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- EMDB-76037: Structure of human CCR4 in complex with AZD2098 -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-76037
TitleStructure of human CCR4 in complex with AZD2098
Map data
Sample
  • Complex: CCR4-BRIL-Fab-AZD2098
    • Protein or peptide: C-C chemokine receptor type 4,Soluble cytochrome b562
    • Protein or peptide: Anti-BRIL Fab heavy chain
    • Protein or peptide: Anti-BRIL Fab light chain
  • Ligand: 2,3-dichloro-N-(3-methoxypyrazin-2-yl)benzene-1-sulfonamide
KeywordsG protein coupled receptor / MEMBRANE PROTEIN
Function / homology
Function and homology information


tolerance induction / chemokine receptor activity / interneuron migration / C-C chemokine receptor activity / C-C chemokine binding / Chemokine receptors bind chemokines / homeostasis of number of cells / cell chemotaxis / calcium-mediated signaling / electron transport chain ...tolerance induction / chemokine receptor activity / interneuron migration / C-C chemokine receptor activity / C-C chemokine binding / Chemokine receptors bind chemokines / homeostasis of number of cells / cell chemotaxis / calcium-mediated signaling / electron transport chain / chemotaxis / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / periplasmic space / electron transfer activity / immune response / iron ion binding / inflammatory response / external side of plasma membrane / heme binding / plasma membrane
Similarity search - Function
CC chemokine receptor 4 / Chemokine receptor family / : / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like ...CC chemokine receptor 4 / Chemokine receptor family / : / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile.
Similarity search - Domain/homology
Soluble cytochrome b562 / C-C chemokine receptor type 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.54 Å
AuthorsQi X / Zhou N / Wang R
Funding support United States, 2 items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT)RR230054 United States
Welch FoundationI-2253-20250403 United States
CitationJournal: To Be Published
Title: Structure of human CCR4 in complex with AZD2098
Authors: Qi X / Zhou N / Wang R
History
DepositionMar 12, 2026-
Header (metadata) releaseApr 1, 2026-
Map releaseApr 1, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76037.png

Downloads & links

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Map

FileDownload / File: emd_76037.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 360 pix.
= 265.68 Å		0.74 Å/pix.
x 360 pix.
= 265.68 Å		0.74 Å/pix.
x 360 pix.
= 265.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.738 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.166
Minimum - Maximum-0.0018039491 - 2.1460702
Average (Standard dev.)0.0006373173 (±0.018725894)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 265.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_76037_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_76037_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CCR4-BRIL-Fab-AZD2098

EntireName: CCR4-BRIL-Fab-AZD2098
Components
  • Complex: CCR4-BRIL-Fab-AZD2098
    • Protein or peptide: C-C chemokine receptor type 4,Soluble cytochrome b562
    • Protein or peptide: Anti-BRIL Fab heavy chain
    • Protein or peptide: Anti-BRIL Fab light chain
  • Ligand: 2,3-dichloro-N-(3-methoxypyrazin-2-yl)benzene-1-sulfonamide

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Supramolecule #1: CCR4-BRIL-Fab-AZD2098

SupramoleculeName: CCR4-BRIL-Fab-AZD2098 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: C-C chemokine receptor type 4,Soluble cytochrome b562

MacromoleculeName: C-C chemokine receptor type 4,Soluble cytochrome b562 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.283961 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MNPTDIADTT LDESIYSNYY LYESIPKPCT KEGIKAFGEL FLPPLYSLVF VFGLLGNSVV VLVLFKYKRL RSMTDVYLLN LAISDLLFV FSLPFWGYYA ADQWVFGLGL CKMISWMYLV GFYSGIFFVM LMSIDRYLAI VHAVFSLRAR TLTYGVITSL A TWSVAVFA ...String:
MNPTDIADTT LDESIYSNYY LYESIPKPCT KEGIKAFGEL FLPPLYSLVF VFGLLGNSVV VLVLFKYKRL RSMTDVYLLN LAISDLLFV FSLPFWGYYA ADQWVFGLGL CKMISWMYLV GFYSGIFFVM LMSIDRYLAI VHAVFSLRAR TLTYGVITSL A TWSVAVFA SLPGFLFSTC YTERNHTYCK TKYSLNSTTW KVLSSLEINI LGLVIPLGIM LFCYSMIIRT LQHARRQLAD LE DNWETLN DNLKVIEKAD NAAQVKDALT KMRAAALDAQ KATPPKLEDK SPDSPEMKDF RHGFDILVGQ IDDALKLANE GKV KEAQAA AEQLKTTRNA YIQKYLERAR STLNEKNKAV KMIFAVVVLF LGFWTPYNIV LFLETLVELE VLQDCTFERY LDYA IQATE TLAFVHCCLN PIIYFFLGEK FRKYILQLFK TCRGLFVLCQ YCGLLQIYSA DTPSSSYTQS TMDHDLHDAL

UniProtKB: C-C chemokine receptor type 4, Soluble cytochrome b562, C-C chemokine receptor type 4

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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: 24.321084 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EISEVQLVES GGGLVQPGGS LRLSCAASGF NVVDFSLHWV RQAPGKGLEW VAYISSSSGS TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARWGYWPGEP WWKAFDYWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW ...String:
EISEVQLVES GGGLVQPGGS LRLSCAASGF NVVDFSLHWV RQAPGKGLEW VAYISSSSGS TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARWGYWPGEP WWKAFDYWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKVEPK S

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Macromolecule #3: Anti-BRIL Fab light chain

MacromoleculeName: Anti-BRIL Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.353947 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYLYYSLVT FGQGTKVEIK RTVAAPSVFI FPPSDSQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ ...String:
SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYLYYSLVT FGQGTKVEIK RTVAAPSVFI FPPSDSQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ DSKDSTYSLS STLTLSKADY EKHKVYACEV THQGLSSPVT KSFNRG

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Macromolecule #4: 2,3-dichloro-N-(3-methoxypyrazin-2-yl)benzene-1-sulfonamide

MacromoleculeName: 2,3-dichloro-N-(3-methoxypyrazin-2-yl)benzene-1-sulfonamide
type: ligand / ID: 4 / Number of copies: 1 / Formula: A1DAN
Molecular weightTheoretical: 334.178 Da

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 138729
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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