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- EMDB-75350: WRAP-TP0698 -

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Basic information

Entry
Database: EMDB / ID: EMD-75350
TitleWRAP-TP0698
Map dataunsharpened
Sample
  • Complex: WRAP-TP0698
    • Protein or peptide: WRAP-TP0698
KeywordsGlpG / membrane protein / WRAP / de novo protein / IMP / enzyme
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.01 Å
AuthorsBorst AJ
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Science / Year: 2026
Title: Membrane protein solubilization and structure determination using de novo-designed proteins.
Authors: Ljubica Mihaljević / David E Kim / Pooja D Bandawane / Helen E Eisenach / Andrew J Borst / Alexis Courbet / Connor Weidle / Kenneth D Carr / Everton Bettin / Qiushi Liu / Aldo T Trejos / ...Authors: Ljubica Mihaljević / David E Kim / Pooja D Bandawane / Helen E Eisenach / Andrew J Borst / Alexis Courbet / Connor Weidle / Kenneth D Carr / Everton Bettin / Qiushi Liu / Aldo T Trejos / Sagardip Majumder / Surabhi Kokane / Alexander Stevens / Edin Muratspahić / Thomas Schlichthaerle / Marc Expòsit / Xinting Li / Mila Lamb / Analisa Nicole Azcárraga Murray / Rashmi Ravichandran / Elizabeth C Williams / Shuyuan Hu / Lynda Stuart / Linda Grillová / Nicholas R Thomson / Michael Landreh / Pengxiang Chang / Lorenzo Giacani / Melissa J Caimano / Kelly L Hawley / Neil P King / David Baker /
Abstract: Developing therapies and vaccines against integral membrane proteins is hindered by their extensive hydrophobic surfaces, which complicate production and structural analysis. Here, we describe a ...Developing therapies and vaccines against integral membrane proteins is hindered by their extensive hydrophobic surfaces, which complicate production and structural analysis. Here, we describe a general deep learning-based design approach for solubilizing native membrane proteins while preserving their sequence, fold, active-site, and ligand-binding properties. Genetically encoded de novo protein WRAPs [water-soluble RFdiffused amphipathic proteins] surround the lipid-interacting hydrophobic surfaces, rendering them thermostable and water-soluble without the need for detergents. We design WRAPs for both monomeric and oligomeric beta-barrel outer membrane proteins and helical multipass transmembrane proteins. A 2.95-angstrom-resolution cryo-electron microscopy structure of WRAPed mycobacterial porin demonstrates that WRAPs can be used for the structural determination of membrane proteins in solution. As a step toward syphilis vaccine development, we generated soluble versions of antigens.
History
DepositionJan 29, 2026-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75350.png

Downloads & links

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Map

FileReleased
Annotationunsharpened
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.42 Å/pix.
x 476 pix.
= 199.92 Å		0.42 Å/pix.
x 476 pix.
= 199.92 Å		0.42 Å/pix.
x 476 pix.
= 199.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.42 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.034162212 - 0.13564967
Average (Standard dev.)0.000006782055 (±0.0024972113)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions476476476
Spacing476476476
CellA=B=C: 199.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: sharpened

Fileemd_75350_additional_1.map
Annotationsharpened
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

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Half map: half b

Fileemd_75350_half_map_1.map
Annotationhalf b
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half a

Fileemd_75350_half_map_2.map
Annotationhalf a
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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Sample components

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Entire : WRAP-TP0698

EntireName: WRAP-TP0698
Components
  • Complex: WRAP-TP0698
    • Protein or peptide: WRAP-TP0698

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Supramolecule #1: WRAP-TP0698

SupramoleculeName: WRAP-TP0698 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: WRAP-TP0698

MacromoleculeName: WRAP-TP0698 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
SequenceString: MSGAIYETIR NLLNELFDRL AEIRPERKEE VEIQRVIMLK ILDIVLAETE EERKKLIEEL LKELAKRSKA AAVLAELVVT FMLRLVEALR RRDRAAFEAA VEEFAEELV KLLKDAEPAA EALRRMLRAL AALYFDRDVD AFVAHLRELA DVLAKHSEEA EEIRYYIDLL ...String:
MSGAIYETIR NLLNELFDRL AEIRPERKEE VEIQRVIMLK ILDIVLAETE EERKKLIEEL LKELAKRSKA AAVLAELVVT FMLRLVEALR RRDRAAFEAA VEEFAEELV KLLKDAEPAA EALRRMLRAL AALYFDRDVD AFVAHLRELA DVLAKHSEEA EEIRYYIDLL IETLRRMLAA GDADAMVDIL RETALKIVDE H EEAKFGRE LVERMMAAFR AAVEARTLAA VEAFTDTMVD AFRDIMNVPE SSAEAIRAMF DTLLALARAG GGGSGGGGSG ALELFLSPKI GITSVYQFGS NG GSDGTSS GKGVSFDRLI GRVDLGLILV NGLTISASAE SSLTNVFVRA QALIGYAVRV GGLRAIVSSG VNICGDSCAT SEGKSSAWYS KLLYSVPLNL EVQ YYLTSF AGVAVAASTA VGVRDFNFKE FTLPLSLTIG PTFRVGSGSH HWGSTHHHHH H

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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 KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.01 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 47941
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsThe design model for WRAP-TP0698 was rigid-body fit into this density map to assess design accuracy.
RefinementProtocol: RIGID BODY FIT

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