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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)

Method: X-RAY DIFFRACTION Dmax: 153.2 Å Quality: SUSPICIOUS
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Duffy receptor

Plasmodium vivax

UniProt P22290

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 211–525 Fragment：unp residues 211-525 Duffy antigen/chemokine receptor × 1 （Q16570） 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
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 211–525 Fragment：unp residues 211-525 No other associated polymer 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

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 4NUU Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3RRC Crystal Structure of Region II from Plasmodium vivax Duffy Binding Protein Deposited 2011-04-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 211–525（315 aa） Fragment：Region II (UNP residues 211-525)
Chain B 211–525（315 aa） Fragment：Region II (UNP residues 211-525)
Not recorded EDO 1,2-ETHANEDIOL × 11 PO4 PHOSPHATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；290 K；0.1 M ammonium phosphate, 23% polyethylene glycol 3350, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 1.95 Å R-free 0.241
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 structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 211–525（315 aa） Fragment：unp residues 211-525
Chain B 211–525（315 aa） Fragment：unp residues 211-525
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 ligand/ion Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 211–525（315 aa） Fragment：unp residues 211-525
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 ligand/ion Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 211–525（315 aa） Fragment：unp residues 211-525
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
4YFS Structure of the synthetic Duffy Binding Protein (DBP) antigen DEKnull relevant for malaria vaccine design Deposited 2015-02-25 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 198–521（324 aa） Fragment：UNP RESIDUES 198-521
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M di-sodium tartrate, 20% PEG 3350, and microseeded into 0.2 M lithium chloride, 20% PEG 3350
Resolution 2.10 Å R-free 0.259
5F3J Crystal structure of DBP in complex with inhibitory monoclonal antibody 2D10 Deposited 2015-12-02 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 211–525（315 aa） Fragment：UNP residues 211-525
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；290 K；1% w/v tryptone, 50 mM HEPES sodium salt pH 7.0, 12% w/v PEG 3,350
Resolution 4.00 Å R-free 0.300
5F3J Crystal structure of DBP in complex with inhibitory monoclonal antibody 2D10 Deposited 2015-12-02 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 211–525（315 aa） Fragment：UNP residues 211-525
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；290 K；1% w/v tryptone, 50 mM HEPES sodium salt pH 7.0, 12% w/v PEG 3,350
Resolution 4.00 Å R-free 0.300
6R2S The structure of Plasmodium vivax Duffy binding protein (PvDBP) bound to human antibody DB9 Deposited 2019-03-18 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 211–508（298 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；45 % v/v polypropylene glycol 400, 10% v/v ethanol
Resolution 3.04 Å R-free 0.238
9EZE Structure of subdomain 3 of the Plasmodium vivx Duffy binding protein (PvDBP) bound to human antibody DB9 Deposited 2024-04-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 211–508（298 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M ammonium acetate, 0.1M sodium acetate pH 4.0, 15% PEG 4000
Resolution 1.55 Å R-free 0.223
9EZE Structure of subdomain 3 of the Plasmodium vivx Duffy binding protein (PvDBP) bound to human antibody DB9 Deposited 2024-04-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 211–508（298 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M ammonium acetate, 0.1M sodium acetate pH 4.0, 15% PEG 4000
Resolution 1.55 Å R-free 0.223

6 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PVDR_PLAVS
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–317； UniProt 211–525 Author chain B； PDBConstruct 3–317； UniProt 211–525

Duffy antigen/chemokine receptor

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 14–43 Fragment：unp residues 14-43 Duffy receptor × 1 （P22290） 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

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 4NUU Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
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 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 ligand/ion 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 ligand/ion 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 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
8JPS Structure of Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 in complex with the chemokine, CCL7 (Composite map) Deposited 2023-06-12 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 46–312（267 aa）
Chain B 46–312（267 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
8YNF Structure of Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 in complex with the chemokine, CXCL8 Deposited 2024-03-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics 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 2
Chains and sequence ranges Author chain C； PDBConstruct 3–32； UniProt 14–43

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 4nuu

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4nuu
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4nuu
Deposition date deposition_date2013-12-04
Structure title titleHeterotrimer structure of Region II from Plasmodium vivax Duffy Binding Protein (PvDBP) bound to the ectodomain of the Duffy Antigen Receptor for Chemokines (DARC)
Keywords keywords;Duffy Binding Like (DBL) Domain Fold, GPCR, Adhesion, Invasion, Red blood cell binding, Chemokine Binding, Duffy Antigen Receptor for Chemokines, Membrane, membrane protein, protein binding, cell invasion ;; membrane protein, cell invasion
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier37.06 Å
Radius of gyration Rg (electron density) rg_electron37.82 Å
Forward intensity I(0) i076983000.00
Molecular weight molecular_weight69736.0 kDa
Excluded volume excluded_volume87267 ų
Envelope volume envelope_volume113840 ų
Hydration-shell volume shell_volume29050 ų
Envelope diameter envelope_diameter162.8 Å
Shell Rg shell_rg36.68 Å
Envelope Rg envelope_rg38.68 Å
Shape Rg shape_rg37.74 Å
Total Rg total_rg38.00 Å
Total atoms total_atoms9747
Residues n_residues586
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 dmax153.2 Å
Rg (real space) rg_real38.00 Å
Rg uncertainty (real space) rg_real_error2.77 Å
I(0) (real space) i0_real7.6980e+07
I(0) uncertainty (real space) i0_real_error1.6300e+06
Rg (reciprocal space) rg_reciprocal37.41 Å
I(0) (reciprocal space) i0_reciprocal76940000.0000
Solution quality estimate total_estimate0.4527
Solution quality rating solution_quality SUSPICIOUS a SUSPICIOUS solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.9 Å
Skewness Skewness skewness0.764
Kurtosis Kurtosis kurtosis0.037
Angular range angular_range— – 0.2150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10420000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.144; Stabil: 1.000; Sysdev: 0.159; Positv: 1.000; Valcen: 0.015; Smooth: 0.957
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd4nuua1
Class classa — All alpha proteins
Fold Fold folda.264 — Duffy binding domain-like
Superfamily Superfamily superfamilya.264.1 — Duffy binding domain-like
Family Family familya.264.1.1 — Duffy binding domain
Domain ID domain_idd4nuua2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4nuub1
Class classa — All alpha proteins
Fold Fold folda.264 — Duffy binding domain-like
Superfamily Superfamily superfamilya.264.1 — Duffy binding domain-like
Family Family familya.264.1.1 — Duffy binding domain
Domain ID domain_idd4nuub2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id4nuuA01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1310 — 5 helical Cullin repeat like
Homologous superfamily homologous superfamily20 — Duffy-antigen binding domain
Domain ID domain_id4nuuA02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily830 —
Domain ID domain_id4nuuB01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1310 — 5 helical Cullin repeat like
Homologous superfamily homologous superfamily20 — Duffy-antigen binding domain
Domain ID domain_id4nuuB02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily830 —
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8. Citations (1)

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9. Files and Curves (10)