7M6J

Human Septin Hexameric Complex SEPT2G/SEPT6/SEPT7 by Single Particle Cryo-EM


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

An atomic model for the human septin hexamer by cryo-EM.

Mendonca, D.C.Guimaraes, S.L.Pereira, H.D.Pinto, A.A.de Farias, M.A.de Godoy, A.S.Araujo, A.P.U.van Heel, M.Portugal, R.V.Garratt, R.C.

(2021) J Mol Biol 433: 167096-167096

  • DOI: https://doi.org/10.1016/j.jmb.2021.167096
  • Primary Citation of Related Structures:  
    7M6J

  • PubMed 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 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 0 helices including their polybasic regions. These are locked into place between the two subunits by interactions made with the α 5 and α 6 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.


  • Organizational Affiliation

    São Carlos Institute of Physics, USP, São Carlos, SP, Brazil.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Septin-2
A, F
275Homo sapiensMutation(s): 0 
Gene Names: SEPTIN2DIFF6KIAA0158NEDD5SEPT2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15019 (Homo sapiens)
Explore Q15019 
Go to UniProtKB:  Q15019
PHAROS:  Q15019
GTEx:  ENSG00000168385 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15019
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Septin-6
B, E
427Homo sapiensMutation(s): 0 
Gene Names: SEPTIN6KIAA0128SEP2SEPT6
UniProt & NIH Common Fund Data Resources
Find proteins for Q14141 (Homo sapiens)
Explore Q14141 
Go to UniProtKB:  Q14141
PHAROS:  Q14141
GTEx:  ENSG00000125354 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14141
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Septin-7
C, D
432Homo sapiensMutation(s): 0 
Gene Names: SEPTIN7CDC10SEPT7
UniProt & NIH Common Fund Data Resources
Find proteins for Q16181 (Homo sapiens)
Explore Q16181 
Go to UniProtKB:  Q16181
PHAROS:  Q16181
GTEx:  ENSG00000122545 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16181
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
H [auth B],
L [auth E]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
GDP
Query on GDP

Download Ideal Coordinates CCD File 
G [auth A],
I [auth C],
J [auth D],
M [auth F]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
K [auth E]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil2014/15546-1
Sao Paulo Research Foundation (FAPESP)Brazil2017/15340-2
Sao Paulo Research Foundation (FAPESP)Brazil2018/20209-5

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-07
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Data collection, Database references, Structure summary