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- PDB-4nuv: Heterotetramer structure of Region II from Plasmodium vivax Duffy... -

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Basic information

Entry
Database: PDB / ID: 4nuv
TitleHeterotetramer structure of Region II from Plasmodium vivax Duffy Binding Protein (PvDBP) bound to the ectodomain of the Duffy Antigen Receptor for Chemokines (DARC)
Components
  • Duffy antigen/chemokine receptor
  • Duffy receptor
Keywordsmembrane protein / cell invasion / Duffy Binding Like (DBL) Domain Fold / GPCR / Adhesion / Invasion / Red blood cell binding / Chemokine Binding / Duffy Antigen Receptor for Chemokines / Membrane / protein binding
Function / homology
Function and homology information


regulation of chemokine production / chemokine-mediated signaling pathway / C-C chemokine binding / Peptide ligand-binding receptors / defense response / G protein-coupled receptor activity / recycling endosome / transmembrane signaling receptor activity / signaling receptor activity / early endosome ...regulation of chemokine production / chemokine-mediated signaling pathway / C-C chemokine binding / Peptide ligand-binding receptors / defense response / G protein-coupled receptor activity / recycling endosome / transmembrane signaling receptor activity / signaling receptor activity / early endosome / host cell surface receptor binding / inflammatory response / identical protein binding / membrane / plasma membrane
Similarity search - Function
Duffy antigen/chemokine receptor / Duffy-antigen binding, C-terminal / Duffy-antigen binding, N-terminal / Duffy-antigen binding protein / Duffy binding protein N terminal / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #830 / Erythrocyte binding antigen 175, C-terminal / Erythrocyte binding antigen 175, C-terminal domain superfamily / Erythrocyte binding antigen 175 / Duffy-antigen binding domain ...Duffy antigen/chemokine receptor / Duffy-antigen binding, C-terminal / Duffy-antigen binding, N-terminal / Duffy-antigen binding protein / Duffy binding protein N terminal / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #830 / Erythrocyte binding antigen 175, C-terminal / Erythrocyte binding antigen 175, C-terminal domain superfamily / Erythrocyte binding antigen 175 / Duffy-antigen binding domain / 5 helical Cullin repeat like / Duffy-antigen binding / Duffy-antigen binding superfamily / Duffy binding domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Duffy receptor / Atypical chemokine receptor 1
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsTolia, N.H.
CitationJournal: Plos Pathog. / Year: 2014
Title: Red Blood Cell Invasion by Plasmodium vivax: Structural Basis for DBP Engagement of DARC.
Authors: Batchelor, J.D. / Malpede, B.M. / Omattage, N.S. / Dekoster, G.T. / Henzler-Wildman, K.A. / Tolia, N.H.
History
DepositionDec 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Mar 13, 2024Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Duffy receptor
B: Duffy receptor
C: Duffy antigen/chemokine receptor
D: Duffy antigen/chemokine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,6626
Polymers82,4774
Non-polymers1842
Water93752
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Duffy receptor
C: Duffy antigen/chemokine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3313
Polymers41,2392
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-7 kcal/mol
Surface area15660 Å2
MethodPISA
3
B: Duffy receptor
D: Duffy antigen/chemokine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3313
Polymers41,2392
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-7 kcal/mol
Surface area16010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.287, 59.391, 91.395
Angle α, β, γ (deg.)103.14, 91.04, 100.31
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Duffy receptor / Erythrocyte-binding protein


Mass: 37610.051 Da / Num. of mol.: 2 / Fragment: unp residues 211-525
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Strain: Salvador I / Gene: PVDR / Production host: Escherichia coli (E. coli) / References: UniProt: P22290
#2: Protein/peptide Duffy antigen/chemokine receptor / Atypical chemokine receptor 1 / Fy glycoprotein / GpFy / Glycoprotein D / Plasmodium vivax receptor


Mass: 3628.606 Da / Num. of mol.: 2 / Fragment: unp residues 14-43
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DARC, ACKR1, FY, GPD / Production host: Escherichia coli (E. coli) / References: UniProt: Q16570
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.59 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.1 M HEPES and 20% (w/v) polyethylene glycol 6000, VAPOR DIFFUSION, HANGING DROP, temperature 290K, pH 7.4

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Dec 20, 2011
RadiationMonochromator: Rosenbaum-Rock monochromator 1: high-resolution double-crystal sagittal focusing, Rosenbaum-Rock monochromator 2: double crystal, Rosenbaum-Rock vertical focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 23251 / Num. obs: 22139 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.6→2.7 Å / % possible all: 93.1

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Processing

Software
NameVersionClassification
Blu-IceICEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3RRC

3rrc


Resolution: 2.6→19.904 Å / SU ML: 0.32 / σ(F): 1.99 / Phase error: 25.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2328 1085 4.9 %Randomly selected 5%
Rwork0.1829 ---
obs0.1854 22121 95.14 %-
all-23251 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→19.904 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5041 0 12 52 5105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025232
X-RAY DIFFRACTIONf_angle_d0.5437030
X-RAY DIFFRACTIONf_dihedral_angle_d11.8612020
X-RAY DIFFRACTIONf_chiral_restr0.034732
X-RAY DIFFRACTIONf_plane_restr0.002893
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5918-2.70950.33921310.27472559X-RAY DIFFRACTION92
2.7095-2.8520.27591430.23862651X-RAY DIFFRACTION96
2.852-3.03010.27131450.20972672X-RAY DIFFRACTION98
3.0301-3.26310.2711260.19392674X-RAY DIFFRACTION97
3.2631-3.58980.24871310.18362669X-RAY DIFFRACTION96
3.5898-4.10520.18941370.16752605X-RAY DIFFRACTION94
4.1052-5.15720.20271350.15862622X-RAY DIFFRACTION95
5.1572-19.90480.23871370.17482584X-RAY DIFFRACTION93

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