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- EMDB-71713: V-shaped (channel-formed), ATP-bound, VX809-bound, T2a-nanobody-b... -

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Basic information

Entry
Database: EMDB / ID: EMD-71713
TitleV-shaped (channel-formed), ATP-bound, VX809-bound, T2a-nanobody-bound conformation of wild-type human CFTR (sharpened WalkerB2 local refinement map from cryoSPARC)
Map data
Sample
  • Complex: Wild-type human CFTR solubilized in digitonin and cholesterol-hemisuccinate plus T2a nanobody in the presence of 2 mM MgATP
    • Organelle or cellular component: Wild type human Cystic Fibrosis Transmembrane Conductance Regulator (hCFTR)
      • Organelle or cellular component: T2a nanobody
Keywordscystic fibrosis / CFTR / nanobody / protein folding / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsHunt JF / Paige AS / Cohen BM / Goldberg PM / Wang C / Loughlin BJ / Kappes JC / Yang Z / Jiang F / Govaerts C ...Hunt JF / Paige AS / Cohen BM / Goldberg PM / Wang C / Loughlin BJ / Kappes JC / Yang Z / Jiang F / Govaerts C / Overtus M / Rich Z
Funding support United States, 1 items
OrganizationGrant numberCountry
Cystic Fibrosis FoundationHUNT13XX0, HUNT18G0, HUNT20G0, 004400G222-Hunt, 007997G224-Hunt, FRANK16XX0, FRANK18G0 United States
CitationJournal: To Be Published
Title: Nanobody-Driven Stabilization Synergistically Rescues F508del-CFTR and Reveals an Alternative Active State of the Channel
Authors: Hunt FJ / Paige AS / Cohen BM / Goldberg PM / Wang C / Loughlin BJ / Kappes JC / Yang Z / Jiang F / Govaerts C / Overtus M / Urbatsch IL / Lukacs G
History
DepositionJul 15, 2025-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71713.png

Downloads & links

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Map

FileDownload / File: emd_71713.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.5309792 - 0.7521399
Average (Standard dev.)0.00027351244 (±0.010137651)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 265.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_71713_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_71713_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Wild-type human CFTR solubilized in digitonin and cholesterol-hem...

EntireName: Wild-type human CFTR solubilized in digitonin and cholesterol-hemisuccinate plus T2a nanobody in the presence of 2 mM MgATP
Components
  • Complex: Wild-type human CFTR solubilized in digitonin and cholesterol-hemisuccinate plus T2a nanobody in the presence of 2 mM MgATP
    • Organelle or cellular component: Wild type human Cystic Fibrosis Transmembrane Conductance Regulator (hCFTR)
      • Organelle or cellular component: T2a nanobody

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Supramolecule #1: Wild-type human CFTR solubilized in digitonin and cholesterol-hem...

SupramoleculeName: Wild-type human CFTR solubilized in digitonin and cholesterol-hemisuccinate plus T2a nanobody in the presence of 2 mM MgATP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Supramolecule #2: Wild type human Cystic Fibrosis Transmembrane Conductance Regulat...

SupramoleculeName: Wild type human Cystic Fibrosis Transmembrane Conductance Regulator (hCFTR)
type: organelle_or_cellular_component / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: T2a nanobody

SupramoleculeName: T2a nanobody / type: organelle_or_cellular_component / ID: 3 / Parent: 2 / Macromolecule list: #2
Source (natural)Organism: Lama glama (llama)

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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

Concentration1.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
200.0 mMNaClSodium Chloride
3.0 mMMgCl2Magnesium Chloride
50.0 mMC4H11NO3Tris buffer
0.06 % (w/v)C56H92O29Digitonin
2.0 mMC10H16N5O13P3ATP
GridModel: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 50 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: OTHER
Details: The grid was treated in a Solarus Plasma Cleaner 950 (Gatan Inc., USA) for 25 sec with O2/H2 flow-rates of 27.5/6.4 sccm and 15 W cleaning power.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 85.0 K / Max: 90.0 K
Specialist opticsEnergy filter - Name: GIF Quantum ER / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 11110 / Average exposure time: 2.5 sec. / Average electron dose: 58.0 e/Å2
Details: Movies comprised 40 frames collected in 2.5 seconds.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.9 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 105000
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: 2635244
CTF correctionSoftware - Name: cryoSPARC (ver. 4.3.1) / Software - details: Patch CTF correction / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 81235
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3.1)
Final 3D classificationNumber classes: 6 / Avg.num./class: 49652 / Software - Name: cryoSPARC (ver. 4.7.0)
FSC plot (resolution estimation)

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