8FWD | pdb_00008fwd

Fast and versatile sequence- independent protein docking for nanomaterials design using RPXDock

• PDB DOI: https://doi.org/10.2210/pdb8FWD/pdb
• EM Map EMD-29502: EMDB EMDataResource

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-01-20 Released: 2023-05-10 
• Deposition Author(s): Skotheim, R., Borst, A.J., Baker, D.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.67 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock.

Sheffler, W., Yang, E.C., Dowling, Q., Hsia, Y., Fries, C.N., Stanislaw, J., Langowski, M.D., Brandys, M., Li, Z., Skotheim, R., Borst, A.J., Khmelinskaia, A., King, N.P., Baker, D.

(2023) PLoS Comput Biol 19: e1010680-e1010680

• PubMed: 37216343 
• DOI: https://doi.org/10.1371/journal.pcbi.1010680
• Primary Citation Related Structures: 
  8FWD


• PubMed Abstract: 
  

  Computationally designed multi-subunit assemblies have shown considerable promise for a variety of applications, including a new generation of potent vaccines. One of the major routes to such materials is rigid body sequence-independent docking of cyclic oligomers into architectures with point group or lattice symmetries. Current methods for docking and designing such assemblies are tailored to specific classes of symmetry and are difficult to modify for novel applications. Here we describe RPXDock, a fast, flexible, and modular software package for sequence-independent rigid-body protein docking across a wide range of symmetric architectures that is easily customizable for further development. RPXDock uses an efficient hierarchical search and a residue-pair transform (RPX) scoring method to rapidly search through multidimensional docking space. We describe the structure of the software, provide practical guidelines for its use, and describe the available functionalities including a variety of score functions and filtering tools that can be used to guide and refine docking results towards desired configurations.

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Organizational Affiliation: 
• Institute for Protein Design, University of Washington, Seattle, Washington, United States of America.
Department of Biochemistry, University of Washington, Seattle, Washington, United States of America.
Graduate Program in Biological Physics, Structure & Design, University of Washington, Seattle, Washington, United States of America.
Department of Bioengineering, University of Washington, Seattle, Washington, United States of America.
Transdisciplinary Research Area "Building Blocks of Matter and Fundamental Interactions (TRA Matter)", University of Bonn, Bonn, Germany.
Life and Medical Sciences Institute, University of Bonn, Bonn, Germany.
Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, Washington, United States of America.
Howard Hughes Medical Institute, University of Washington, Seattle, Washington, United States of America.

Biological Assembly 1  

Global Symmetry: Octahedral - O  (Explore in 3D)
Global Stoichiometry: Hetero 48-mer - A24B24 Pseudo Symmetry: Octahedral - O  (Explore in 3D)
Pseudo Stoichiometry: Homo 48-mer - A48 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 1,005.43 kDa 
• Atom Count: 43,080 
• Modeled Residue Count: 5,736 
• Deposited Residue Count: 9,144 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O43-rpxdoc-EK1_A	A [auth 0], BA [auth R], C [auth 2], DA [auth T], E [auth 4], FA [auth V], G [auth 6], HA [auth X], I [auth 8], JA [auth Z], L [auth B], LA [auth b], N [auth D], NA [auth d], P [auth F], PA [auth f], R [auth H], RA [auth h], T [auth J], TA [auth j], V [auth L], VA [auth l], X [auth N], Z [auth P]	242	synthetic construct	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
O43-rpxdoc-EK1_B	AA [auth Q], B [auth 1], CA [auth S], D [auth 3], EA [auth U], F [auth 5], GA [auth W], H [auth 7], IA [auth Y], J [auth 9], K [auth A], KA [auth a], M [auth C], MA [auth c], O [auth E], OA [auth e], Q [auth G], QA [auth g], S [auth I], SA [auth i], U [auth K], UA [auth k], W [auth M], Y [auth O]	139	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.67 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-05-10 
Deposition Author(s): Skotheim, R., Borst, A.J., Baker, D.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2023-05-10
  Type: Initial release
  
• Version 1.1: 2023-06-14
  Changes: Database references
• Version 1.2: 2024-06-19
  Changes: Data collection
• Version 1.3: 2025-06-04
  Changes: Data collection, Structure summary