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8jps

Structure of Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 in complex with the chemokine, CCL7 (Composite map)

Method: ELECTRON MICROSCOPY Dmax: 124.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Atypical chemokine receptor 1

Homo sapiens

UniProt Q16570

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 46–312 Chain B； UniProt 46–312 Not recorded C-C motif chemokine 7 × 2 （P80098） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.65 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8JPS Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4NUU Heterotrimer structure of Region II from Plasmodium vivax Duffy Binding Protein (PvDBP) bound to the ectodomain of the Duffy Antigen Receptor for Chemokines (DARC) Deposited 2013-12-04 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 14–43（30 aa） Fragment：unp residues 14-43
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；0.1 M HEPES and 20% (w/v) polyethylene glycol 6000, VAPOR DIFFUSION, HANGING DROP, temperature 290K, pH 7.4
Resolution 1.95 Å R-free 0.202
4NUV Heterotetramer structure of Region II from Plasmodium vivax Duffy Binding Protein (PvDBP) bound to the ectodomain of the Duffy Antigen Receptor for Chemokines (DARC) Deposited 2013-12-04 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 14–43（30 aa） Fragment：unp residues 14-43
Chain D 14–43（30 aa） Fragment：unp residues 14-43
Not recorded GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；0.1 M HEPES and 20% (w/v) polyethylene glycol 6000, VAPOR DIFFUSION, HANGING DROP, temperature 290K, pH 7.4
Resolution 2.60 Å R-free 0.233
4NUV Heterotetramer structure of Region II from Plasmodium vivax Duffy Binding Protein (PvDBP) bound to the ectodomain of the Duffy Antigen Receptor for Chemokines (DARC) Deposited 2013-12-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 14–43（30 aa） Fragment：unp residues 14-43
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；0.1 M HEPES and 20% (w/v) polyethylene glycol 6000, VAPOR DIFFUSION, HANGING DROP, temperature 290K, pH 7.4
Resolution 2.60 Å R-free 0.233
4NUV Heterotetramer structure of Region II from Plasmodium vivax Duffy Binding Protein (PvDBP) bound to the ectodomain of the Duffy Antigen Receptor for Chemokines (DARC) Deposited 2013-12-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 14–43（30 aa） Fragment：unp residues 14-43
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；0.1 M HEPES and 20% (w/v) polyethylene glycol 6000, VAPOR DIFFUSION, HANGING DROP, temperature 290K, pH 7.4
Resolution 2.60 Å R-free 0.233
7P93 Crystal Structure of leukotoxin LukE from Staphylococcus aureus in complex with a sulfated ACKR1 N-terminal peptide Deposited 2021-07-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 34–46（13 aa）
Chain M 34–46（13 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293.15 K；0.1 M Imidazole.HCl pH 8.0, 30% (w/v) MPD, 10% (w/v) PEG 4000
Resolution 1.55 Å R-free 0.204
8YNF Structure of Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 in complex with the chemokine, CXCL8 Deposited 2024-03-11 Different construct Different oligomeric state Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 2–336（335 aa）
Chain B 2–336（335 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.65 Å

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ACKR1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–267； UniProt 46–312 Author chain B； PDBConstruct 1–267； UniProt 46–312

C-C motif chemokine 7

Homo sapiens

UniProt P80098

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain C； UniProt 31–93 Chain D； UniProt 31–93 Not recorded Atypical chemokine receptor 1 × 2 （Q16570） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.65 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8JPS Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BO0 MONOCYTE CHEMOATTRACTANT PROTEIN-3, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1998-08-10 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–99（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.1；303 K
Resolution not provided
1NCV DETERMINATION CC-CHEMOKINE MCP-3, NMR, 7 STRUCTURES Deposited 1997-02-05 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 24–99（76 aa）
Chain B 24–99（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5；290 K
Resolution not provided
4ZKC The chemokine binding protein of orf virus complexed with CCL7 Deposited 2015-04-30 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 24–99（76 aa） Fragment：UNP residues 24-99
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；289 K；0.2M potassium sodium tartrate tetrahydrate, 0.1M sodium citrate tribasic dihydrate pH5.6, 2.0M ammonium citrate
Resolution 3.15 Å R-free 0.327
7S58 Crystal Structure of the tick evasin EVA-P974 complexed to human chemokine CCL7 Deposited 2021-09-10 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 24–99（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.1 M BIS-TRIS 6.5 pH (Buffer) 25 %w/v PEG 3350 (Precipitant)
Resolution 1.82 Å R-free 0.244
7S58 Crystal Structure of the tick evasin EVA-P974 complexed to human chemokine CCL7 Deposited 2021-09-10 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 24–99（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.1 M BIS-TRIS 6.5 pH (Buffer) 25 %w/v PEG 3350 (Precipitant)
Resolution 1.82 Å R-free 0.244
7S58 Crystal Structure of the tick evasin EVA-P974 complexed to human chemokine CCL7 Deposited 2021-09-10 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain J 24–99（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.1 M BIS-TRIS 6.5 pH (Buffer) 25 %w/v PEG 3350 (Precipitant)
Resolution 1.82 Å R-free 0.244
7S58 Crystal Structure of the tick evasin EVA-P974 complexed to human chemokine CCL7 Deposited 2021-09-10 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 24–99（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.1 M BIS-TRIS 6.5 pH (Buffer) 25 %w/v PEG 3350 (Precipitant)
Resolution 1.82 Å R-free 0.244
7S59 Crystal structure of the tick evasin EVA-P974 complexed to a chimera made of human chemokines CCL7 and CCL8 Deposited 2021-09-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain 2 39–99（61 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.1 M TRIS 8.5 pH (Buffer) 2 M (NH4)2SO4 (Precipitant)
Resolution 2.39 Å R-free 0.268
7S59 Crystal structure of the tick evasin EVA-P974 complexed to a chimera made of human chemokines CCL7 and CCL8 Deposited 2021-09-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain 4 39–99（61 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.1 M TRIS 8.5 pH (Buffer) 2 M (NH4)2SO4 (Precipitant)
Resolution 2.39 Å R-free 0.268
7SCU Crystal Structure of the Tick Evasin EVA-AAM1001 Complexed to Human Chemokine CCL7 Deposited 2021-09-29 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 24–99（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Na Acet 4.6 pH (Buffer),2 M NaCl (Precipitant)
Resolution 1.86 Å R-free 0.210
8FJ3 Crystal Structure of the Tick Evasin EVA-AAM1001 Complexed to Human Chemokine CCL7(Y13A) Deposited 2022-12-19 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 24–99（76 aa）
Mutation：Y13A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；2 M NH2SO4, 0.1 Na acetate, pH 4.8
Resolution 2.07 Å R-free 0.229
8FK6 Crystal Structure of the Tick Evasin EVA-AAM1001(Y44A) Complexed to Human Chemokine CCL7 Deposited 2022-12-20 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 24–99（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；2 M Ammonium sulfate
Resolution 1.74 Å R-free 0.223
8FK8 Crystal Structure of the Tick Evasin EVA-AAM1001(L39P) Complexed to Human Chemokine CCL7 Deposited 2022-12-20 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 24–99（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；2 M Ammonium sulfate
Resolution 1.96 Å R-free 0.263

9 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CCL7_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 1–63； UniProt 31–93 Author chain D； PDBConstruct 1–63； UniProt 31–93

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 8jps

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8jps
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8jps
Deposition date deposition_date2023-06-12
Structure title titleStructure of Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 in complex with the chemokine, CCL7 (Composite map)
Keywords keywordsGPCR, SIGNALING PROTEIN, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier32.93 Å
Radius of gyration Rg (electron density) rg_electron32.30 Å
Forward intensity I(0) i059766100.00
Molecular weight molecular_weight65531.0 kDa
Excluded volume excluded_volume83976 ų
Envelope volume envelope_volume117940 ų
Hydration-shell volume shell_volume31863 ų
Envelope diameter envelope_diameter131.8 Å
Shell Rg shell_rg36.46 Å
Envelope Rg envelope_rg33.63 Å
Shape Rg shape_rg32.28 Å
Total Rg total_rg32.77 Å
Total atoms total_atoms4616
Residues n_residues640
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax124.3 Å
Rg (real space) rg_real33.41 Å
Rg uncertainty (real space) rg_real_error1.58 Å
I(0) (real space) i0_real5.9770e+07
I(0) uncertainty (real space) i0_real_error1.0530e+06
Rg (reciprocal space) rg_reciprocal33.20 Å
I(0) (reciprocal space) i0_reciprocal59760000.0000
Solution quality estimate total_estimate0.7927
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary36.3 Å
Skewness Skewness skewness0.670
Kurtosis Kurtosis kurtosis0.287
Angular range angular_range— – 0.2400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5996000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.642; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.607; Smooth: 0.767
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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9. Files and Curves (10)