4F8C | pdb_00004f8c

Structure of the Cif:Nedd8 complex - Yersinia pseudotuberculosis Cycle Inhibiting Factor in complex with human Nedd8

• PDB DOI: https://doi.org/10.2210/pdb4F8C/pdb

• Classification: CELL CYCLE/PROTEIN BINDING
• Organism(s): Yersinia pseudotuberculosis YPIII, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-05-17 Released: 2012-06-20 
• Deposition Author(s): Crow, A., Banfield, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.235 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

The molecular basis of Nedd8 deamidation by the bacterial effector protein Cif

Crow, A., Hughes, R.K., Taieb, F., Oswald, E., Banfield, M.J.

(2012) Proc Natl Acad Sci U S A 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 81.96 kDa 
• Atom Count: 5,747 
• Modeled Residue Count: 644 
• Deposited Residue Count: 726 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cycle Inhibiting Factor	A, C	275	Yersinia pseudotuberculosis YPIII	Mutation(s): 1  Gene Names: YPK_1971 EC: 3.5.1.44
UniProt
Find proteins for A0A0H3B1Q8 (Yersinia pseudotuberculosis serotype O:3 (strain YPIII)) Explore A0A0H3B1Q8  Go to UniProtKB:  A0A0H3B1Q8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NEDD8	B, D	88	Homo sapiens	Mutation(s): 0  Gene Names: NEDD8
UniProt & NIH Common Fund Data Resources
Find proteins for Q15843 (Homo sapiens) Explore Q15843  Go to UniProtKB:  Q15843
PHAROS:  Q15843 GTEx:  ENSG00000129559

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	E [auth A], F [auth A], G [auth C], H [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.235 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.359	α = 90
b = 125.359	β = 90
c = 169.93	γ = 120

Software Package:

Software Name	Purpose
GDA	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-20 
Deposition Author(s): Crow, A., Banfield, M.

Revision History  

• Version 1.0: 2012-06-20
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description