SAXSdb — 4nuv

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Duffy receptor

Plasmodium vivax

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Duffy antigen/chemokine receptor × 2 （Q16570） GLYCEROL × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Duffy antigen/chemokine receptor × 1 （Q16570） GLYCEROL × 1 water × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Duffy antigen/chemokine receptor × 1 （Q16570） GLYCEROL × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Duffy receptor × 2 （P22290） GLYCEROL × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Duffy receptor × 1 （P22290） GLYCEROL × 1 water × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Duffy receptor × 1 （P22290） GLYCEROL × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ACKR1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 5–34； UniProt 14–43 Author chain D； PDBConstruct 5–34； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4nuv
Deposition date deposition_date	2013-12-04
Structure title title	Heterotetramer 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 method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

4nuv__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4nuv__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4nuv__assembly_3__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	22.81 Å
Rg (electron density)	22.34 Å
Total Rg	23.16 Å
Atom count	5030
Residues	300
Excluded volume	45009 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4nuv__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4nuv__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4nuv__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Duffy receptor
Molecular weight formula_weight	37610.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	10227

ASNTVMKNCNYKRKRRERDWDCNTKKDVCIPDRRYQLCMKELTNLVNNTDTNFHRDITFRKLYLKRKLIYDAAVEGDLLLKLNNYRYNKDFCKDIRWSLGDFGDIIMGTDMEGIGYSKVVENNLRSIFGTDEKAQQRRKQWWNESKAQIWTAMMYSVKKRLKGNFIWICKLNVAVNIEPQIYRWIREWGRDYVSELPTEVQKLKEKCDGKINYTDKKVCKVPPCQNACKSYDQWITRKKNQWDVLSNKFISVKNAEKVQTAGIVTPYDILKQELDEFNEVAFENEINKRDGAYIELCVCSVEEAKKNTQEVVTNVDN

Source Source

Source organism organism	Plasmodium vivax
NCBI taxonomy ID ncbi_taxonomy_id	126793
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Duffy antigen/chemokine receptor
Molecular weight formula_weight	3628.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

GPTGTENSSQLDFEDVWNSSYGVNDSFPDGDYGA

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	52

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4nuva_
Class class	a — All alpha proteins
Fold Fold fold	a.264 — Duffy binding domain-like
Superfamily Superfamily superfamily	a.264.1 — Duffy binding domain-like
Family Family family	a.264.1.1 — Duffy binding domain

Domain ID domain_id	d4nuvb_
Class class	a — All alpha proteins
Fold Fold fold	a.264 — Duffy binding domain-like
Superfamily Superfamily superfamily	a.264.1 — Duffy binding domain-like
Family Family family	a.264.1.1 — Duffy binding domain

CATH v4.4 (4 domains)

Domain ID domain_id	4nuvA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1310 — 5 helical Cullin repeat like
Homologous superfamily homologous superfamily	20 — Duffy-antigen binding domain

Domain ID domain_id	4nuvA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	830 —

Domain ID domain_id	4nuvB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1310 — 5 helical Cullin repeat like
Homologous superfamily homologous superfamily	20 — Duffy-antigen binding domain

Domain ID domain_id	4nuvB02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	830 —

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Unit-cell length a length_a	37.287 Å
Unit-cell length b length_b	59.391 Å
Unit-cell length c length_c	91.395 Å
Unit-cell angle α angle_alpha	103.14 °
Unit-cell angle β angle_beta	91.04 °
Unit-cell angle γ angle_gamma	100.31 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	19.904 Å
R factor r_factor	0.1854
R_work r_work	0.1829
R_free r_free	0.2328

Heterotetramer structure of Region II from Plasmodium vivax Duffy Binding Protein (PvDBP) bound to the ectodomain of the Duffy Antigen Receptor for Chemokines (DARC)

1. Protein Identity and Related Structures Protein Identity & Related Structures

Duffy receptor

State in the Current Structure

Other States of the Same Protein in the Database

Duffy antigen/chemokine receptor

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4nuv__assembly_3__model_1

4nuv__assembly_3__model_1 | I(q)

4nuv__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Heterotetramer structure of Region II from Plasmodium vivax Duffy Binding Protein (PvDBP) bound to the ectodomain of the Duffy Antigen Receptor for Chemokines (DARC)

1. Protein Identity and Related Structures Protein Identity & Related Structures

Duffy receptor

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Duffy antigen/chemokine receptor

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4nuv__assembly_3__model_1

4nuv__assembly_3__model_1 | I(q)

4nuv__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)