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- EMDB-62732: Focused refinement in chemerin and receptor regions of the chemok... -

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Basic information

Entry
Database: EMDB / ID: EMD-62732
TitleFocused refinement in chemerin and receptor regions of the chemokine-like receptor 1 (CMKLR1) in complex with chemerin and Gi1
Map dataFocused refinement in chemerin and receptor regions of the chemokine-like receptor 1 (CMKLR1) in complex with chemerin and Gi1
Sample
  • Complex: The full length chemerin bound CMKLR1-Gi complex
KeywordsGPCR / CMKLR1 / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.47 Å
AuthorsZhu Y / He M / Wu B / Zhao Q
Funding support China, 3 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)2022YFA1302900 China
National Natural Science Foundation of China (NSFC)82121005 China
National Natural Science Foundation of China (NSFC)32401012 China
CitationJournal: Protein Cell / Year: 2025
Title: Structural insights into the distinct ligand recognition and signaling of the chemerin receptors CMKLR1 and GPR1.
Authors: Xiaowen Lin / Lechen Zhao / Heng Cai / Xiaohua Chang / Yuxuan Tang / Tianyu Luo / Mengdan Wu / Cuiying Yi / Limin Ma / Xiaojing Chu / Shuo Han / Qiang Zhao / Beili Wu / Maozhou He / Ya Zhu /
History
DepositionDec 13, 2024-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62732.png

Downloads & links

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Map

FileDownload / File: emd_62732.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused refinement in chemerin and receptor regions of the chemokine-like receptor 1 (CMKLR1) in complex with chemerin and Gi1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 300 pix.
= 321.3 Å		1.07 Å/pix.
x 300 pix.
= 321.3 Å		1.07 Å/pix.
x 300 pix.
= 321.3 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.071 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.58
Minimum - Maximum-5.8650274 - 7.37949
Average (Standard dev.)-0.0011669534 (±0.06329505)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 321.3 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half 2

Fileemd_62732_half_map_1.map
Annotationhalf 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half 1

Fileemd_62732_half_map_2.map
Annotationhalf 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The full length chemerin bound CMKLR1-Gi complex

EntireName: The full length chemerin bound CMKLR1-Gi complex
Components
  • Complex: The full length chemerin bound CMKLR1-Gi complex

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Supramolecule #1: The full length chemerin bound CMKLR1-Gi complex

SupramoleculeName: The full length chemerin bound CMKLR1-Gi complex / 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 89786
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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