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- EMDB-33086: Cryo-EM structure of the CCL2 bound CCR2-Gi complex -

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Entry
Database: EMDB / ID: EMD-33086
TitleCryo-EM structure of the CCL2 bound CCR2-Gi complex
Map data
Sample
  • Complex: Cryo-EM structure of the apo CCR3-Gi complex
    • Protein or peptide: Isoform B of C-C chemokine receptor type 2
    • Protein or peptide: C-C motif chemokine 2
    • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Protein or peptide: scFv16
KeywordsGPCR / CCR2 / Chemokine Receptor / MEMBRNE PROTEIN / MEMBRANE PROTEIN
Function / homology
Function and homology information


T-helper 17 cell chemotaxis / chemokine (C-C motif) ligand 2 binding / chemokine (C-C motif) ligand 12 binding / negative regulation of eosinophil degranulation / positive regulation of immune complex clearance by monocytes and macrophages / positive regulation of CD8-positive, alpha-beta T cell extravasation / positive regulation of astrocyte chemotaxis / leukocyte adhesion to vascular endothelial cell / chemokine (C-C motif) ligand 7 binding / helper T cell extravasation ...T-helper 17 cell chemotaxis / chemokine (C-C motif) ligand 2 binding / chemokine (C-C motif) ligand 12 binding / negative regulation of eosinophil degranulation / positive regulation of immune complex clearance by monocytes and macrophages / positive regulation of CD8-positive, alpha-beta T cell extravasation / positive regulation of astrocyte chemotaxis / leukocyte adhesion to vascular endothelial cell / chemokine (C-C motif) ligand 7 binding / helper T cell extravasation / chemokine (C-C motif) ligand 2 signaling pathway / positive regulation of thymocyte migration / positive regulation of hematopoietic stem cell migration / monocyte extravasation / CCR2 chemokine receptor binding / regulation of vascular endothelial growth factor production / negative regulation of natural killer cell chemotaxis / negative regulation of type 2 immune response / Beta defensins / positive regulation of monocyte extravasation / regulation of macrophage migration / macrophage migration / positive regulation of leukocyte tethering or rolling / neutrophil clearance / astrocyte cell migration / regulation of T cell cytokine production / chemokine receptor activity / positive regulation of T-helper 1 type immune response / positive regulation of T cell chemotaxis / CCR chemokine receptor binding / positive regulation of apoptotic cell clearance / positive regulation of alpha-beta T cell proliferation / inflammatory response to wounding / ATF4 activates genes in response to endoplasmic reticulum stress / negative regulation of glial cell apoptotic process / positive regulation of glutamate receptor signaling pathway / C-C chemokine receptor activity / negative regulation of adenylate cyclase activity / NFE2L2 regulating inflammation associated genes / chemokine-mediated signaling pathway / eosinophil chemotaxis / C-C chemokine binding / cellular homeostasis / positive regulation of monocyte chemotaxis / chemokine activity / Chemokine receptors bind chemokines / negative regulation of vascular endothelial cell proliferation / dendritic cell chemotaxis / regulation of T cell differentiation / negative regulation of G1/S transition of mitotic cell cycle / positive regulation of macrophage chemotaxis / positive regulation of calcium ion import / chemoattractant activity / macrophage chemotaxis / Interleukin-10 signaling / monocyte chemotaxis / humoral immune response / hemopoiesis / positive regulation of endothelial cell apoptotic process / cellular response to interleukin-1 / blood vessel remodeling / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / cell surface receptor signaling pathway via JAK-STAT / cellular defense response / positive regulation of synaptic transmission, glutamatergic / adenylate cyclase inhibitor activity / positive regulation of protein localization to cell cortex / T cell migration / Adenylate cyclase inhibitory pathway / D2 dopamine receptor binding / response to prostaglandin E / cellular response to fibroblast growth factor stimulus / adenylate cyclase regulator activity / G protein-coupled serotonin receptor binding / adenylate cyclase-inhibiting serotonin receptor signaling pathway / cytoskeleton organization / sensory perception of pain / positive regulation of interleukin-2 production / homeostasis of number of cells within a tissue / cellular response to forskolin / regulation of mitotic spindle organization / viral genome replication / negative regulation of angiogenesis / animal organ morphogenesis / cell chemotaxis / response to bacterium / Regulation of insulin secretion / calcium-mediated signaling / positive regulation of cholesterol biosynthetic process / negative regulation of insulin secretion / G protein-coupled receptor binding / response to peptide hormone / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / positive regulation of T cell activation / cellular response to type II interferon / response to wounding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G-protein beta/gamma-subunit complex binding / centriolar satellite / Olfactory Signaling Pathway
Similarity search - Function
CC chemokine receptor 2 / CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / Chemokine receptor family / : / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like ...CC chemokine receptor 2 / CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / Chemokine receptor family / : / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / G-protein alpha subunit, group I / Serpentine type 7TM GPCR chemoreceptor Srsx / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / G protein beta WD-40 repeat protein / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / 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) / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
C-C motif chemokine 2 / C-C chemokine receptor type 2 / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(i) subunit alpha-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsShao Z / Tan Y / Shen Q / Yao B / Hou L / Qin J / Xu P / Mao C / Chen L / Zhang H ...Shao Z / Tan Y / Shen Q / Yao B / Hou L / Qin J / Xu P / Mao C / Chen L / Zhang H / Shen D / Zhang C / Li W / Du X / Li F / Chen Z / Jiang Y / Xu HE / Ying S / Ma H / Zhang Y / Shen H
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Discov / Year: 2022
Title: Molecular insights into ligand recognition and activation of chemokine receptors CCR2 and CCR3.
Authors: Zhehua Shao / Yangxia Tan / Qingya Shen / Li Hou / Bingpeng Yao / Jiao Qin / Peiyu Xu / Chunyou Mao / Li-Nan Chen / Huibing Zhang / Dan-Dan Shen / Chao Zhang / Weijie Li / Xufei Du / Fei Li ...Authors: Zhehua Shao / Yangxia Tan / Qingya Shen / Li Hou / Bingpeng Yao / Jiao Qin / Peiyu Xu / Chunyou Mao / Li-Nan Chen / Huibing Zhang / Dan-Dan Shen / Chao Zhang / Weijie Li / Xufei Du / Fei Li / Zhi-Hua Chen / Yi Jiang / H Eric Xu / Songmin Ying / Honglei Ma / Yan Zhang / Huahao Shen /
Abstract: Chemokine receptors are a family of G-protein-coupled receptors with key roles in leukocyte migration and inflammatory responses. Here, we present cryo-electron microscopy structures of two human CC ...Chemokine receptors are a family of G-protein-coupled receptors with key roles in leukocyte migration and inflammatory responses. Here, we present cryo-electron microscopy structures of two human CC chemokine receptor-G-protein complexes: CCR2 bound to its endogenous ligand CCL2, and CCR3 in the apo state. The structure of the CCL2-CCR2-G-protein complex reveals that CCL2 inserts deeply into the extracellular half of the transmembrane domain, and forms substantial interactions with the receptor through the most N-terminal glutamine. Extensive hydrophobic and polar interactions are present between both two chemokine receptors and the Gα-protein, contributing to the constitutive activity of these receptors. Notably, complemented with functional experiments, the interactions around intracellular loop 2 of the receptors are found to be conserved and play a more critical role in G-protein activation than those around intracellular loop 3. Together, our findings provide structural insights into chemokine recognition and receptor activation, shedding lights on drug design targeting chemokine receptors.
History
DepositionMar 17, 2022-
Header (metadata) releaseAug 24, 2022-
Map releaseAug 24, 2022-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33086.png

Downloads & links

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Map

FileDownload / File: emd_33086.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 224 pix.
= 227.136 Å		1.01 Å/pix.
x 224 pix.
= 227.136 Å		1.01 Å/pix.
x 224 pix.
= 227.136 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.014 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.057
Minimum - Maximum-0.049808424 - 1.6913521
Average (Standard dev.)0.0016351518 (±0.02728221)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 227.13602 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Cryo-EM structure of the apo CCR3-Gi complex

EntireName: Cryo-EM structure of the apo CCR3-Gi complex
Components
  • Complex: Cryo-EM structure of the apo CCR3-Gi complex
    • Protein or peptide: Isoform B of C-C chemokine receptor type 2
    • Protein or peptide: C-C motif chemokine 2
    • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Protein or peptide: scFv16

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Supramolecule #1: Cryo-EM structure of the apo CCR3-Gi complex

SupramoleculeName: Cryo-EM structure of the apo CCR3-Gi complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Isoform B of C-C chemokine receptor type 2

MacromoleculeName: Isoform B of C-C chemokine receptor type 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.104332 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MLSTSRSRFI RNTNESGEEV TTFFDYDYGA PCHKFDVKQI GAQLLPPLYS LVFIFGFVGN MLVVLILINC KKLKCLTDIY LLNLAISDL LFLITLPLWA HSAANEWVFG NAMCKLFTGL YHIGYFGGIF FIILLTIDRY LAIVHAVFAL KARTVTFGVV T SVITWLVA ...String:
MLSTSRSRFI RNTNESGEEV TTFFDYDYGA PCHKFDVKQI GAQLLPPLYS LVFIFGFVGN MLVVLILINC KKLKCLTDIY LLNLAISDL LFLITLPLWA HSAANEWVFG NAMCKLFTGL YHIGYFGGIF FIILLTIDRY LAIVHAVFAL KARTVTFGVV T SVITWLVA VFASVPGIIF TKCQKEDSVY VCGPYFPRGW NNFHTIMRNI LGLVLPLLIM VICYSGILKT LLRCRNEKKR HR AVRVIFT IMIVYFLFWT PYNIVILLNT FQEFFGLSNC ESTSQLDQAT QVTETLGMTH CCINPIIYAF VGEKFRRYLS VFF RKHITK RFCKQCPVFY RETVDGVTST NTPSTGEQEV SAGL

UniProtKB: C-C chemokine receptor type 2

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Macromolecule #2: C-C motif chemokine 2

MacromoleculeName: C-C motif chemokine 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.913181 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
QPDAINAPVT CCYNFTNRKI SVQRLASYRR ITSSKCPKEA VIFKTIVAKE ICADPKQKWV QDSMDHLDK

UniProtKB: C-C motif chemokine 2

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Macromolecule #3: Guanine nucleotide-binding protein G(i) subunit alpha-1

MacromoleculeName: Guanine nucleotide-binding protein G(i) subunit alpha-1
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.445059 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGCTLSAEDK AAVERSKMID RNLREDGEKA AREVKLLLLG AGESGKSTIV KQMKIIHEAG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI ...String:
MGCTLSAEDK AAVERSKMID RNLREDGEKA AREVKLLLLG AGESGKSTIV KQMKIIHEAG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI PTQQDVLRTR VKTTGIVETH FTFKDLHFKM FDVGAQRSER KKWIHCFEGV TAIIFCVALS DYDLVLAEDE EM NRMHESM KLFDSICNNK WFTDTSIILF LNKKDLFEEK IKKSPLTICY PEYAGSNTYE EAAAYIQCQF EDLNKRKDTK EIY THFTCS TDTKNVQFVF DAVTDVIIKN NLKDCGLF

UniProtKB: Guanine nucleotide-binding protein G(i) subunit alpha-1

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Macromolecule #4: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.59723 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SELDQLRQEA EQLKNQIRDA RKACADATLS QITNNIDPVG RIQMRTRRTL RGHLAKIYAM HWGTDSRLLV SASQDGKLII WDSYTTNKV HAIPLRSSWV MTCAYAPSGN YVACGGLDNI CSIYNLKTRE GNVRVSRELA GHTGYLSCCR FLDDNQIVTS S GDTTCALW ...String:
SELDQLRQEA EQLKNQIRDA RKACADATLS QITNNIDPVG RIQMRTRRTL RGHLAKIYAM HWGTDSRLLV SASQDGKLII WDSYTTNKV HAIPLRSSWV MTCAYAPSGN YVACGGLDNI CSIYNLKTRE GNVRVSRELA GHTGYLSCCR FLDDNQIVTS S GDTTCALW DIETGQQTTT FTGHTGDVMS LSLAPDTRLF VSGACDASAK LWDVREGMCR QTFTGHESDI NAICFFPNGN AF ATGSDDA TCRLFDLRAD QELMTYSHDN IICGITSVSF SKSGRLLLAG YDDFNCNVWD ALKADRAGVL AGHDNRVSCL GVT DDGMAV ATGSWDSFLK IWNGSSGGGG SGGGGSSGVS GWRLFKKIS

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

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Macromolecule #5: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.861143 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI L

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

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Macromolecule #6: scFv16

MacromoleculeName: scFv16 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.37051 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGSSDIV MTQATSSVPV TPGESVSISC R SSKSLLHS ...String:
DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGSSDIV MTQATSSVPV TPGESVSISC R SSKSLLHS NGNTYLYWFL QRPGQSPQLL IYRMSNLASG VPDRFSGSGS GTAFTLTISR LEAEDVGVYY CMQHLEYPLT FG AGTKLEL KGSLEVLFQ

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 62.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 142391
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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