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- EMDB-29502: Fast and versatile sequence- independent protein docking for nano... -

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Basic information

Entry
Database: EMDB / ID: EMD-29502
TitleFast and versatile sequence- independent protein docking for nanomaterials design using RPXDock
Map dataSharpened map
Sample
  • Complex: O43-rpxdock-EK1
    • Protein or peptide: O43-rpxdoc-EK1_A
    • Protein or peptide: O43-rpxdoc-EK1_B
Keywordsoctahedra / oligomer / de novo design / rosetta / cryoEM / interface / DE NOVO PROTEIN
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.67 Å
AuthorsSkotheim R / Borst AJ / Baker D
Funding support United States, 1 items
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, 2023-
Header (metadata) releaseMay 10, 2023-
Map releaseMay 10, 2023-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29502.png

Downloads & links

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Map

FileDownload / File: emd_29502.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 380 pix.
= 336.3 Å		0.89 Å/pix.
x 380 pix.
= 336.3 Å		0.89 Å/pix.
x 380 pix.
= 336.3 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.885 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.257
Minimum - Maximum-1.1822803 - 1.5615345
Average (Standard dev.)0.0015904247 (±0.0476506)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 336.3 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map

Fileemd_29502_additional_1.map
AnnotationUnsharpened map
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Additional map: DeepEMhancer

Fileemd_29502_additional_2.map
AnnotationDeepEMhancer
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Half map: Half map A

Fileemd_29502_half_map_1.map
AnnotationHalf map A
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Half map: Half map B

Fileemd_29502_half_map_2.map
AnnotationHalf map B
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Sample components

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Entire : O43-rpxdock-EK1

EntireName: O43-rpxdock-EK1
Components
  • Complex: O43-rpxdock-EK1
    • Protein or peptide: O43-rpxdoc-EK1_A
    • Protein or peptide: O43-rpxdoc-EK1_B

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Supramolecule #1: O43-rpxdock-EK1

SupramoleculeName: O43-rpxdock-EK1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: O43-rpxdoc-EK1_A

MacromoleculeName: O43-rpxdoc-EK1_A / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 26.624115 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EEAELAYLLG ELAYKLGEYR IAIRAYRIAL KRDPNNAEAW YNLGNAYTKQ GDYDEAIEYY LRALVLDPNN AEAATNLGQA YMNQGDKDR AKLMLLLALK LDPNNDSARV ILGVAKVGIE ELAKLASQAQ QEGDSEKQKA IELAAEAARV AQEVGDPELE K LALEAARR ...String:
EEAELAYLLG ELAYKLGEYR IAIRAYRIAL KRDPNNAEAW YNLGNAYTKQ GDYDEAIEYY LRALVLDPNN AEAATNLGQA YMNQGDKDR AKLMLLLALK LDPNNDSARV ILGVAKVGIE ELAKLASQAQ QEGDSEKQKA IELAAEAARV AQEVGDPELE K LALEAARR GDSEKAKAIL LAAEAARVAK EVGDPELIKL ALEAARRGDS EKARAILEAA ERAREAKERG DPEQIKKARE LA KR

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Macromolecule #2: O43-rpxdoc-EK1_B

MacromoleculeName: O43-rpxdoc-EK1_B / type: protein_or_peptide / ID: 2 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 15.268709 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
DVSALAYVML GLLLSLLNRL SLAAEAYKKA IELDPNDALA WLLLGSVLEK LKRLDEAAEA YKKAIELKPN DASAWKELGK VLEKLGRLD EAAEAYLIAI MLDPEDAEAA KELGKVLEKL GELEMAEEAY KLAIKLDPND

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.8 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R2/2 / Support film - Material: CARBON
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm

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Image processing

Particle selectionNumber selected: 771134
CTF correctionType: NONE
Startup modelType of model: NONE / Details: Ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 130778
Initial angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC (ver. 3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0)
FSC plot (resolution estimation)

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