5CYO

High resolution Septin 9 GTPase domain in complex with GDP

• PDB DOI: https://doi.org/10.2210/pdb5CYO/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: 2.04 Å
• R-Value Free: 0.228 
• R-Value Work: 0.183 
• R-Value Observed: 0.186 

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

Macromolecule Content

• Total Structure Weight: 64.74 kDa 
• Atom Count: 4,474 
• Modelled Residue Count: 524 
• Deposited Residue Count: 548 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Septin-9	A, B	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
GDP	C [auth A], E [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 0.228 
• R-Value Work: 0.183 
• R-Value Observed: 0.186 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.497	α = 90
b = 78.049	β = 105.92
c = 77.443	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	2014/15556-1

Revision History  

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