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- EMDB-75291: cryoEM map of OmpA helical WRAP -

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Basic information

Entry
Database: EMDB / ID: EMD-75291
TitlecryoEM map of OmpA helical WRAP
Map dataRefined cryoEM map of OmpA helical WRAP
Sample
  • Complex: Ompa WRAP expressed in E coli
KeywordsMembrane protein solubilization and structure determination using de novo-designed amphipathic proteins / MEMBRANE PROTEIN
Biological speciesE coli (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.88 Å
AuthorsCourbet A / Mihaljevic L
Funding support United States, 2 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-043758 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19AI144177 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 27, 2026-
Header (metadata) releaseApr 22, 2026-
Map releaseApr 22, 2026-
UpdateJul 15, 2026-
Current statusJul 15, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75291.png

Downloads & links

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Map

FileDownload / File: emd_75291.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRefined cryoEM map of OmpA helical WRAP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 220 pix.
= 193.6 Å		0.88 Å/pix.
x 220 pix.
= 193.6 Å		0.88 Å/pix.
x 220 pix.
= 193.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.331
Minimum - Maximum-2.1689026 - 6.6832685
Average (Standard dev.)0.0006322215 (±0.06814244)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 193.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_75291_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B for cryoEM map of OmpA helical WRAP

Fileemd_75291_half_map_1.map
AnnotationHalf Map B for cryoEM map of OmpA helical WRAP
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A for cryoEM map of OmpA helical WRAP

Fileemd_75291_half_map_2.map
AnnotationHalf Map A for cryoEM map of OmpA helical WRAP
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ompa WRAP expressed in E coli

EntireName: Ompa WRAP expressed in E coli
Components
  • Complex: Ompa WRAP expressed in E coli

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Supramolecule #1: Ompa WRAP expressed in E coli

SupramoleculeName: Ompa WRAP expressed in E coli / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: E coli (bacteria) / Strain: BL21
Molecular weightTheoretical: 41.4 kDa/nm

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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: 8.4
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 correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.88 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 133256
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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