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- PDB-11tl: Structure of human CCR4 in complex with GSK2239633A -

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Basic information

Entry
Database: PDB / ID: 11tl
TitleStructure of human CCR4 in complex with GSK2239633A
Components
  • Anti-BRIL Fab heavy chain
  • Anti-BRIL Fab light chain
  • C-C chemokine receptor type 4,Soluble cytochrome b562
KeywordsMEMBRANE PROTEIN / G protein coupled receptor
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)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsQi, X. / Zhou, N. / Wang, R.
Funding support United States, 2items
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 GSK2239633A
Authors: Qi, X. / Zhou, N. / Wang, R.
History
DepositionMar 12, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
R: C-C chemokine receptor type 4,Soluble cytochrome b562
H: Anti-BRIL Fab heavy chain
L: Anti-BRIL Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,5084
Polymers101,9593
Non-polymers5491
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein C-C chemokine receptor type 4,Soluble cytochrome b562 / C-C CKR-4 / CC-CKR-4 / CCR-4 / CCR4 / K5-5 / Cytochrome b-562


Mass: 54283.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: CCR4, CMKBR4, cybC / Production host: Homo sapiens (human) / References: UniProt: P51679, UniProt: P0ABE7
#2: Antibody Anti-BRIL Fab heavy chain


Mass: 24321.084 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody Anti-BRIL Fab light chain


Mass: 23353.947 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Chemical ChemComp-A1DAM / N-[(3-{[3-(5-chlorothiophene-2-sulfonamido)-4-methoxy-1H-indazol-1-yl]methyl}phenyl)methyl]-2-hydroxy-2-methylpropanamide


Mass: 549.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H25ClN4O5S2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: CCR4-BRIL-Fab-GSK2239633A / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
9PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 171380 / Symmetry type: POINT
RefinementHighest resolution: 3.9 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0045072
ELECTRON MICROSCOPYf_angle_d0.6536893
ELECTRON MICROSCOPYf_dihedral_angle_d6.907687
ELECTRON MICROSCOPYf_chiral_restr0.042773
ELECTRON MICROSCOPYf_plane_restr0.004848

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