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- EMDB-72769: RSV-F SC-DM bound to a designed protein minibinder, cb13 -

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Basic information

Entry
Database: EMDB / ID: EMD-72769
TitleRSV-F SC-DM bound to a designed protein minibinder, cb13
Map dataUnsharpened
Sample
  • Complex: RSV-F SC-DM bound to de novo minibinder, cb13
    • Protein or peptide: cb13
    • Protein or peptide: Fusion glycoprotein F0
KeywordsRSV / SC-DM / RSV-F / DE NOVO PROTEIN / minibinder / glycoprotein / respiratory syncytial virus / cryoEM / cryo-EM / PROTEIN BINDING
Function / homology
Function and homology information


symbiont-mediated induction of syncytium formation / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0
Similarity search - Domain/homology
Fusion glycoprotein F0
Similarity search - Component
Biological speciesunidentified (others) / synthetic construct (others) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.63 Å
AuthorsBorst AJ / Skotheim R
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat Commun / Year: 2026
Title: Accelerating protein design by scaling experimental characterization.
Authors: Jason Qian / Lukas F Milles / Basile I M Wicky / Robert J Ragotte / Amir Motmaen / Andrew J Borst / Rebecca Skotheim / Sebastian Ols / Brian Coventry / Xinting Li / Ryan D Kibler / Inna ...Authors: Jason Qian / Lukas F Milles / Basile I M Wicky / Robert J Ragotte / Amir Motmaen / Andrew J Borst / Rebecca Skotheim / Sebastian Ols / Brian Coventry / Xinting Li / Ryan D Kibler / Inna Goreshnik / Marc Expòsit / Karin Loré / Lance Stewart / David Baker /
Abstract: Recent advances in de novo protein design have greatly outpaced standard protein biochemistry workflows, making experimental validation a bottleneck. Here, we describe workflows to address the scale, ...Recent advances in de novo protein design have greatly outpaced standard protein biochemistry workflows, making experimental validation a bottleneck. Here, we describe workflows to address the scale, speed and reproducibility of common in vitro protein testing methods, enabling at least an order of magnitude increase in throughput while reducing wetlab time. Semi-Automated Protein Production (SAPP) is a rapid, modular, scalable and cost-effective protocol, enabling up to milligram-scale protein production and standardized characterization - including yield, dispersity, and oligomeric state - of hundreds of designs per day, at the cost-equivalent of a few DNA oligos per construct. End-to-end protocol execution takes 48 hours, with ~6 hours spent benchside using standard laboratory equipment. We showcase the platform by rapidly screening redesigned fluorescent proteins, as well as identifying de novo binders that potently neutralize respiratory syncytial virus. We also developed a barcoding and demultiplexing protocol (DMX) to further reduce gene synthesis cost 5-fold by leveraging oligo pools as input DNA for the generation of thousands of sequence-verified arrayed clones. These protocols which combine optimized molecular biology, automated analysis, and optional open-source robotics should be widely adoptable, accelerating protein design.
History
DepositionSep 18, 2025-
Header (metadata) releaseJul 15, 2026-
Map releaseJul 15, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72769.png

Downloads & links

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Map

FileDownload / File: emd_72769.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 400 pix.
= 354. Å		0.89 Å/pix.
x 400 pix.
= 354. Å		0.89 Å/pix.
x 400 pix.
= 354. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.885 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0538
Minimum - Maximum-0.057222784 - 0.18029515
Average (Standard dev.)0.00006230119 (±0.0050083087)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 354.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened

Fileemd_72769_additional_1.map
AnnotationSharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half B

Fileemd_72769_half_map_1.map
AnnotationHalf B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half A

Fileemd_72769_half_map_2.map
AnnotationHalf A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RSV-F SC-DM bound to de novo minibinder, cb13

EntireName: RSV-F SC-DM bound to de novo minibinder, cb13
Components
  • Complex: RSV-F SC-DM bound to de novo minibinder, cb13
    • Protein or peptide: cb13
    • Protein or peptide: Fusion glycoprotein F0

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Supramolecule #1: RSV-F SC-DM bound to de novo minibinder, cb13

SupramoleculeName: RSV-F SC-DM bound to de novo minibinder, cb13 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: unidentified (others)

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Macromolecule #1: cb13

MacromoleculeName: cb13 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 8.798856 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSHHHHHHHH SENLYFQSGL EKQLENLVRT AEVLVRHNDR LNAFFILEQA KDLAERLNDP ETLREVKELH KEL

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Macromolecule #2: Fusion glycoprotein F0

MacromoleculeName: Fusion glycoprotein F0 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.201781 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QNITEEFYQS TCSAVSKGYL SALRTGWYTS VITIELSNIK EIKCNGTDAK VKLINQELDK YKNAVTELQL LMQSTTAANN RARGSGSGR FLGFLLGVGS AIASGIAVSK VLHLEGEVNK IKSALLSTNK AVVSLSNGVS VLTSKVLDLK NYIDKQLLPI V NKQSCRIP ...String:
QNITEEFYQS TCSAVSKGYL SALRTGWYTS VITIELSNIK EIKCNGTDAK VKLINQELDK YKNAVTELQL LMQSTTAANN RARGSGSGR FLGFLLGVGS AIASGIAVSK VLHLEGEVNK IKSALLSTNK AVVSLSNGVS VLTSKVLDLK NYIDKQLLPI V NKQSCRIP NIETVIEFQQ KNNRLLEITR EFSVNAGVTT PVSTYMLTNS ELLSLINDMP ITNDQKKLMS NNVQIVRQQS YS IMSIIKE EVLAYVVQLP LYGVIDTPCW KLHTSPLCTT NTKEGSNICL TRTDRGWYCD NAGSVSFFPQ AETCKVQSNR VFC DTMNSL TLPSEVNLCN VDIFNPKYDC KIMTSKTDVS SSVITSLGAI VSCYGKTKCT ASNKNRGIIK TFSNGCDYVS NKGV DTVSV GNTLYYVNKQ EGKSLYVKGE PIINFYDPLV FPSDEFDASI SQVNEKINQS LAFIRKSDEL LSAIGGYIPE APRDG OAYV RKDGEWVLLS TFLGSGSGSH HHHHH

UniProtKB: Fusion glycoprotein F0

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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

BufferpH: 7.5
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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.63 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 89296
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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