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- PDB-8vi3: TehA from Haemophilus influenzae purified in GDN -

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Basic information

Entry
Database: PDB / ID: 8vi3
TitleTehA from Haemophilus influenzae purified in GDN
ComponentsTellurite resistance protein TehA homolog
KeywordsMEMBRANE PROTEIN / ANION CHANNEL / ALPHA HELICAL INTEGRAL MEMBRANE PROTEIN
Function / homology
Function and homology information


monoatomic cation efflux transmembrane transporter activity / response to tellurium ion / response to antibiotic / identical protein binding / plasma membrane
Similarity search - Function
Tellurite resistance protein TehA/malic acid transport protein / Tellurite resistance protein TehA / Transporter protein SLAC1/Mae1/ Ssu1/TehA / Voltage-dependent anion channel superfamily / Voltage-dependent anion channel
Similarity search - Domain/homology
Tellurite resistance protein TehA homolog
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsCatalano, C. / Senko, S. / Tran, N.L. / Lucier, K.W. / Farwell, A.C. / Silva, M.S. / Dip, P.V. / Poweleit, N. / Scapin, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int J Mol Sci / Year: 2024
Title: High-Resolution Cryo-Electron Microscopy Structure Determination of Tellurite-Resistance Protein A via 200 kV Transmission Electron Microscopy.
Authors: Nhi L Tran / Skerdi Senko / Kyle W Lucier / Ashlyn C Farwell / Sabrina M Silva / Phat V Dip / Nicole Poweleit / Giovanna Scapin / Claudio Catalano /
Abstract: Membrane proteins constitute about 20% of the human proteome and play crucial roles in cellular functions. However, a complete understanding of their structure and function is limited by their ...Membrane proteins constitute about 20% of the human proteome and play crucial roles in cellular functions. However, a complete understanding of their structure and function is limited by their hydrophobic nature, which poses significant challenges in purification and stabilization. Detergents, essential in the isolation process, risk destabilizing or altering the proteins' native conformations, thus affecting stability and functionality. This study leverages single-particle cryo-electron microscopy to elucidate the structural nuances of membrane proteins, focusing on the SLAC1 bacterial homolog from (TehA) purified with diverse detergents, including n-dodecyl β-D-maltopyranoside (DDM), glycodiosgenin (GDN), β-D-octyl-glucoside (OG), and lauryl maltose neopentyl glycol (LMNG). This research not only contributes to the understanding of membrane protein structures but also addresses detergent effects on protein purification. By showcasing that the overall structural integrity of the channel is preserved, our study underscores the intricate interplay between proteins and detergents, offering insightful implications for drug design and membrane biology.
History
DepositionJan 3, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tellurite resistance protein TehA homolog
B: Tellurite resistance protein TehA homolog
C: Tellurite resistance protein TehA homolog


Theoretical massNumber of molelcules
Total (without water)105,7583
Polymers105,7583
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Tellurite resistance protein TehA homolog


Mass: 35252.547 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: tehA, HI_0511
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P44741

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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: TELLURITE RESISTANCE PROTEIN TEHA / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.108 MDa / Experimental value: NO
Source (natural)Organism: Haemophilus influenzae (bacteria)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 8
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 240000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 36.43 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 7352

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4particle selection
2Leginon3.6image acquisition
4cryoSPARC4CTF correction
7UCSF ChimeraX1.2.5model fitting
9PHENIX1.19.2model refinement
10Coot0.9.6model refinement
11cryoSPARC4initial Euler assignment
12cryoSPARCfinal Euler assignment
14cryoSPARC43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 227571
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40701 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 3M7C

3m7c


Accession code: 3M7C / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0027603
ELECTRON MICROSCOPYf_angle_d0.42110372
ELECTRON MICROSCOPYf_dihedral_angle_d3.372992
ELECTRON MICROSCOPYf_chiral_restr0.0361171
ELECTRON MICROSCOPYf_plane_restr0.0031258

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