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- EMDB-63520: Cryo-EM structure of chimeric receptor in complex with transduce -

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Basic information

Entry
Database: EMDB / ID: EMD-63520
TitleCryo-EM structure of chimeric receptor in complex with transduce
Map data
Sample
  • Complex: Cryo-EM structure of ligand-bound form of the chimeric receptor in complex with the transduce
KeywordsCryo-EM structure / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsZhai X / Mao C / Shen Q / Zang S / Shen D / Zhang H / Chen Z / Wang G / Zhang C / Zhang Y / Liu Z
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2026
Title: Core conformation of arrestin coupling to parathyroid hormone type 1 receptor.
Authors: Xiuwen Zhai / Jia Guo / Qingya Shen / Li-Nan Chen / Gang Wang / Dan-Dan Shen / Changming Zhang / Xiaodong Xu / Chunyou Mao / Yan Zhang / Zhihong Liu /
Abstract: The recruitment of β-arrestin (βarr) by G-protein-coupled receptor (GPCR) holds imperative importance in physiological processes, while the mechanisms underlying arrestin engagement with receptors ...The recruitment of β-arrestin (βarr) by G-protein-coupled receptor (GPCR) holds imperative importance in physiological processes, while the mechanisms underlying arrestin engagement with receptors remain obscure. The parathyroid hormone type 1 receptor (PTH1R), as a prototypical class B1 receptor, incorporates arrestin for signaling and regulates G-protein signaling by distinct mechanisms. Here, we report three cryo-electron microscopy structures of β-arrestin1 (βarr1) engaged with the activated wild-type and chimeric PTH1R in core conformation, revealing a distinctive binding mode of βarr1 coupling to PTH1R compared to other GPCRs. In addition to the pronounced kinking of transmembrane (TM) 6, βarr1 establishes extensive interactions with the core cavity of PTH1R by promoting the outward movement of TM5 and intracellular loop (ICL) 2, stabilizing the core conformation of the complex. Further, our work shows that the core coupling mode of βarr with PTH1R mediates receptor internalization and trafficking. Collectively, our work offers a paradigm for the arrestin coupling to class B1 GPCR and regulating the signaling transduction.
History
DepositionFeb 21, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63520.png

Downloads & links

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Map

FileDownload / File: emd_63520.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 320 pix.
= 297.6 Å		0.93 Å/pix.
x 320 pix.
= 297.6 Å		0.93 Å/pix.
x 320 pix.
= 297.6 Å

Surface

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Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.246
Minimum - Maximum-0.04217962 - 2.5559514
Average (Standard dev.)0.00036281487 (±0.010366696)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 297.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_63520_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63520_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of ligand-bound form of the chimeric receptor i...

EntireName: Cryo-EM structure of ligand-bound form of the chimeric receptor in complex with the transduce
Components
  • Complex: Cryo-EM structure of ligand-bound form of the chimeric receptor in complex with the transduce

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Supramolecule #1: Cryo-EM structure of ligand-bound form of the chimeric receptor i...

SupramoleculeName: Cryo-EM structure of ligand-bound form of the chimeric receptor in complex with the transduce
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Frames/image: 1-40 / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6nbi

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 345754
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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