[English] 日本語
Yorodumi
- EMDB-43277: cryoEM structure of human ACKR3 phosphorylated by GRK5 in complex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-43277
TitlecryoEM structure of human ACKR3 phosphorylated by GRK5 in complex with Arrestin3 variant with the C edge loop from Arrestin2 inserted
Map data
Sample
  • Complex: human ACKR3 phosphorylated by GRK5 in complex with Arrestin3
    • Protein or peptide: Fab7 heavy chain
    • Protein or peptide: Fab7 light chain
    • Protein or peptide: Atypical chemokine receptor 3
    • Protein or peptide: Beta-arrestin-2
KeywordsGPCR / arrestin / signaling / SIGNALING PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


oculomotor nerve development / positive regulation of mesenchymal stem cell migration / C-X-C chemokine binding / angiotensin receptor binding / C-X-C chemokine receptor activity / desensitization of G protein-coupled receptor signaling pathway / C-C chemokine receptor activity / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / chemokine-mediated signaling pathway / C-C chemokine binding ...oculomotor nerve development / positive regulation of mesenchymal stem cell migration / C-X-C chemokine binding / angiotensin receptor binding / C-X-C chemokine receptor activity / desensitization of G protein-coupled receptor signaling pathway / C-C chemokine receptor activity / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / chemokine-mediated signaling pathway / C-C chemokine binding / G protein-coupled receptor internalization / inositol hexakisphosphate binding / Chemokine receptors bind chemokines / scavenger receptor activity / phosphatidylinositol-3,4,5-trisphosphate binding / positive regulation of receptor internalization / endocytic vesicle / vasculogenesis / coreceptor activity / clathrin-coated pit / phosphatidylinositol binding / cell chemotaxis / calcium-mediated signaling / recycling endosome / receptor internalization / protein transport / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / angiogenesis / early endosome / positive regulation of ERK1 and ERK2 cascade / endosome / cell adhesion / immune response / external side of plasma membrane / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / cell surface / signal transduction / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Atypical chemokine receptor 3 / : / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain ...Atypical chemokine receptor 3 / : / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin-like, C-terminal / 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) / Immunoglobulin E-set
Similarity search - Domain/homology
Atypical chemokine receptor 3 / Beta-arrestin-2
Similarity search - Component
Biological speciesBos taurus (domestic cattle) / synthetic construct (others) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsChen Q / Tesmer JJG
Funding support United States, 12 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA254402 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM117372 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI161880 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA221289 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA023168 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM137505 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL071818 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM151033 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA023168 United States
Walther Cancer Foundation United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM151033 United States
Ralph W. and Grace M. Showalter Research Trust United States
CitationJournal: Nature / Year: 2025
Title: Effect of phosphorylation barcodes on arrestin binding to a chemokine receptor.
Authors: Qiuyan Chen / Christopher T Schafer / Somnath Mukherjee / Kai Wang / Martin Gustavsson / James R Fuller / Katelyn Tepper / Thomas D Lamme / Yasmin Aydin / Parth Agrawal / Genki Terashi / Xin- ...Authors: Qiuyan Chen / Christopher T Schafer / Somnath Mukherjee / Kai Wang / Martin Gustavsson / James R Fuller / Katelyn Tepper / Thomas D Lamme / Yasmin Aydin / Parth Agrawal / Genki Terashi / Xin-Qiu Yao / Daisuke Kihara / Anthony A Kossiakoff / Tracy M Handel / John J G Tesmer /
Abstract: Unique phosphorylation 'barcodes' installed in different regions of an active seven-transmembrane receptor by different G-protein-coupled receptor (GPCR) kinases (GRKs) have been proposed to promote ...Unique phosphorylation 'barcodes' installed in different regions of an active seven-transmembrane receptor by different G-protein-coupled receptor (GPCR) kinases (GRKs) have been proposed to promote distinct cellular outcomes, but it is unclear whether or how arrestins differentially engage these barcodes. Here, to address this, we developed an antigen-binding fragment (Fab7) that recognizes both active arrestin2 (β-arrestin1) and arrestin3 (β-arrestin2) without interacting with bound receptor polypeptides. We used Fab7 to determine the structures of both arrestins in complex with atypical chemokine receptor 3 (ACKR3) phosphorylated in different regions of its C-terminal tail by either GRK2 or GRK5 (ref. ). The GRK2-phosphorylated ACKR3 resulted in more heterogeneous 'tail-mode' assemblies, whereas phosphorylation by GRK5 resulted in more rigid 'ACKR3-adjacent' assemblies. Unexpectedly, the finger loops of both arrestins engaged the micelle surface rather than the receptor intracellular pocket, with arrestin3 being more dynamic, partly because of its lack of a membrane-anchoring motif. Thus, both the region of the barcode and the arrestin isoform involved can alter the structure and dynamics of GPCR-arrestin complexes, providing a possible mechanistic basis for unique downstream cellular effects, such as the efficiency of chemokine scavenging and the robustness of arrestin binding in ACKR3.
History
DepositionJan 6, 2024-
Header (metadata) releaseJan 22, 2025-
Map releaseJan 22, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_43277.png

Downloads & links

-
Map

FileDownload / File: emd_43277.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 320 pix.
= 337.28 Å		1.05 Å/pix.
x 320 pix.
= 337.28 Å		1.05 Å/pix.
x 320 pix.
= 337.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.054 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.126
Minimum - Maximum-1.2170221 - 1.8153596
Average (Standard dev.)-0.0001849145 (±0.019624734)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 337.28 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_43277_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_43277_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : human ACKR3 phosphorylated by GRK5 in complex with Arrestin3

EntireName: human ACKR3 phosphorylated by GRK5 in complex with Arrestin3
Components
  • Complex: human ACKR3 phosphorylated by GRK5 in complex with Arrestin3
    • Protein or peptide: Fab7 heavy chain
    • Protein or peptide: Fab7 light chain
    • Protein or peptide: Atypical chemokine receptor 3
    • Protein or peptide: Beta-arrestin-2

-
Supramolecule #1: human ACKR3 phosphorylated by GRK5 in complex with Arrestin3

SupramoleculeName: human ACKR3 phosphorylated by GRK5 in complex with Arrestin3
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bos taurus (domestic cattle)

-
Macromolecule #1: Fab7 heavy chain

MacromoleculeName: Fab7 heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 25.720758 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EISEVQLVES GGGLVQPGGS LRLSCAASGF NVSSSYIHWV RQAPGKGLEW VASISSYYGY TYYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARKSMYHRGW GWLSWVYGAM DYWGQGTLVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP ...String:
EISEVQLVES GGGLVQPGGS LRLSCAASGF NVSSSYIHWV RQAPGKGLEW VASISSYYGY TYYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARKSMYHRGW GWLSWVYGAM DYWGQGTLVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP VTVSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK KVEPKSCDKT HT

-
Macromolecule #2: Fab7 light chain

MacromoleculeName: Fab7 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 23.471031 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQSYYYPITF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQSYYYPITF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

-
Macromolecule #3: Atypical chemokine receptor 3

MacromoleculeName: Atypical chemokine receptor 3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.356367 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GAPDLHLFDY SEPGNFSDIS WPCNSSDCIV VDTVMCPNMP NKSVLLYTLS FIYIFIFVIG MIANSVVVWV NIQAKTTGYD THCYILNLA IADLWVVLTI PVWVVSLVQH NQWPMGELTC KVTHLIFSIN LFGSIFFLTC MSVDRYLSIT YFTNTPSSRK K MVRRVVCI ...String:
GAPDLHLFDY SEPGNFSDIS WPCNSSDCIV VDTVMCPNMP NKSVLLYTLS FIYIFIFVIG MIANSVVVWV NIQAKTTGYD THCYILNLA IADLWVVLTI PVWVVSLVQH NQWPMGELTC KVTHLIFSIN LFGSIFFLTC MSVDRYLSIT YFTNTPSSRK K MVRRVVCI LVWLLAFCVS LPDTYYLKTV TSASNNETYC RSFYPEHSIK EWLIGMELVS VVLGFAVPFS IIAVFYFLLA RA ISASSDQ EKHSSRKIIF SYVVVFLVCW LPYHVAVLLD IFSILHYIPF TCRLEHALFT ALHVTQCLSL VHCCVNPVLY SFI NRNYRY ELMKAFIFKY SAK(TPO)GL(TPO)KLI DASRVSETEY SALEQSTKGR PLEVLFQGPH HHHHHHHHHD YKDDDD K

UniProtKB: Atypical chemokine receptor 3

-
Macromolecule #4: Beta-arrestin-2

MacromoleculeName: Beta-arrestin-2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 44.863176 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGEKPGTRVF KKSSPNCKLT VYLGKRDFVD HLDKVDPVDG VVLVDPDYLK DRKVFVTLTC AFRYGREDLD VLGLSFRKDL FIANYQAFP PTPNPPRPPT RLQERLLRKL GQHAHPFFFT IPQNLPCSVT LQPGPEDTGK ACGVDFEIRA FCAKSLEEKS H KRNSVRLV ...String:
MGEKPGTRVF KKSSPNCKLT VYLGKRDFVD HLDKVDPVDG VVLVDPDYLK DRKVFVTLTC AFRYGREDLD VLGLSFRKDL FIANYQAFP PTPNPPRPPT RLQERLLRKL GQHAHPFFFT IPQNLPCSVT LQPGPEDTGK ACGVDFEIRA FCAKSLEEKS H KRNSVRLV IRKVQFAPEK PGPQPSAETT RHFLMSDRSL HLEASLDKEL YYHGEPLNVN VHVTNNSTKT VKKIKVSVRQ YA DICLFST AQYKCPVAQV EQDDQVSPSS TFCKVYTITP LLSNNREKRG LALDGKLKHE DTNLASSTIV KEGANKEVLG ILV SYRVKV KLVVSRGGLL GDLASSDVSV ELPFVLMHPK PHDHIALPRP QSAVPETDAP VDTNLIEFET NYATDDDIVF EDFA

UniProtKB: Beta-arrestin-2

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.7 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 56.0 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: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 214953
Initial angle assignmentType: COMMON LINE / Software - Name: cryoSPARC
Final angle assignmentType: COMMON LINE / Software - Name: cryoSPARC
FSC plot (resolution estimation)

+
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