3VCD

Computationally Designed Self-assembling Octahedral Cage protein, O333, Crystallized in space group R32


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Computational design of self-assembling protein nanomaterials with atomic level accuracy.

King, N.P.Sheffler, W.Sawaya, M.R.Vollmar, B.S.Sumida, J.P.Andre, I.Gonen, T.Yeates, T.O.Baker, D.

(2012) Science 336: 1171-1174

  • DOI: 10.1126/science.1219364
  • Primary Citation of Related Structures:  
    4DCL, 4DDF, 4EGG, 3VCD

  • PubMed Abstract: 
  • We describe a general computational method for designing proteins that self-assemble to a desired symmetric architecture. Protein building blocks are docked together symmetrically to identify complementary packing arrangements, and low-energy protein-protein interfaces are then designed between the building blocks in order to drive self-assembly ...

    We describe a general computational method for designing proteins that self-assemble to a desired symmetric architecture. Protein building blocks are docked together symmetrically to identify complementary packing arrangements, and low-energy protein-protein interfaces are then designed between the building blocks in order to drive self-assembly. We used trimeric protein building blocks to design a 24-subunit, 13-nm diameter complex with octahedral symmetry and a 12-subunit, 11-nm diameter complex with tetrahedral symmetry. The designed proteins assembled to the desired oligomeric states in solution, and the crystal structures of the complexes revealed that the resulting materials closely match the design models. The method can be used to design a wide variety of self-assembling protein nanomaterials.


    Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Propanediol utilization polyhedral body protein PduTA, B, C, D, E, F, G, H192Salmonella entericaMutation(s): 10 
Gene Names: pduT
UniProt
Find proteins for Q9XDM8 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore Q9XDM8 
Go to UniProtKB:  Q9XDM8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth F] , BA [auth F] , CA [auth G] , DA [auth G] , EA [auth H] , FA [auth H] , GA [auth H] , HA [auth H] , 
AA [auth F],  BA [auth F],  CA [auth G],  DA [auth G],  EA [auth H],  FA [auth H],  GA [auth H],  HA [auth H],  I [auth A],  J [auth A],  K [auth B],  L [auth B],  M [auth B],  N [auth C],  O [auth C],  P [auth C],  Q [auth D],  R [auth D],  S [auth D],  T [auth D],  U [auth D],  V [auth E],  W [auth E],  X [auth E],  Y [auth E],  Z [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
IA [auth H]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.92α = 90
b = 137.92β = 90
c = 560.57γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-06
    Type: Initial release
  • Version 1.1: 2012-06-13
    Changes: Database references