4Q7O | pdb_00004q7o

The crystal structure of an immunity protein NMB0503 from Neisseria meningitidis MC58

• PDB DOI: https://doi.org/10.2210/pdb4Q7O/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Neisseria meningitidis MC58
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-04-25 Released: 2014-05-14 
• Deposition Author(s): Tan, K., Stols, L., Eschenfeldt, W., Babnigg, G., Low, D.A., Hayes, C.S., Goulding, C.W., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes (UC4CDI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.189 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.149 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Literature

The structure of a contact-dependent growth-inhibition (CDI) immunity protein from Neisseria meningitidis MC58.

Tan, K., Johnson, P.M., Stols, L., Boubion, B., Eschenfeldt, W., Babnigg, G., Hayes, C.S., Joachimiak, A., Goulding, C.W.

(2015) Acta Crystallogr F Struct Biol Commun 71: 702-709

• PubMed: 26057799 
• DOI: https://doi.org/10.1107/S2053230X15006585
• Primary Citation of Related Structures:  
  4Q7O


• PubMed Abstract: 
  

  Contact-dependent growth inhibition (CDI) is an important mechanism of intercellular competition between neighboring Gram-negative bacteria. CDI systems encode large surface-exposed CdiA effector proteins that carry a variety of C-terminal toxin domains (CdiA-CTs). All CDI(+) bacteria also produce CdiI immunity proteins that specifically bind to the cognate CdiA-CT and neutralize its toxin activity to prevent auto-inhibition. Here, the X-ray crystal structure of a CdiI immunity protein from Neisseria meningitidis MC58 is presented at 1.45 Å resolution. The CdiI protein has structural homology to the Whirly family of RNA-binding proteins, but appears to lack the characteristic nucleic acid-binding motif of this family. Sequence homology suggests that the cognate CdiA-CT is related to the eukaryotic EndoU family of RNA-processing enzymes. A homology model is presented of the CdiA-CT based on the structure of the XendoU nuclease from Xenopus laevis. Molecular-docking simulations predict that the CdiA-CT toxin active site is occluded upon binding to the CdiI immunity protein. Together, these observations suggest that the immunity protein neutralizes toxin activity by preventing access to RNA substrates.

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Organizational Affiliation: 
• Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL 60439, USA.
Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA 92697, USA.
Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 35.13 kDa 
• Atom Count: 2,529 
• Modeled Residue Count: 268 
• Deposited Residue Count: 292 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunity protein	A, B	146	Neisseria meningitidis MC58	Mutation(s): 0  Gene Names: NMB0503
UniProt
Find proteins for Q7DDN8 (Neisseria meningitidis serogroup B (strain ATCC BAA-335 / MC58)) Explore Q7DDN8  Go to UniProtKB:  Q7DDN8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BR	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M
FMT	I [auth A], J [auth A], Q [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.189 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.149 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.383	α = 90
b = 53.532	β = 98.04
c = 59.699	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-05-14 
Deposition Author(s): Tan, K., Stols, L., Eschenfeldt, W., Babnigg, G., Low, D.A., Hayes, C.S., Goulding, C.W., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes (UC4CDI)

Revision History  

• Version 1.0: 2014-05-14
  Type: Initial release
  
• Version 1.1: 2015-07-01
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations