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- EMDB-62799: Cryo-EM structure of the inactive chemokine-like receptor 1 (CMKLR1) -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-62799
TitleCryo-EM structure of the inactive chemokine-like receptor 1 (CMKLR1)
Map data
Sample
  • Complex: CMKLR1 with ICL3-BRIL complex with anti-BRIL Fab and the antagonist LRH7-C2
    • Protein or peptide: The light chain of anti-BRIL Fab
    • Protein or peptide: Chemerin-like receptor 1,Soluble cytochrome b562
  • Protein or peptide: The heavy chain of anti-BRIL Fab
  • Protein or peptide: LRH7-C2
KeywordsGPCR / CMKLR1 / MEMBRANE PROTEIN/IMMUNE SYSTEM / MEMBRANE PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


adipokinetic hormone binding / adipokinetic hormone receptor activity / complement receptor activity / chemokine receptor activity / complement receptor mediated signaling pathway / negative regulation of interleukin-12 production / Class A/1 (Rhodopsin-like receptors) / positive regulation of macrophage chemotaxis / negative regulation of NF-kappaB transcription factor activity / positive regulation of fat cell differentiation ...adipokinetic hormone binding / adipokinetic hormone receptor activity / complement receptor activity / chemokine receptor activity / complement receptor mediated signaling pathway / negative regulation of interleukin-12 production / Class A/1 (Rhodopsin-like receptors) / positive regulation of macrophage chemotaxis / negative regulation of NF-kappaB transcription factor activity / positive regulation of fat cell differentiation / regulation of calcium-mediated signaling / skeletal system development / electron transport chain / G protein-coupled receptor activity / chemotaxis / signaling receptor activity / positive regulation of cold-induced thermogenesis / positive regulation of cytosolic calcium ion concentration / phospholipase C-activating G protein-coupled receptor signaling pathway / periplasmic space / electron transfer activity / immune response / G protein-coupled receptor signaling pathway / inflammatory response / iron ion binding / heme binding / membrane / plasma membrane
Similarity search - Function
Chemerin-like receptor 1 / Formyl peptide receptor-related / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
Soluble cytochrome b562 / Chemerin-like receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 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 19, 2024-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62799.png

Downloads & links

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Map

FileDownload / File: emd_62799.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 274.176 Å		1.07 Å/pix.
x 256 pix.
= 274.176 Å		1.07 Å/pix.
x 256 pix.
= 274.176 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: 0.15
Minimum - Maximum-0.0007284089 - 3.2198277
Average (Standard dev.)0.0036116086 (±0.042761914)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 274.176 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62799_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_62799_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 : CMKLR1 with ICL3-BRIL complex with anti-BRIL Fab and the antagoni...

EntireName: CMKLR1 with ICL3-BRIL complex with anti-BRIL Fab and the antagonist LRH7-C2
Components
  • Complex: CMKLR1 with ICL3-BRIL complex with anti-BRIL Fab and the antagonist LRH7-C2
    • Protein or peptide: The light chain of anti-BRIL Fab
    • Protein or peptide: Chemerin-like receptor 1,Soluble cytochrome b562
  • Protein or peptide: The heavy chain of anti-BRIL Fab
  • Protein or peptide: LRH7-C2

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Supramolecule #1: CMKLR1 with ICL3-BRIL complex with anti-BRIL Fab and the antagoni...

SupramoleculeName: CMKLR1 with ICL3-BRIL complex with anti-BRIL Fab and the antagonist LRH7-C2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: The heavy chain of anti-BRIL Fab

MacromoleculeName: The heavy chain of anti-BRIL Fab / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 26.917025 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: EISEVQLVES GGGLVQPGGS LRLSCAASGF NVVDFSLHWV RQAPGKGLEW VAYISSSSGS TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARWGYWPGEP WWKAFDYWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW ...String:
EISEVQLVES GGGLVQPGGS LRLSCAASGF NVVDFSLHWV RQAPGKGLEW VAYISSSSGS TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARWGYWPGEP WWKAFDYWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKVEPK SGPISTINPC LE VLFQGPH HHHHH

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Macromolecule #2: The light chain of anti-BRIL Fab

MacromoleculeName: The light chain of anti-BRIL Fab / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.586205 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYLYYSLVT FGQGTKVEIK RTVAAPSVFI FPPSDSQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ ...String:
SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYLYYSLVT FGQGTKVEIK RTVAAPSVFI FPPSDSQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ DSKDSTYSLS STLTLSKADY EKHKVYACEV THQGLSSPVT KSFNRGEC

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Macromolecule #3: Chemerin-like receptor 1,Soluble cytochrome b562

MacromoleculeName: Chemerin-like receptor 1,Soluble cytochrome b562 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.102949 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MRMEDEDYNT SISYGDEYPD YLDSIVVLED LSPLEARVTR IFLVVVYSIV CFLGILGNGL VIIIATFKMK KTVNMVWFLN LAVADFLFN VFLPIHITYA AMDYHWVFGT AMCKISNFLL IHNMFTSVFL LTIISSDRCI SVLLPVWSQN HRSVRLAYMA C MVIWVLAF ...String:
MRMEDEDYNT SISYGDEYPD YLDSIVVLED LSPLEARVTR IFLVVVYSIV CFLGILGNGL VIIIATFKMK KTVNMVWFLN LAVADFLFN VFLPIHITYA AMDYHWVFGT AMCKISNFLL IHNMFTSVFL LTIISSDRCI SVLLPVWSQN HRSVRLAYMA C MVIWVLAF FLSSPSLVFR DTANLHGKIS CFNNFSLSTP GSSSWPTHSQ MDPVGYSRHM VVTVTRFLCG FLVPVLIITA CY LTIVCKL QRNARRQLAD LEDNWETLND NLKVIEKADN AAQVKDALTK MRAAALDAQK ATPPKLEDKS PDSPEMKDFR HGF DILVGQ IDDALKLANE GKVKEAQAAA EQLKTTRNAY IQKYLERARS TLTKKPDKII VTIIITFFLC WCPYHTLNLL ELHH TAMPG SVFSLGLPLA TALAIANSCM NPILYVFMGQ DFKKFKVALF SRLVNALEFL EVLFQGPWSH PQFEKGGGSG GGSGG SAWS HPQFEKDYKD DDDK

UniProtKB: Chemerin-like receptor 1, Soluble cytochrome b562, Chemerin-like receptor 1

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Macromolecule #4: LRH7-C2

MacromoleculeName: LRH7-C2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 842.918 Da
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
H(DTR)NTVVS

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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: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 260967
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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