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- EMDB-70780: CryoEM structure of the soluble-WRAPed membranous portion of MspA... -

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Basic information

Entry
Database: EMDB / ID: EMD-70780
TitleCryoEM structure of the soluble-WRAPed membranous portion of MspA (Mycobacterium smegmatis porin), dimerized along the native interface.
Map data
Sample
  • Complex: souble-WRAPed MspA
    • Protein or peptide: Soluble-WRAPed MspA
KeywordsMspA / Mycobacterium smegmatis porin / WRAPs / Water-soluble RFdiffused Amphipathic Proteins / DE NOVO PROTEIN
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsCarr KD / Weidle C / Alexis C / Borst AJ
Funding support United States, 4 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
Bill & Melinda Gates FoundationINV-040928 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: Solubilization of Membrane Proteins using designed protein WRAPS
Authors: Mihaljevic L / Kim DE / Bandawane PD / Eisenach HE / Borst AJ / Courbet A / Weidle C / Bettin E / Liu Q / Trejos AT / Majumder S / Muratspahic E / Schlichthaerle T / Exposit M / Li X / Lamb ...Authors: Mihaljevic L / Kim DE / Bandawane PD / Eisenach HE / Borst AJ / Courbet A / Weidle C / Bettin E / Liu Q / Trejos AT / Majumder S / Muratspahic E / Schlichthaerle T / Exposit M / Li X / Lamb M / Murray ANA / Thomson NR / Chang P / Giacani L / Caimano MJ / Hawley KL / King NP / Baker D
History
DepositionMay 22, 2025-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70780.png

Downloads & links

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Map

FileDownload / File: emd_70780.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 350 pix.
= 290.5 Å		0.83 Å/pix.
x 350 pix.
= 290.5 Å		0.83 Å/pix.
x 350 pix.
= 290.5 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0668
Minimum - Maximum-0.021538813 - 1.842694
Average (Standard dev.)0.0014189879 (±0.026303004)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 290.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #2

Fileemd_70780_additional_1.map
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Additional map: #1

Fileemd_70780_additional_2.map
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Half map: #2

Fileemd_70780_half_map_1.map
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Half map: #1

Fileemd_70780_half_map_2.map
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Sample components

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Entire : souble-WRAPed MspA

EntireName: souble-WRAPed MspA
Components
  • Complex: souble-WRAPed MspA
    • Protein or peptide: Soluble-WRAPed MspA

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Supramolecule #1: souble-WRAPed MspA

SupramoleculeName: souble-WRAPed MspA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: The membranous portion of MspA (Mycobacterium smegmatis porin)is expressed with a computationally designed protein Water-soluble RFdiffused Amphipathic Protein (WRAP). 8 chains form the ...Details: The membranous portion of MspA (Mycobacterium smegmatis porin)is expressed with a computationally designed protein Water-soluble RFdiffused Amphipathic Protein (WRAP). 8 chains form the porin. Additionally, the porin is dimerized along the native interface. (Artifact that is not biologically relevant)
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)

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Macromolecule #1: Soluble-WRAPed MspA

MacromoleculeName: Soluble-WRAPed MspA / type: protein_or_peptide / ID: 1 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 16.97099 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MTNEQNIQAV MDFFDLVGEI RRRRAERLRE EIERLREREK EDGELARGII LLGEAMYYAG SHGPVEGLYY TLKKLQEAQK VLTEWSLGV GINFSYTTPN ILIDDGDITR PPFGLNSVIT PNLFPGVSIS ADLGNGSGSH 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

Concentration1 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMTris/HCltris(hydroxymethyl)aminomethane, hydrogen chloride
100.0 mMNaClSodium Chloride

Details: 20 mM Tris / HCl, 100 mM NaCl, pH 8.0
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 20 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Pressure: 39.0 kPa / Details: 15 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV
DetailsThe sample contained soluble-WRAPed MspA (8 polypeptide chains). Monomers and Dimers of the

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 3 / Number real images: 12234 / Average exposure time: 5.0 sec. / 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
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 7804230 / Details: Template Picker was Used
CTF correctionDetails: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: Ab Initio
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D8 (2x8 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 64941
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Details: 2D classification
Final angle assignmentType: MAXIMUM LIKELIHOOD / Details: Non Uniform Refinement
Final 3D classificationNumber classes: 2 / Avg.num./class: 40686 / Details: heterogeneous refinement, to remove any monomers
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: experimental model / Details: MspA and De Novo Design
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9orp:
CryoEM structure of the soluble-WRAPed membranous portion of MspA (Mycobacterium smegmatis porin), dimerized along the native interface.

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