3M4E | pdb_00003m4e

Crystal structure of the M113N mutant of alpha-hemolysin bound to beta-cyclodextrin

• PDB DOI: https://doi.org/10.2210/pdb3M4E/pdb

• Classification: CELL INVASION
• Organism(s): Staphylococcus aureus
• Expression System: Staphylococcus aureus
• Mutation(s): Yes 
• Membrane Protein: Yes  MemProtMDmpstruc


• Deposited: 2010-03-10 Released: 2010-05-05 
• Deposition Author(s): Montoya, M., Gouaux, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.269 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.232 (DCC) 

Literature

Molecular bases of cyclodextrin adapter interactions with engineered protein nanopores.

Banerjee, A., Mikhailova, E., Cheley, S., Gu, L.Q., Montoya, M., Nagaoka, Y., Gouaux, E., Bayley, H.

(2010) Proc Natl Acad Sci U S A 107: 8165-8170

• PubMed: 20400691 
• DOI: https://doi.org/10.1073/pnas.0914229107
• Primary Citation Related Structures: 
  3M2L, 3M3R, 3M4D, 3M4E


• PubMed Abstract: 
  

  Engineered protein pores have several potential applications in biotechnology: as sensor elements in stochastic detection and ultrarapid DNA sequencing, as nanoreactors to observe single-molecule chemistry, and in the construction of nano- and micro-devices. One important class of pores contains molecular adapters, which provide internal binding sites for small molecules. Mutants of the alpha-hemolysin (alphaHL) pore that bind the adapter beta-cyclodextrin (betaCD) approximately 10(4) times more tightly than the wild type have been obtained. We now use single-channel electrical recording, protein engineering including unnatural amino acid mutagenesis, and high-resolution x-ray crystallography to provide definitive structural information on these engineered protein nanopores in unparalleled detail.

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Organizational Affiliation: 
• Department of Chemistry, University of Oxford, Oxford, OX1 3TA, United Kingdom.

Biological Assembly 1  

Global Symmetry: Cyclic - C7  (Explore in 3D)
Global Stoichiometry: Homo 7-mer - A7 

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

Macromolecule Content 

• Total Structure Weight: 234.06 kDa 
• Atom Count: 16,774 
• Modeled Residue Count: 2,051 
• Deposited Residue Count: 2,051 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-hemolysin	A, B, C, D, E, F, G	293	Staphylococcus aureus	Mutation(s): 1  Gene Names: hla, hly Membrane Entity: Yes
UniProt
Find proteins for P09616 (Staphylococcus aureus) Explore P09616  Go to UniProtKB:  P09616

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
Cycloheptakis-(1-4)-(alpha-D-glucopyranose)	H	7		N/A
Glycosylation Resources
GlyTouCan: G01435GL GlyCosmos: G01435GL

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900012	H	beta-cyclodextrin	Oligosaccharide / Drug delivery

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.269 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.232 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.35	α = 90
b = 134.27	β = 90.97
c = 132.06	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-05 
Deposition Author(s): Montoya, M., Gouaux, E.

Revision History  

• Version 1.0: 2010-05-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2021-10-06
  Changes: Advisory, Database references, Structure summary
• Version 2.2: 2024-02-21
  Changes: Data collection