6N0B

Structure of GTPase Domain of Human Septin 7 at High Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Revisiting SEPT7 and the slippage of beta-strands in the septin family.

Brognara, G.Pereira, H.M.Brandao-Neto, J.Araujo, A.P.U.Garratt, R.C.

(2019) J Struct Biol 207: 67-73

  • DOI: 10.1016/j.jsb.2019.04.015
  • Primary Citation of Related Structures:  
    6N12, 6N0B

  • PubMed Abstract: 
  • Septins are GTP-binding proteins that will often spontaneously assemble into filaments. In some species, particularly budding yeast, it is well known that these are capable of associating with membranes in order to fulfill their cellular role as a component of the cytoskeleton ...

    Septins are GTP-binding proteins that will often spontaneously assemble into filaments. In some species, particularly budding yeast, it is well known that these are capable of associating with membranes in order to fulfill their cellular role as a component of the cytoskeleton. Different from other human septins, SEPT7 appears to be unique in that it is an essential component of all hetero-oligomeric complexes described to date. As a step towards understanding the molecular basis of filament assembly, here we present two high-resolution structures of the SEPT7 GTPase domain complexed with GDP. One of these reveals a previously unreported coordination for the magnesium ion involving four water molecules and only a tenuous connection to the protein. The higher resolution structures provide unambiguous insight into the interactions at the G-interface where a structural motif based on an antiparallel β-bridge allows for the rationalization of why some septins show nucleotide-dependent β-strand slippage and others do not.


    Organizational Affiliation

    São Carlos Institute of Physics, University of São Paulo, São Carlos, São Paulo, Brazil. Electronic address: richard@ifsc.usp.br.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Septin-7B [auth A], C [auth B], A [auth C], D285Homo sapiensMutation(s): 0 
Gene Names: SEPT7CDC10SEPTIN7
UniProt & NIH Common Fund Data Resources
Find proteins for Q16181 (Homo sapiens)
Explore Q16181 
Go to UniProtKB:  Q16181
PHAROS:  Q16181
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download Ideal Coordinates CCD File 
E [auth C], F [auth A], G [auth B], H [auth D]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.513α = 90
b = 68.866β = 112.76
c = 150.519γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data scaling
PHASERphasing
PDB_EXTRACTdata extraction
xia2data reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil2014/15546-1

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-01
    Type: Initial release
  • Version 1.1: 2019-06-19
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence