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- PDB-7m6j: Human Septin Hexameric Complex SEPT2G/SEPT6/SEPT7 by Single Parti... -

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Basic information

Entry
Database: PDB / ID: 7m6j
TitleHuman Septin Hexameric Complex SEPT2G/SEPT6/SEPT7 by Single Particle Cryo-EM
Components
  • Septin-2
  • Septin-6
  • Septin-7
KeywordsCELL CYCLE / Complex / SPA / Cytoskeleton
Function / homology
Function and homology information


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 / cleavage furrow / axoneme / 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
Septin 2 / Septin 7 / Septin-type guanine nucleotide-binding (G) domain / Septin / Septin-type guanine nucleotide-binding (G) domain profile. / Septin / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Septin-6 / Septin-2 / Septin-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsMendonca, D.C. / Pereira, H.M. / van Heel, M. / Portugal, R.V. / Garratt, R.C.
Funding support Brazil, 3items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2014/15546-1 Brazil
Sao Paulo Research Foundation (FAPESP)2017/15340-2 Brazil
Sao Paulo Research Foundation (FAPESP)2018/20209-5 Brazil
CitationJournal: J Mol Biol / Year: 2021
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
DepositionMar 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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Assembly

Deposited unit
A: Septin-2
B: Septin-6
C: Septin-7
D: Septin-7
E: Septin-6
F: Septin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,15113
Polymers262,3076
Non-polymers2,8437
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area24750 Å2
ΔGint-138 kcal/mol
Surface area71900 Å2

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Components

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Protein , 3 types, 6 molecules AFBECD

#1: Protein Septin-2 / Neural precursor cell expressed developmentally down-regulated protein 5 / NEDD-5


Mass: 31748.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEPTIN2, DIFF6, KIAA0158, NEDD5, SEPT2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15019
#2: Protein Septin-6


Mass: 48948.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEPTIN6, KIAA0128, SEP2, SEPT6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14141
#3: Protein Septin-7 / CDC10 protein homolog


Mass: 50456.645 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEPTIN7, CDC10, SEPT7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16181

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Non-polymers , 3 types, 7 molecules

#4: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human Septin Hexameric Complex SEPT2G/SEPT6/SEPT7 / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 30 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 1/2 BIT CUT-OFF / Num. of particles: 108262 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00413171
ELECTRON MICROSCOPYf_angle_d0.69317879
ELECTRON MICROSCOPYf_dihedral_angle_d10.9931813
ELECTRON MICROSCOPYf_chiral_restr0.0482039
ELECTRON MICROSCOPYf_plane_restr0.0042267

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