5CYP

GTPase domain of Septin 9 in complex with GTP-gamma-S

• PDB DOI: https://doi.org/10.2210/pdb5CYP/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-07-30 Released: 2016-08-03 
• Deposition Author(s): Matos, S.S., Leonardo, D.A., Pereira, H.M., Horjales, E., Araujo, A.P.U., Garratt, R.C.
• Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free: 0.297 
• R-Value Work: 0.252 
• R-Value Observed: 0.254 

Literature

A complete compendium of crystal structures for the human SEPT3 subgroup reveals functional plasticity at a specific septin interface

Castro, D.K.S.V., da Silva, S.M.O., Pereira, H.M., Macedo, J.N.A., Leonardo, D.A., Valadares, N.F., Kumagai, P.S., Brandao-Neto, J., Araujo, A.P.U., Garratt, R.C.

(2020) IUCrJ 

• DOI: https://doi.org/10.1107/S2052252520002973

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 130.16 kDa 
• Atom Count: 7,249 
• Modelled Residue Count: 940 
• Deposited Residue Count: 1,096 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Septin-9	A, B, C, D	274	Homo sapiens	Mutation(s): 0  Gene Names: SEPT9, KIAA0991, MSF
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHD8 (Homo sapiens) Explore Q9UHD8  Go to UniProtKB:  Q9UHD8
PHAROS:  Q9UHD8 GTEx:  ENSG00000184640

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GSP	E [auth A], G [auth B], I [auth C], K [auth D]	5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE C10 H16 N5 O13 P3 S XOFLBQFBSOEHOG-UUOKFMHZSA-N
MG	F [auth A], H [auth B], J [auth C], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free: 0.297 
• R-Value Work: 0.252 
• R-Value Observed: 0.254 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.587	α = 90
b = 79.156	β = 100.38
c = 108.217	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-08-03 
Deposition Author(s): Matos, S.S., Leonardo, D.A., Pereira, H.M., Horjales, E., Araujo, A.P.U., Garratt, R.C.

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Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	2014/15546-1

Revision History  

• Version 1.0: 2016-08-03
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence, Derived calculations, Refinement description
• Version 1.2: 2017-11-01
  Changes: Author supporting evidence
• Version 1.3: 2019-04-17
  Changes: Author supporting evidence, Data collection
• Version 1.4: 2020-01-01
  Changes: Author supporting evidence
• Version 1.5: 2020-04-22
  Changes: Database references
• Version 1.6: 2020-05-13
  Changes: Database references
• Version 1.7: 2024-03-06
  Changes: Data collection, Database references, Derived calculations