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- PDB-9orp: CryoEM structure of the soluble-WRAPed membranous portion of MspA... -

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Basic information

Entry
Database: PDB / ID: 9orp
TitleCryoEM structure of the soluble-WRAPed membranous portion of MspA (Mycobacterium smegmatis porin), dimerized along the native interface.
ComponentsSoluble-WRAPed MspA
KeywordsDE NOVO PROTEIN / MspA / Mycobacterium smegmatis porin / WRAPs / Water-soluble RFdiffused Amphipathic Proteins
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsCarr, K.D. / Weidle, C. / Alexis, C. / Borst, A.J.
Funding support United States, 4items
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, D.E. / Bandawane, P.D. / Eisenach, H.E. / Borst, A.J. / Courbet, A. / Weidle, C. / Bettin, E. / Liu, Q. / Trejos, A.T. / Majumder, S. / Muratspahic, E. / ...Authors: Mihaljevic, L. / Kim, D.E. / Bandawane, P.D. / Eisenach, H.E. / Borst, A.J. / Courbet, A. / Weidle, C. / Bettin, E. / Liu, Q. / Trejos, A.T. / Majumder, S. / Muratspahic, E. / Schlichthaerle, T. / Exposit, M. / Li, X. / Lamb, M. / Murray, A.N.A. / Thomson, N.R. / Chang, P. / Giacani, L. / Caimano, M.J. / Hawley, K.L. / King, N.P. / Baker, D.
History
DepositionMay 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Soluble-WRAPed MspA
B: Soluble-WRAPed MspA
C: Soluble-WRAPed MspA
D: Soluble-WRAPed MspA
E: Soluble-WRAPed MspA
F: Soluble-WRAPed MspA
G: Soluble-WRAPed MspA
H: Soluble-WRAPed MspA
I: Soluble-WRAPed MspA
J: Soluble-WRAPed MspA
K: Soluble-WRAPed MspA
L: Soluble-WRAPed MspA
M: Soluble-WRAPed MspA
N: Soluble-WRAPed MspA
O: Soluble-WRAPed MspA
P: Soluble-WRAPed MspA


Theoretical massNumber of molelcules
Total (without water)271,53616
Polymers271,53616
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Soluble-WRAPed MspA


Mass: 16970.990 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Production host: Escherichia coli (E. coli)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: souble-WRAPed MspA / Type: COMPLEX
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)
Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 8 / Details: 20 mM Tris / HCl, 100 mM NaCl, pH 8.0
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMtris(hydroxymethyl)aminomethane, hydrogen chlorideTris/HCl1
2100 mMSodium ChlorideNaCl1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The sample contained soluble-WRAPed MspA (8 polypeptide chains). Monomers and Dimers of the
Specimen supportDetails: 15 mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 5 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 3 / Num. of real images: 12234

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Processing

EM software
IDNameCategory
7UCSF Chimeramodel fitting
13UCSF Chimeramodel refinement
14UCSF ChimeraXmodel refinement
15Cootmodel refinement
16PHENIXmodel refinement
17ISOLDEmodel refinement
CTF correctionDetails: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 7804230 / Details: Template Picker was Used
SymmetryPoint symmetry: D8 (2x8 fold dihedral)
3D reconstructionResolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 64941 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingDetails: MspA and De Novo Design / Source name: Other / Type: experimental model
RefinementHighest resolution: 2.95 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00316656
ELECTRON MICROSCOPYf_angle_d0.66722592
ELECTRON MICROSCOPYf_dihedral_angle_d5.7012402
ELECTRON MICROSCOPYf_chiral_restr0.0442544
ELECTRON MICROSCOPYf_plane_restr0.0072992

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