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- PDB-8fwd: Fast and versatile sequence- independent protein docking for nano... -

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Basic information

Entry
Database: PDB / ID: 8fwd
TitleFast and versatile sequence- independent protein docking for nanomaterials design using RPXDock
Components
  • O43-rpxdoc-EK1_A
  • O43-rpxdoc-EK1_B
KeywordsDE NOVO PROTEIN / octahedra / oligomer / de novo design / rosetta / cryoEM / interface
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.67 Å
AuthorsSkotheim, R. / Borst, A.J. / Baker, D.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: PLoS Comput Biol / Year: 2023
Title: Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock.
Authors: William Sheffler / Erin C Yang / Quinton Dowling / Yang Hsia / Chelsea N Fries / Jenna Stanislaw / Mark D Langowski / Marisa Brandys / Zhe Li / Rebecca Skotheim / Andrew J Borst / Alena ...Authors: William Sheffler / Erin C Yang / Quinton Dowling / Yang Hsia / Chelsea N Fries / Jenna Stanislaw / Mark D Langowski / Marisa Brandys / Zhe Li / Rebecca Skotheim / Andrew J Borst / Alena Khmelinskaia / Neil P King / David Baker /
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 ...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.
History
DepositionJan 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.0May 10, 2023Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.0May 10, 2023Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 10, 2023Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 10, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 10, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 10, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 10, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0May 10, 2023Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
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Revision 1.0May 10, 2023Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 10, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 10, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 10, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 10, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0May 10, 2023Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 10, 2023Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 10, 2023Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 10, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 10, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 10, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 10, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.3Jun 4, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 4, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: O43-rpxdoc-EK1_A
1: O43-rpxdoc-EK1_B
2: O43-rpxdoc-EK1_A
3: O43-rpxdoc-EK1_B
4: O43-rpxdoc-EK1_A
5: O43-rpxdoc-EK1_B
6: O43-rpxdoc-EK1_A
7: O43-rpxdoc-EK1_B
8: O43-rpxdoc-EK1_A
9: O43-rpxdoc-EK1_B
A: O43-rpxdoc-EK1_B
B: O43-rpxdoc-EK1_A
C: O43-rpxdoc-EK1_B
D: O43-rpxdoc-EK1_A
E: O43-rpxdoc-EK1_B
F: O43-rpxdoc-EK1_A
G: O43-rpxdoc-EK1_B
H: O43-rpxdoc-EK1_A
I: O43-rpxdoc-EK1_B
J: O43-rpxdoc-EK1_A
K: O43-rpxdoc-EK1_B
L: O43-rpxdoc-EK1_A
M: O43-rpxdoc-EK1_B
N: O43-rpxdoc-EK1_A
O: O43-rpxdoc-EK1_B
P: O43-rpxdoc-EK1_A
Q: O43-rpxdoc-EK1_B
R: O43-rpxdoc-EK1_A
S: O43-rpxdoc-EK1_B
T: O43-rpxdoc-EK1_A
U: O43-rpxdoc-EK1_B
V: O43-rpxdoc-EK1_A
W: O43-rpxdoc-EK1_B
X: O43-rpxdoc-EK1_A
Y: O43-rpxdoc-EK1_B
Z: O43-rpxdoc-EK1_A
a: O43-rpxdoc-EK1_B
b: O43-rpxdoc-EK1_A
c: O43-rpxdoc-EK1_B
d: O43-rpxdoc-EK1_A
e: O43-rpxdoc-EK1_B
f: O43-rpxdoc-EK1_A
g: O43-rpxdoc-EK1_B
h: O43-rpxdoc-EK1_A
i: O43-rpxdoc-EK1_B
j: O43-rpxdoc-EK1_A
k: O43-rpxdoc-EK1_B
l: O43-rpxdoc-EK1_A


Theoretical massNumber of molelcules
Total (without water)1,005,42848
Polymers1,005,42848
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, nsEM, cryoEM
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
O43-rpxdoc-EK1_A


Mass: 26624.115 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein ...
O43-rpxdoc-EK1_B


Mass: 15268.709 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: O43-rpxdock-EK1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: synthetic construct (others)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenConc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM software
IDNameVersionCategory
9PHENIXmodel refinement
10cryoSPARC3.2initial Euler assignment
11cryoSPARC4final Euler assignment
CTF correctionType: NONE
Particle selectionNum. of particles selected: 771134
3D reconstructionResolution: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 130778 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00343632
ELECTRON MICROSCOPYf_angle_d0.49959112
ELECTRON MICROSCOPYf_dihedral_angle_d12.69315864
ELECTRON MICROSCOPYf_chiral_restr0.0316840
ELECTRON MICROSCOPYf_plane_restr0.0037608

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