[English] 日本語
Yorodumi
- EMDB-46534: Cryo-EM structure of CCR6 bound by SQA1 and OXM1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-46534
TitleCryo-EM structure of CCR6 bound by SQA1 and OXM1
Map dataCryo-EM reconstruction of CCR6 bound by SQA1 and OXM1
Sample
  • Complex: CCR6-BRIL/Fab/Nb in complex with SQA1 and OXM1
    • Protein or peptide: CCR6, Soluble cytochrome b562
    • Protein or peptide: anti-BRIL Fab Heavy chain
    • Protein or peptide: anti-BRIL Fab Nanobody
    • Protein or peptide: anti-BRIL Fab Light chain
  • Ligand: CHOLESTEROL
  • Ligand: 4-[[3,4-bis(oxidanylidene)-2-[[(1~{R})-1-(4-propan-2-ylfuran-2-yl)propyl]amino]cyclobuten-1-yl]amino]-~{N},~{N}-dimethyl-3-oxidanyl-pyridine-2-carboxamide
  • Ligand: 1-(4-chlorophenyl)-N-{[(2R)-4-(2,3-dihydro-1H-inden-2-yl)-5-oxomorpholin-2-yl]methyl}cyclopropane-1-carboxamide
KeywordsGPCR / Antagonist / CCR6 / BRIL / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsWasilko DJ / Wu H
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis for CCR6 modulation by allosteric antagonists.
Authors: David Jonathan Wasilko / Brian S Gerstenberger / Kathleen A Farley / Wei Li / Jennifer Alley / Mark E Schnute / Ray J Unwalla / Jorge Victorino / Kimberly K Crouse / Ru Ding / Parag V ...Authors: David Jonathan Wasilko / Brian S Gerstenberger / Kathleen A Farley / Wei Li / Jennifer Alley / Mark E Schnute / Ray J Unwalla / Jorge Victorino / Kimberly K Crouse / Ru Ding / Parag V Sahasrabudhe / Fabien Vincent / Richard K Frisbie / Alpay Dermenci / Andrew Flick / Chulho Choi / Gary Chinigo / James J Mousseau / John I Trujillo / Philippe Nuhant / Prolay Mondal / Vincent Lombardo / Daniel Lamb / Barbara J Hogan / Gurdeep Singh Minhas / Elena Segala / Christine Oswald / Ian W Windsor / Seungil Han / Mathieu Rappas / Robert M Cooke / Matthew F Calabrese / Gabriel Berstein / Atli Thorarensen / Huixian Wu /
Abstract: The CC chemokine receptor 6 (CCR6) is a potential target for chronic inflammatory diseases. Previously, we reported an active CCR6 structure in complex with its cognate chemokine CCL20, revealing the ...The CC chemokine receptor 6 (CCR6) is a potential target for chronic inflammatory diseases. Previously, we reported an active CCR6 structure in complex with its cognate chemokine CCL20, revealing the molecular basis of CCR6 activation. Here, we present two inactive CCR6 structures in ternary complexes with different allosteric antagonists, CCR6/SQA1/OXM1 and CCR6/SQA1/OXM2. The oxomorpholine analogues, OXM1 and OXM2 are highly selective CCR6 antagonists which bind to an extracellular pocket and disrupt the receptor activation network. An energetically favoured U-shaped conformation in solution that resembles the bound form is observed for the active analogues. SQA1 is a squaramide derivative with close-in analogues reported as antagonists of chemokine receptors including CCR6. SQA1 binds to an intracellular pocket which overlaps with the G protein site, stabilizing a closed pocket that is a hallmark of inactive GPCRs. Minimal communication between the two allosteric pockets is observed, in contrast to the prevalent allosteric cooperativity model of GPCRs. This work highlights the versatility of GPCR antagonism by small molecules, complementing previous knowledge of CCR6 activation, and sheds light on drug discovery targeting CCR6.
History
DepositionAug 10, 2024-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_46534.png

Downloads & links

-
Map

FileDownload / File: emd_46534.map.gz / Format: CCP4 / Size: 536.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM reconstruction of CCR6 bound by SQA1 and OXM1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.58 Å/pix.
x 520 pix.
= 299. Å		0.58 Å/pix.
x 520 pix.
= 299. Å		0.58 Å/pix.
x 520 pix.
= 299. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.575 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.083
Minimum - Maximum-0.9692936 - 1.3107519
Average (Standard dev.)-0.00021160119 (±0.012765196)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions520520520
Spacing520520520
CellA=B=C: 299.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: EM half map 1

Fileemd_46534_half_map_1.map
AnnotationEM half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: EM half map 2

Fileemd_46534_half_map_2.map
AnnotationEM half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : CCR6-BRIL/Fab/Nb in complex with SQA1 and OXM1

EntireName: CCR6-BRIL/Fab/Nb in complex with SQA1 and OXM1
Components
  • Complex: CCR6-BRIL/Fab/Nb in complex with SQA1 and OXM1
    • Protein or peptide: CCR6, Soluble cytochrome b562
    • Protein or peptide: anti-BRIL Fab Heavy chain
    • Protein or peptide: anti-BRIL Fab Nanobody
    • Protein or peptide: anti-BRIL Fab Light chain
  • Ligand: CHOLESTEROL
  • Ligand: 4-[[3,4-bis(oxidanylidene)-2-[[(1~{R})-1-(4-propan-2-ylfuran-2-yl)propyl]amino]cyclobuten-1-yl]amino]-~{N},~{N}-dimethyl-3-oxidanyl-pyridine-2-carboxamide
  • Ligand: 1-(4-chlorophenyl)-N-{[(2R)-4-(2,3-dihydro-1H-inden-2-yl)-5-oxomorpholin-2-yl]methyl}cyclopropane-1-carboxamide

-
Supramolecule #1: CCR6-BRIL/Fab/Nb in complex with SQA1 and OXM1

SupramoleculeName: CCR6-BRIL/Fab/Nb in complex with SQA1 and OXM1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: CCR6-BRIL/Fab/Nb complex co-purified with SQA1 and OXM1.
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 120 kDa/nm

-
Macromolecule #1: CCR6, Soluble cytochrome b562

MacromoleculeName: CCR6, Soluble cytochrome b562 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.62302 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKTIIALSYI FCLVFADYKD DDDAKLQTMH HHHHHHHHHE NLYFQGGTSV DSEMLLCSLQ EVRQFSRAFV PIAYSLICVF GLLGNILVV ITFAFYKKAR SMTDVYLANM AIADILFALT LPFWAVSHAT GAWVFSNATC KLLKGIYAIN FNCGMWLLTC I AMDRYIAI ...String:
MKTIIALSYI FCLVFADYKD DDDAKLQTMH HHHHHHHHHE NLYFQGGTSV DSEMLLCSLQ EVRQFSRAFV PIAYSLICVF GLLGNILVV ITFAFYKKAR SMTDVYLANM AIADILFALT LPFWAVSHAT GAWVFSNATC KLLKGIYAIN FNCGMWLLTC I AMDRYIAI VQATKSFRLR SATLPRSKII CLVVWGLSVI ISSSTFVFNQ KYNTQGSDVC EPKYQTVSEP IRWKLLMLGL EL LFGFFIP LMFMIFCYTA IVKTLRRQLA DLEDNWETLN DNLKVIEKAD NAAQVKDALT KMRAAALDAQ KATPPKLEDK SPD SPEMKD FRHGFDILVG QIDDALKLAN EGKVKEAQAA AEQLKTTRNA YIQKYLERAR STLQKEVKAI RVIIAVVLVF LACQ IPHNM VLLVTAANLG KMNRSCQSEK LIAYTKTVTE VLAFLHCCLN PVLYAFIGQK FRNYFLKILK DLWCVRRKYK SSGFS

-
Macromolecule #2: anti-BRIL Fab Heavy chain

MacromoleculeName: anti-BRIL Fab Heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.832098 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHSE ISEVQLVESG GGLVQPGGSL RLSCAASGFN VVDFSLHWVR QAPGKGLEWV AYISSSSGST SYADSVKGR FTISADTSKN TAYLQMNSLR AEDTAVYYCA RWGYWPGEPW WKAFDYWGQG TLVTVSSAST KGPSVFPLAP S SKSTSGGT ...String:
MGWSCIILFL VATATGVHSE ISEVQLVESG GGLVQPGGSL RLSCAASGFN VVDFSLHWVR QAPGKGLEWV AYISSSSGST SYADSVKGR FTISADTSKN TAYLQMNSLR AEDTAVYYCA RWGYWPGEPW WKAFDYWGQG TLVTVSSAST KGPSVFPLAP S SKSTSGGT AALGCLVKDY FPEPVTVSWN SGALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KV DKKVEPK SGGSENLYFQ GSHHHHHHHH HH

-
Macromolecule #3: anti-BRIL Fab Nanobody

MacromoleculeName: anti-BRIL Fab Nanobody / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 15.755214 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGHHHHHHHH HHENLYFQGS QVQLQESGGG LVQPGGSLRL SCAASGRTIS RYAMSWFRQA PGKEREFVAV ARRSGDGAFY ADSVQGRFT VSRDDAKNTV YLQMNSLKPE DTAVYYCAID SDTFYSGSYD YWGQGTQVTV SS

-
Macromolecule #4: anti-BRIL Fab Light chain

MacromoleculeName: anti-BRIL Fab Light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.343348 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHSS DIQMTQSPSS LSASVGDRVT ITCRASQSVS SAVAWYQQKP GKAPKLLIYS ASSLYSGVPS RFSGSRSGT DFTLTISSLQ PEDFATYYCQ QYLYYSLVTF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN F YPREAKVQ ...String:
MGWSCIILFL VATATGVHSS DIQMTQSPSS LSASVGDRVT ITCRASQSVS SAVAWYQQKP GKAPKLLIYS ASSLYSGVPS RFSGSRSGT DFTLTISSLQ PEDFATYYCQ QYLYYSLVTF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN F YPREAKVQ WKVDNALQSG NSQESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRG

-
Macromolecule #5: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 5 / Number of copies: 1 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

-
Macromolecule #6: 4-[[3,4-bis(oxidanylidene)-2-[[(1~{R})-1-(4-propan-2-ylfuran-2-yl...

MacromoleculeName: 4-[[3,4-bis(oxidanylidene)-2-[[(1~{R})-1-(4-propan-2-ylfuran-2-yl)propyl]amino]cyclobuten-1-yl]amino]-~{N},~{N}-dimethyl-3-oxidanyl-pyridine-2-carboxamide
type: ligand / ID: 6 / Number of copies: 1 / Formula: EBX
Molecular weightTheoretical: 426.466 Da
Chemical component information

ChemComp-EBX:
4-[[3,4-bis(oxidanylidene)-2-[[(1~{R})-1-(4-propan-2-ylfuran-2-yl)propyl]amino]cyclobuten-1-yl]amino]-~{N},~{N}-dimethyl-3-oxidanyl-pyridine-2-carboxamide

-
Macromolecule #7: 1-(4-chlorophenyl)-N-{[(2R)-4-(2,3-dihydro-1H-inden-2-yl)-5-oxomo...

MacromoleculeName: 1-(4-chlorophenyl)-N-{[(2R)-4-(2,3-dihydro-1H-inden-2-yl)-5-oxomorpholin-2-yl]methyl}cyclopropane-1-carboxamide
type: ligand / ID: 7 / Number of copies: 1 / Formula: A1A2A
Molecular weightTheoretical: 424.92 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
Details: 50 mM HEPES pH 7.5, 150 mM NaCl, 0.003% LMNG, 0.0003% CHS, 50 uM OXM1 and 50 uM of SQA1
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsCCR6-BRIL/Fab/Nb complex co-purified with SQA1 and OXM1.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 215000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 5332464
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 482484
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC (ver. 3.3.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9d3g:
Cryo-EM structure of CCR6 bound by SQA1 and OXM1

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more