | ||||||||||||
Function / homology | ![]() septin collar / regulation of embryonic cell shape / sperm annulus / positive regulation of non-motile cilium assembly / septin complex / photoreceptor connecting cilium / septin ring / cytoskeleton-dependent cytokinesis / regulation of exocytosis / non-motile cilium ...septin collar / regulation of embryonic cell shape / sperm annulus / positive regulation of non-motile cilium assembly / septin complex / photoreceptor connecting cilium / septin ring / cytoskeleton-dependent cytokinesis / regulation of exocytosis / non-motile cilium / ciliary membrane / smoothened signaling pathway / intercellular bridge / cell division site / axoneme / cleavage furrow / mitotic cytokinesis / cilium assembly / stress fiber / axon terminus / Anchoring of the basal body to the plasma membrane / MAPK6/MAPK4 signaling / kinetochore / spindle / microtubule cytoskeleton / protein localization / actin cytoskeleton / synaptic vesicle / midbody / spermatogenesis / molecular adaptor activity / cell differentiation / cadherin binding / GTPase activity / GTP binding / structural molecule activity / extracellular exosome / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||||||||
![]() | Mendonca, D.C. / Pereira, H.M. / van Heel, M. / Portugal, R.V. / Garratt, R.C. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: An atomic model for the human septin hexamer by cryo-EM. Authors: Deborah C Mendonça / Samuel L Guimarães / Humberto D'Muniz Pereira / Andressa A Pinto / Marcelo A de Farias / Andre S de Godoy / Ana P U Araujo / Marin van Heel / Rodrigo V Portugal / Richard C Garratt / ![]() Abstract: In order to form functional filaments, human septins must assemble into hetero-oligomeric rod-like particles which polymerize end-to-end. The rules governing the assembly of these particles and the ...In order to form functional filaments, human septins must assemble into hetero-oligomeric rod-like particles which polymerize end-to-end. The rules governing the assembly of these particles and the subsequent filaments are incompletely understood. Although crystallographic approaches have been successful in studying the separate components of the system, there has been difficulty in obtaining high resolution structures of the full particle. Here we report a first cryo-EM structure for a hexameric rod composed of human septins 2, 6 and 7 with a global resolution of ~3.6 Å and a local resolution of between ~3.0 Å and ~5.0 Å. By fitting the previously determined high-resolution crystal structures of the component subunits into the cryo-EM map, we are able to provide an essentially complete model for the particle. This exposes SEPT2 NC-interfaces at the termini of the hexamer and leaves internal cavities between the SEPT6-SEPT7 pairs. The floor of the cavity is formed by the two α helices including their polybasic regions. These are locked into place between the two subunits by interactions made with the α and α helices of the neighbouring monomer together with its polyacidic region. The cavity may serve to provide space allowing the subunits to move with respect to one another. The elongated particle shows a tendency to bend at its centre where two copies of SEPT7 form a homodimeric G-interface. Such bending is almost certainly related to the ability of septin filaments to recognize and even induce membrane curvature. | ||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 302 KB | Display | ![]() |
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PDB format | ![]() | 244.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 23698MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 3 types, 6 molecules AFBECD
#1: Protein | Mass: 31748.352 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 48948.723 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 50456.645 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 3 types, 7 molecules ![](data/chem/img/GDP.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
#4: Chemical | ChemComp-GDP / #5: Chemical | #6: Chemical | ChemComp-MG / | |
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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: single particle reconstruction |
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Sample preparation
Component | Name: Human Septin Hexameric Complex SEPT2G/SEPT6/SEPT7 / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.8 |
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 |
Image recording | Electron dose: 30 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 1/2 BIT CUT-OFF / Num. of particles: 108262 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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