[English] 日本語
![](img/lk-miru.gif)
- EMDB-21950: Cryo-EM structure of the human chemokine receptor CCR6 in complex... -
+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-21950 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the human chemokine receptor CCR6 in complex with CCL20 and a Go protein | |||||||||
![]() | Chemokine receptor CCR6 in complex with CCL20 and a Go protein | |||||||||
![]() |
| |||||||||
Function / homology | ![]() isotype switching to IgA isotypes / DN3 thymocyte differentiation / thymocyte migration / positive regulation of flagellated sperm motility involved in capacitation / CCR6 chemokine receptor binding / Beta defensins / sperm principal piece / positive regulation of dendritic cell chemotaxis / regulation of T cell migration / T cell migration ...isotype switching to IgA isotypes / DN3 thymocyte differentiation / thymocyte migration / positive regulation of flagellated sperm motility involved in capacitation / CCR6 chemokine receptor binding / Beta defensins / sperm principal piece / positive regulation of dendritic cell chemotaxis / regulation of T cell migration / T cell migration / DN2 thymocyte differentiation / lymphocyte migration / chemokine receptor activity / CCR chemokine receptor binding / lymphocyte chemotaxis / leukocyte migration involved in inflammatory response / C-C chemokine receptor activity / C-C chemokine binding / G-protein activation / Activation of the phototransduction cascade / Glucagon-type ligand receptors / Thromboxane signalling through TP receptor / Sensory perception of sweet, bitter, and umami (glutamate) taste / G beta:gamma signalling through PI3Kgamma / G beta:gamma signalling through CDC42 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Ca2+ pathway / G alpha (z) signalling events / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / vesicle docking involved in exocytosis / chemokine-mediated signaling pathway / G alpha (q) signalling events / G alpha (i) signalling events / Chemokine receptors bind chemokines / Thrombin signalling through proteinase activated receptors (PARs) / chemokine activity / alkylglycerophosphoethanolamine phosphodiesterase activity / dendritic cell chemotaxis / sperm plasma membrane / G protein-coupled dopamine receptor signaling pathway / photoreceptor outer segment membrane / regulation of heart contraction / spectrin binding / positive regulation of epithelial cell migration / plasma membrane => GO:0005886 / Interleukin-10 signaling / monocyte chemotaxis / humoral immune response / : / mu-type opioid receptor binding / photoreceptor outer segment / corticotropin-releasing hormone receptor 1 binding / sperm flagellum / positive regulation of T cell migration / cellular response to interleukin-1 / negative regulation of insulin secretion / cellular defense response / G protein-coupled serotonin receptor binding / sperm midpiece / cardiac muscle cell apoptotic process / photoreceptor inner segment / neutrophil chemotaxis / cell chemotaxis / locomotory behavior / muscle contraction / calcium-mediated signaling / electron transport chain / G-protein beta/gamma-subunit complex binding / 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 / 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 / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through BTK / Adrenaline,noradrenaline inhibits insulin secretion / Glucagon-type ligand receptors / Vasopressin regulates renal water homeostasis via Aquaporins / cellular response to type II interferon / G alpha (z) signalling events / cellular response to catecholamine stimulus / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / 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 / GPER1 signaling Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.34 Å | |||||||||
![]() | Wasilko DJ / Johnson ZL / Ammirati M / Han S / Wu H | |||||||||
![]() | ![]() Title: Structural basis for chemokine receptor CCR6 activation by the endogenous protein ligand CCL20. Authors: David Jonathan Wasilko / Zachary Lee Johnson / Mark Ammirati / Ye Che / Matthew C Griffor / Seungil Han / Huixian Wu / ![]() Abstract: Chemokines are important protein-signaling molecules that regulate various immune responses by activating chemokine receptors which belong to the G protein-coupled receptor (GPCR) superfamily. ...Chemokines are important protein-signaling molecules that regulate various immune responses by activating chemokine receptors which belong to the G protein-coupled receptor (GPCR) superfamily. Despite the substantial progression of our structural understanding of GPCR activation by small molecule and peptide agonists, the molecular mechanism of GPCR activation by protein agonists remains unclear. Here, we present a 3.3-Å cryo-electron microscopy structure of the human chemokine receptor CCR6 bound to its endogenous ligand CCL20 and an engineered Go. CCL20 binds in a shallow extracellular pocket, making limited contact with the core 7-transmembrane (TM) bundle. The structure suggests that this mode of binding induces allosterically a rearrangement of a noncanonical toggle switch and the opening of the intracellular crevice for G protein coupling. Our results demonstrate that GPCR activation by a protein agonist does not always require substantial interactions between ligand and the 7TM core region. | |||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 201.9 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 25.5 KB 25.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.7 KB | Display | ![]() |
Images | ![]() | 119.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 494.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 493.8 KB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 17.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6wwzMC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Chemokine receptor CCR6 in complex with CCL20 and a Go protein | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.87 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
+Entire : CCR6-CCL20-Go complex
+Supramolecule #1: CCR6-CCL20-Go complex
+Supramolecule #2: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1,...
+Supramolecule #3: C-C motif chemokine 20, Guanine nucleotide-binding protein G(o) s...
+Supramolecule #4: scFv16
+Macromolecule #1: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
+Macromolecule #2: C-C motif chemokine 20
+Macromolecule #3: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
+Macromolecule #4: Guanine nucleotide-binding protein G(o) subunit alpha,Guanine nuc...
+Macromolecule #5: scFv16
+Macromolecule #6: C-C chemokine receptor type 6,C-C chemokine receptor type 6
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Concentration | 6.8 mg/mL | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 7.5 Component:
| |||||||||||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING | |||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.0 K / Instrument: FEI VITROBOT MARK IV |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Temperature | Min: 80.0 K / Max: 100.0 K |
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-50 / Number grids imaged: 1 / Number real images: 5303 / Average exposure time: 8.0 sec. / Average electron dose: 81.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 165000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
+
Image processing
-Atomic model buiding 1
Initial model |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
Refinement | Space: REAL / Protocol: RIGID BODY FIT | ||||||||
Output model | ![]() PDB-6wwz: |