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- EMDB-75346: Membrane protein solubilization and structure determination using... -

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Basic information

Entry
Database: EMDB / ID: EMD-75346
TitleMembrane protein solubilization and structure determination using de novo-designed amphipathic proteins
Map datasharpened
Sample
  • Complex: WRAP-GlpG
    • Protein or peptide: WRAP-GlpG
KeywordsGlpG / membrane protein / WRAP / de novo protein / IMP / enzyme
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.74 Å
AuthorsBorst AJ / Weidle C
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_75346.png

Downloads & links

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Map

FileReleased
Annotationsharpened
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 288 pix.
= 242.784 Å		0.84 Å/pix.
x 288 pix.
= 242.784 Å		0.84 Å/pix.
x 288 pix.
= 242.784 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.843 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.105
Minimum - Maximum-0.272682 - 0.5623357
Average (Standard dev.)0.00030520238 (±0.011717815)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 242.784 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpened

Fileemd_75346_additional_1.map
Annotationunsharpened
Projections & Slices
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Half map: half b

Fileemd_75346_half_map_1.map
Annotationhalf b
Projections & Slices
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Histogram

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Half map: half a

Fileemd_75346_half_map_2.map
Annotationhalf a
Projections & Slices
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Sample components

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Entire : WRAP-GlpG

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

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Supramolecule #1: WRAP-GlpG

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

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Macromolecule #1: WRAP-GlpG

MacromoleculeName: WRAP-GlpG / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
SequenceString: MSGRERLDRL YLEVLELRAE VLELVQEGAP AEELVRAAER LVDATLELLD LEAEEAEDLM ERATLLTMRA VVLAMRLFLA VGVGAPEEEI ERLVEELERV IEETEKLLE EIKGGVESLL TALALKILLS LVKSLVLTLL GAPAEEIKEF TDKQLKELLE LLRETIEKAR ...String:
MSGRERLDRL YLEVLELRAE VLELVQEGAP AEELVRAAER LVDATLELLD LEAEEAEDLM ERATLLTMRA VVLAMRLFLA VGVGAPEEEI ERLVEELERV IEETEKLLE EIKGGVESLL TALALKILLS LVKSLVLTLL GAPAEEIKEF TDKQLKELLE LLRETIEKAR EAGAQGELFE ARVLLTGLEV MKKLRETGSV L PSDELVFE LVSGILRALL ETAARVTGAE EEMRRLYEEA EERLRRGLAE IASLPAEEAD EAFALLLAQV LRDVLVAILE LVDKRAAELV RALLDFIIAL AE TKLEVLK EKDEEEAKKK ALEGLEKVEE LAKKLIELRF KDSPILENLK NAITYATELF KALVEGAELE EIEALFDKLA EYMDKAVELE VKSLPPVEAA RLR HTARAG LALLRAAAAA RAGRREEAER EALREFNRLV LEAARETLEL ERRADYQGGG GSGGGGSGGG GSGGGGSERA GPVTWVMMIA CVVVFIAMQI LGDQ EVMLW LAWPFDPTLK FEFWRYFTHA LMHFSLMHIL FNLLWWWYLG GAVEKRLGSG KLIVITLISA LLSGYVQQKF SGPWFGGLSG VVYALMGYVW LRGER DPQS GIYLQRGLII FALIWIVAGW FDLFGMSMAN GAHIAGLAVG LAMAFVDSLN AGSGSHHWGS THHHHHH

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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: 4.74 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 43571
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-GlpG was rigid-body fit into this density map to assess design accuracy.
RefinementProtocol: RIGID BODY FIT

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