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- PDB-8a44: Plasmodium vivax Duffy binding protein region II bound the DARC e... -

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Basic information

Entry
Database: PDB / ID: 8a44
TitlePlasmodium vivax Duffy binding protein region II bound the DARC ectodomain and monoclonal antibody DB1
Components
  • Atypical chemokine receptor 1
  • Duffy binding protein
  • Heavy chain of monoclonal antibody DB1
  • Light chain of monoclonal antibody DB1
KeywordsCELL ADHESION / Plasmodium vivax / malaria / reticulocyte invasion / Duffy binding protein / DARC / sulphotyrosine.
Function / homology
Function and homology information


chemokine binding / chemokine-mediated signaling pathway / G protein-coupled receptor activity / recycling endosome / early endosome / host cell surface receptor binding / inflammatory response / membrane
Similarity search - Function
Duffy antigen/chemokine receptor / Duffy-antigen binding / Duffy-antigen binding superfamily / Duffy binding domain / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Atypical chemokine receptor 1 / Duffy binding protein
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsMoskovitz, R. / Higgins, M.K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Nat Commun / Year: 2023
Title: Structural basis for DARC binding in reticulocyte invasion by Plasmodium vivax.
Authors: Moskovitz, R. / Pholcharee, T. / DonVito, S.M. / Guloglu, B. / Lowe, E. / Mohring, F. / Moon, R.W. / Higgins, M.K.
History
DepositionJun 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Duffy binding protein
B: Atypical chemokine receptor 1
C: Heavy chain of monoclonal antibody DB1
D: Light chain of monoclonal antibody DB1


Theoretical massNumber of molelcules
Total (without water)88,8534
Polymers88,8534
Non-polymers00
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8390 Å2
ΔGint-46 kcal/mol
Surface area35080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.204, 97.949, 287.987
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Duffy binding protein


Mass: 35105.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Gene: dbpII / Production host: Homo sapiens (human) / References: UniProt: A0A7M1C9Q0
#2: Protein Atypical chemokine receptor 1 / Duffy antigen/chemokine receptor


Mass: 6512.702 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DARC / Production host: Homo sapiens (human) / References: UniProt: A0A1P8P1S7
#3: Antibody Heavy chain of monoclonal antibody DB1


Mass: 24012.893 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody Light chain of monoclonal antibody DB1


Mass: 23221.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 4.14 Å3/Da / Density % sol: 70.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 15% w/v jeffamine D-2003 10% v/v ethanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS EIGER2 S 4M / Detector: PIXEL / Date: Dec 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.49→72 Å / Num. obs: 52982 / % possible obs: 100 % / Redundancy: 1.9 % / CC1/2: 0.993 / Rpim(I) all: 0.07 / Net I/σ(I): 5.7
Reflection shellResolution: 2.49→2.57 Å / Num. unique obs: 4488 / CC1/2: 0.463 / Rpim(I) all: 0.735

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Processing

Software
NameVersionClassification
BUSTERrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6R2S

6r2s


Resolution: 2.49→72 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2246 2632 4.98 %
Rwork0.1962 --
obs0.1977 52884 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 170.32 Å2 / Biso mean: 67.6063 Å2 / Biso min: 36.27 Å2
Refinement stepCycle: final / Resolution: 2.49→72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6008 0 0 250 6258
Biso mean---59.19 -
Num. residues----760
Refinement TLS params.Method: refined / Origin x: -20.0781 Å / Origin y: 12.5177 Å / Origin z: -44.4272 Å
111213212223313233
T0.4276 Å20.0159 Å20.0351 Å2-0.48 Å20.0761 Å2--0.42 Å2
L0.819 °2-0.7186 °20.7108 °2-1.0534 °2-0.7508 °2--1.1066 °2
S-0.0849 Å °-0.1452 Å °0.0244 Å °0.1533 Å °0.0216 Å °-0.037 Å °0.039 Å °0.0679 Å °0.0561 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|216-508}A216 - 508
2X-RAY DIFFRACTION1{B|19-47}B19 - 47
3X-RAY DIFFRACTION1{C|20-244}C20 - 244
4X-RAY DIFFRACTION1{D|21-233}D21 - 233
5X-RAY DIFFRACTION1{A|601-646}A601 - 646
6X-RAY DIFFRACTION1{B|101-101}B101
7X-RAY DIFFRACTION1{C|301-406}C301 - 406
8X-RAY DIFFRACTION1{D|302-397}D302 - 397

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