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- PDB-9l3z: Cryo-EM structure of the inactive chemokine-like receptor 1 (CMKLR1) -

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Basic information

Entry
Database: PDB / ID: 9l3z
TitleCryo-EM structure of the inactive chemokine-like receptor 1 (CMKLR1)
Components
  • Chemerin-like receptor 1,Soluble cytochrome b562
  • LRH7-C2
  • The heavy chain of anti-BRIL Fab
  • The light chain of anti-BRIL Fab
KeywordsMEMBRANE PROTEIN/IMMUNE SYSTEM / GPCR / CMKLR1 / 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) / negative regulation of NF-kappaB transcription factor activity / positive regulation of macrophage chemotaxis / 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) / negative regulation of NF-kappaB transcription factor activity / positive regulation of macrophage chemotaxis / positive regulation of fat cell differentiation / regulation of calcium-mediated signaling / skeletal system development / G protein-coupled receptor activity / electron transport chain / 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 speciesMus musculus (house mouse)
Homo sapiens (human)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsZhu, Y. / He, M. / Wu, B. / Zhao, Q.
Funding support China, 3items
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, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: The heavy chain of anti-BRIL Fab
L: The light chain of anti-BRIL Fab
A: Chemerin-like receptor 1,Soluble cytochrome b562
C: LRH7-C2


Theoretical massNumber of molelcules
Total (without water)107,4494
Polymers107,4494
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 26917.025 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm)
#2: Antibody The light chain of anti-BRIL Fab


Mass: 23586.205 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm)
#3: Protein Chemerin-like receptor 1,Soluble cytochrome b562 / Chemokine-like receptor 1 / G-protein coupled receptor ChemR23 / G-protein coupled receptor DEZ / ...Chemokine-like receptor 1 / G-protein coupled receptor ChemR23 / G-protein coupled receptor DEZ / Cytochrome b-562


Mass: 56102.949 Da / Num. of mol.: 1 / Mutation: F259D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: CMKLR1, CHEMR23, DEZ, cybC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q99788, UniProt: P0ABE7
#4: Protein/peptide LRH7-C2


Mass: 842.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: CMKLR1 with ICL3-BRIL complex with anti-BRIL Fab and the antagonist LRH7-C2
Type: COMPLEX / Entity ID: #2-#3 / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Homo sapiens (human)9606
21Escherichia coli (E. coli)562
31Mus musculus (house mouse)10090
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 70 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 260967 / Symmetry type: POINT
RefinementHighest resolution: 3.9 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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