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- EMDB-43248: TehA from Haemophilus influenzae purified in LMNG -

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Basic information

Entry
Database: EMDB / ID: EMD-43248
TitleTehA from Haemophilus influenzae purified in LMNG
Map data
Sample
  • Complex: TELLURITE RESISTANCE PROTEIN TEHA
    • Protein or peptide: Tellurite resistance protein TehA homolog
KeywordsANION CHANNEL / ALPHA HELICAL INTEGRAL MEMBRANE PROTEIN / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsCatalano C / Senko S / Tran NL / Lucier KW / Farwell AC / Silva MS / Dip PV / Poweleit N / Scapin G
Funding support1 items
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, 2024-
Header (metadata) releaseMay 8, 2024-
Map releaseMay 8, 2024-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43248.png

Downloads & links

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Map

FileDownload / File: emd_43248.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.57 Å/pix.
x 440 pix.
= 249.04 Å		0.57 Å/pix.
x 440 pix.
= 249.04 Å		0.57 Å/pix.
x 440 pix.
= 249.04 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.566 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.121
Minimum - Maximum-0.3426128 - 0.5760214
Average (Standard dev.)0.00019503517 (±0.015100617)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 249.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_43248_msk_1.map
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Half map: #1

Fileemd_43248_half_map_1.map
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Half map: #2

Fileemd_43248_half_map_2.map
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Sample components

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Entire : TELLURITE RESISTANCE PROTEIN TEHA

EntireName: TELLURITE RESISTANCE PROTEIN TEHA
Components
  • Complex: TELLURITE RESISTANCE PROTEIN TEHA
    • Protein or peptide: Tellurite resistance protein TehA homolog

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Supramolecule #1: TELLURITE RESISTANCE PROTEIN TEHA

SupramoleculeName: TELLURITE RESISTANCE PROTEIN TEHA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Haemophilus influenzae (bacteria)
Molecular weightTheoretical: 108 KDa

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Macromolecule #1: Tellurite resistance protein TehA homolog

MacromoleculeName: Tellurite resistance protein TehA homolog / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Haemophilus influenzae (bacteria)
Molecular weightTheoretical: 35.252547 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MNITKPFPLP TGYFGIPLGL AALSLAWFHL ENLFPAARMV SDVLGIVASA VWILFILMYA YKLRYYFEEV RAEYHSPVRF SFIALIPIT TMLVGDILYR WNPLIAEVLI WIGTIGQLLF STLRVSELWQ GGVFEQKSTH PSFYLPAVAA NFTSASSLAL L GYHDLGYL ...String:
MNITKPFPLP TGYFGIPLGL AALSLAWFHL ENLFPAARMV SDVLGIVASA VWILFILMYA YKLRYYFEEV RAEYHSPVRF SFIALIPIT TMLVGDILYR WNPLIAEVLI WIGTIGQLLF STLRVSELWQ GGVFEQKSTH PSFYLPAVAA NFTSASSLAL L GYHDLGYL FFGAGMIAWI IFEPVLLQHL RISSLEPQFR ATMGIVLAPA FVCVSAYLSI NHGEVDTLAK ILWGYGFLQL FF LLRLFPW IVEKGLNIGL WAFSFGLASM ANSATAFYHG NVLQGVSIFA FVFSNVMIGL LVLMTIYKLT KGQFFLK

UniProtKB: Tellurite resistance protein TehA homolog

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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

Concentration3 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 240000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 11370 / Average electron dose: 36.43 e/Å2

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Image processing

Particle selectionNumber selected: 252535
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3m7c

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 36758
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

3m7c


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8vi4:
TehA from Haemophilus influenzae purified in LMNG

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