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- EMDB-63428: A focused Cryo EM structure of PTH1R from PTH1R with arrestin1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-63428
TitleA focused Cryo EM structure of PTH1R from PTH1R with arrestin1 complex
Map data
Sample
  • Complex: A focused Cryo EM structure of PTH1R from PTH1R with arrestin1 complex
    • Protein or peptide: PTH1R
KeywordsPTH1R / arrestin / GPCR / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsYuan Q / Zhao L
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: A Cryo-EM structure of PTH1R-arrestin2 complex
Authors: Zhao L / Yuan Q
History
DepositionFeb 13, 2025-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63428.png

Downloads & links

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Map

FileDownload / File: emd_63428.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 440 pix.
= 321.2 Å		0.73 Å/pix.
x 440 pix.
= 321.2 Å		0.73 Å/pix.
x 440 pix.
= 321.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.471
Minimum - Maximum-1.5575501 - 2.4451637
Average (Standard dev.)-0.00038475424 (±0.029850392)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 321.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_63428_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63428_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 : A focused Cryo EM structure of PTH1R from PTH1R with arrestin1 complex

EntireName: A focused Cryo EM structure of PTH1R from PTH1R with arrestin1 complex
Components
  • Complex: A focused Cryo EM structure of PTH1R from PTH1R with arrestin1 complex
    • Protein or peptide: PTH1R

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Supramolecule #1: A focused Cryo EM structure of PTH1R from PTH1R with arrestin1 complex

SupramoleculeName: A focused Cryo EM structure of PTH1R from PTH1R with arrestin1 complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: PTH1R

MacromoleculeName: PTH1R / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DADDVMTKEE QIFLLHRAQA QCEKRLKEVL QRPASIMESD KGWTSASTSG KPRKDKASGK LYPESEEDKE APTGSRYRGR PCLPEWDHIL CWPLGAPGEV VAVPCPDYIY DFNHKGHAYR RCDRNGSWEL VPGHNRTWAN YSECVKFLTN ETREREVFDR LGMIYTVGYS ...String:
DADDVMTKEE QIFLLHRAQA QCEKRLKEVL QRPASIMESD KGWTSASTSG KPRKDKASGK LYPESEEDKE APTGSRYRGR PCLPEWDHIL CWPLGAPGEV VAVPCPDYIY DFNHKGHAYR RCDRNGSWEL VPGHNRTWAN YSECVKFLTN ETREREVFDR LGMIYTVGYS VSLASLTVAV LILAYFRRLH CTRNYIHMHL FLSFMLRAVS IFVKDAVLYS GATLDEAERL TEEELRAIAQ APPPPATAAA GYAGCRVAVT FFLYFLATNY YWILVEGLYL HSLIFMAFFS EKKYLWGFTV FGWGLPAVFV AVWVSVRATL ANTGCWDLSS GNKKWIIQVP ILASIVLNFI LFINIVRVLA TKLRETNAGR CDTRQQYRKL LKSTLVLMPL FGVHYIVFMA TPYTEVSGTL WQVQMHYEML FNSFQGFFVA IIYCFCNGEV QAEIKKSWSR WTLALDFKRK ARSGSSSYSY GPMV(SEP)H(TPO)(SEP)V(TPO) NG

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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: 7.04
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 18.0 µm / Nominal defocus min: 8.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 107599
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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