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- EMDB-31422: Cryo-EM structure of the chemokine receptor CCR5 in complex with ... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-31422 | |||||||||
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Title | Cryo-EM structure of the chemokine receptor CCR5 in complex with MIP-1a and Gi | |||||||||
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Function / homology | ![]() chemokine (C-C motif) ligand 5 binding / granulocyte chemotaxis / CCR1 chemokine receptor binding / positive regulation of microglial cell migration / positive regulation of natural killer cell chemotaxis / negative regulation of macrophage apoptotic process / signaling / regulation of behavior / chemokine receptor activity / astrocyte cell migration ...chemokine (C-C motif) ligand 5 binding / granulocyte chemotaxis / CCR1 chemokine receptor binding / positive regulation of microglial cell migration / positive regulation of natural killer cell chemotaxis / negative regulation of macrophage apoptotic process / signaling / regulation of behavior / chemokine receptor activity / astrocyte cell migration / CCR5 chemokine receptor binding / eosinophil degranulation / regulation of sensory perception of pain / negative regulation of bone mineralization / CCR chemokine receptor binding / positive regulation of microglial cell activation / lymphocyte chemotaxis / cell activation / phosphatidylinositol phospholipase C activity / C-C chemokine receptor activity / T cell chemotaxis / C-C chemokine binding / positive regulation of calcium ion transport / eosinophil chemotaxis / response to cholesterol / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / chemokine activity / dendritic cell chemotaxis / phospholipase activator activity / positive regulation of calcium ion import / exocytosis / chemoattractant activity / negative regulation of osteoclast differentiation / macrophage chemotaxis / Interleukin-10 signaling / monocyte chemotaxis / negative regulation by host of viral transcription / Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / Binding and entry of HIV virion / cellular response to interleukin-1 / regulation of cAMP-mediated signaling / cellular defense response / D2 dopamine receptor binding / G protein-coupled serotonin receptor binding / coreceptor activity / positive regulation of calcium-mediated signaling / regulation of mitotic spindle organization / cellular response to forskolin / cytoskeleton organization / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / neutrophil chemotaxis / cell chemotaxis / positive regulation of interleukin-1 beta production / Regulation of insulin secretion / G protein-coupled receptor binding / calcium-mediated signaling / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / Activation of the phototransduction cascade / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G-protein activation / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / response to toxic substance / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through BTK / response to peptide hormone / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Sensory perception of sweet, bitter, and umami (glutamate) taste / photoreceptor disc membrane / Adrenaline,noradrenaline inhibits insulin secretion / Glucagon-type ligand receptors / cellular response to type II interferon / Vasopressin regulates renal water homeostasis via Aquaporins / intracellular calcium ion homeostasis / G alpha (z) signalling events / positive regulation of inflammatory response / cellular response to catecholamine stimulus / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / osteoblast differentiation / sensory perception of taste / ADP signalling through P2Y purinoceptor 1 / adenylate cyclase-activating dopamine receptor signaling pathway / G beta:gamma signalling through PI3Kgamma / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / calcium ion transport / GPER1 signaling / GDP binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
![]() | Zhang H / Chen K / Tan Q / Han S / Zhu Y / Zhao Q / Wu B | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for chemokine recognition and receptor activation of chemokine receptor CCR5. Authors: Hui Zhang / Kun Chen / Qiuxiang Tan / Qiang Shao / Shuo Han / Chenhui Zhang / Cuiying Yi / Xiaojing Chu / Ya Zhu / Yechun Xu / Qiang Zhao / Beili Wu / ![]() Abstract: The chemokine receptor CCR5 plays a vital role in immune surveillance and inflammation. However, molecular details that govern its endogenous chemokine recognition and receptor activation remain ...The chemokine receptor CCR5 plays a vital role in immune surveillance and inflammation. However, molecular details that govern its endogenous chemokine recognition and receptor activation remain elusive. Here we report three cryo-electron microscopy structures of G protein-coupled CCR5 in a ligand-free state and in complex with the chemokine MIP-1α or RANTES, as well as the crystal structure of MIP-1α-bound CCR5. These structures reveal distinct binding modes of the two chemokines and a specific accommodate pattern of the chemokine for the distal N terminus of CCR5. Together with functional data, the structures demonstrate that chemokine-induced rearrangement of toggle switch and plasticity of the receptor extracellular region are critical for receptor activation, while a conserved tryptophan residue in helix II acts as a trigger of receptor constitutive activation. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 59.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.7 KB 13.7 KB | Display Display | ![]() |
Images | ![]() | 26 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 471.7 KB | Display | ![]() |
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Full document | ![]() | 471.3 KB | Display | |
Data in XML | ![]() | 6 KB | Display | |
Data in CIF | ![]() | 6.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7f1qMC ![]() 7f1rC ![]() 7f1sC ![]() 7f1tC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.045 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Chemokine receptor CCR5 in complex with MIP-1a and Gi
Entire | Name: Chemokine receptor CCR5 in complex with MIP-1a and Gi |
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Components |
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-Supramolecule #1: Chemokine receptor CCR5 in complex with MIP-1a and Gi
Supramolecule | Name: Chemokine receptor CCR5 in complex with MIP-1a and Gi / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #1: C-C motif chemokine 3,C-C chemokine receptor type 5
Macromolecule | Name: C-C motif chemokine 3,C-C chemokine receptor type 5 / type: protein_or_peptide / ID: 1 / Details: Fusion protein of MIP-1a and CCR5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 51.241047 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: SLAADTPTAC CFSYCSRQIP QNFIADYFET SSQCSKPGVI FLTKRSRQVC ADPSEEWVQK YVSDLELSAG SGSGSGSGSG SGSGSGSGS GSGSDYQVSS PIYDINYYCS EPCQKINVKQ IAARLLPPLY SLVFIFGFVG NMLVILILIN CKRLKSMTDI Y LLNLAISD ...String: SLAADTPTAC CFSYCSRQIP QNFIADYFET SSQCSKPGVI FLTKRSRQVC ADPSEEWVQK YVSDLELSAG SGSGSGSGSG SGSGSGSGS GSGSDYQVSS PIYDINYYCS EPCQKINVKQ IAARLLPPLY SLVFIFGFVG NMLVILILIN CKRLKSMTDI Y LLNLAISD LFFLLTVPFW AHYAAAQWDF GNTMCQLLTG LYFIGFFSGI FFIILLTIDR YLAVVHAVFA LKARTVTFGV VT SVITWVV AVFASLPNII FTRSQKEGLH YTCSSHFPYS QYQFWKNFQT LKIVILGLVL PLLVMVICYS GILKTLLRCR NEK KRHRAV RLIFTIMIVY FLFWAPYNIV LLLNTFQEFF GLNNCSSSNR LDQAMQVTET LGMTHCCINP IIYAFVGEKF RNYL LVFFQ KHIAKRLEVL FQGPGSWSHP QFEKGSGAGA SAGSWSHPQF EKGSDYKDDD DK |
-Macromolecule #2: Guanine nucleotide-binding protein G(i) subunit alpha-1
Macromolecule | Name: Guanine nucleotide-binding protein G(i) subunit alpha-1 type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 40.447141 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MGCTLSAEDK AAVERSKMID RNLREDGEKA AREVKLLLLG AGESGKCTIV KQMKIIHEAG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI ...String: MGCTLSAEDK AAVERSKMID RNLREDGEKA AREVKLLLLG AGESGKCTIV KQMKIIHEAG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI PTQQDVLRTR VKTTGIVETH FTFKDLHFKM FDVTAQRSER KKWIHCFEGV TAIIFCVALS DYDLVLAEDE EM NRMHASM KLFDSICNNK WFTDTSIILF LNKKDLFEEK IKKSPLTICY PEYAGSNTYE EAAAYIQCQF EDLNKRKDTK EIY THFTCS TDTKNVQFVF DAVTDVIIKN NLKDCGLF |
-Macromolecule #3: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
Macromolecule | Name: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 37.41693 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKLI IWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC RFLDDNQIVT S SGDTTCAL ...String: MSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKLI IWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC RFLDDNQIVT S SGDTTCAL WDIETGQQTT TFTGHTGDVM SLSLAPDTRL FVSGACDASA KLWDVREGMC RQTFTGHESD INAICFFPNG NA FATGSDD ATCRLFDLRA DQELMTYSHD NIICGITSVS FSKSGRLLLA GYDDFNCNVW DALKADRAGV LAGHDNRVSC LGV TDDGMA VATGSWDSFL KIWN |
-Macromolecule #4: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
Macromolecule | Name: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 7.861143 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI L |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 2.1875 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 7095732 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |