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- PDB-6r2s: The structure of Plasmodium vivax Duffy binding protein (PvDBP) b... -

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Basic information

Entry
Database: PDB / ID: 6r2s
TitleThe structure of Plasmodium vivax Duffy binding protein (PvDBP) bound to human antibody DB9
Components
  • Antibody DB9 heavy chain
  • Antibody DB9 light chain
  • Duffy receptor
KeywordsIMMUNE SYSTEM / Plasmodium vivax / Invasion / Broadly-neutralising human monoclonal antibody
Function / homology
Function and homology information


host cell surface receptor binding / membrane / identical protein binding
Similarity search - Function
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, 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 / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Plasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.04 Å
AuthorsBarber, N.M. / Higgins, M.K.
Funding support1items
OrganizationGrant numberCountry
Wellcome Trust101020/Z/13/Z
CitationJournal: Nat Microbiol / Year: 2019
Title: Structural basis for inhibition of Plasmodium vivax invasion by a broadly neutralizing vaccine-induced human antibody.
Authors: Rawlinson, T.A. / Barber, N.M. / Mohring, F. / Cho, J.S. / Kosaisavee, V. / Gerard, S.F. / Alanine, D.G.W. / Labbe, G.M. / Elias, S.C. / Silk, S.E. / Quinkert, D. / Jin, J. / Marshall, J.M. ...Authors: Rawlinson, T.A. / Barber, N.M. / Mohring, F. / Cho, J.S. / Kosaisavee, V. / Gerard, S.F. / Alanine, D.G.W. / Labbe, G.M. / Elias, S.C. / Silk, S.E. / Quinkert, D. / Jin, J. / Marshall, J.M. / Payne, R.O. / Minassian, A.M. / Russell, B. / Renia, L. / Nosten, F.H. / Moon, R.W. / Higgins, M.K. / Draper, S.J.
History
DepositionMar 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 21, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Sep 4, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antibody DB9 light chain
B: Antibody DB9 heavy chain
C: Duffy receptor


Theoretical massNumber of molelcules
Total (without water)90,5643
Polymers90,5643
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-24 kcal/mol
Surface area33560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.560, 173.560, 169.730
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Antibody Antibody DB9 light chain


Mass: 25440.494 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Antibody DB9 heavy chain


Mass: 29428.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein Duffy receptor / Erythrocyte-binding protein


Mass: 35695.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (strain Salvador I) (eukaryote)
Strain: Salvador I / Gene: PVDR / Production host: Escherichia coli (E. coli) / References: UniProt: P22290

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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: 4.07 Å3/Da / Density % sol: 69.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 45 % v/v polypropylene glycol 400, 10% v/v ethanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3→42.04 Å / Num. obs: 30707 / % possible obs: 100 % / Redundancy: 19.6 % / Biso Wilson estimate: 109.78 Å2 / Net I/σ(I): 12.8
Reflection shellResolution: 3→3.09 Å / Num. unique obs: 1442

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NUV and 3DIF

4nuv

3dif


Resolution: 3.04→42.04 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.919 / SU R Cruickshank DPI: 0.523 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.516 / SU Rfree Blow DPI: 0.303 / SU Rfree Cruickshank DPI: 0.308
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1550 5.05 %RANDOM
Rwork0.202 ---
obs0.204 30707 99.9 %-
Displacement parametersBiso mean: 115.38 Å2
Baniso -1Baniso -2Baniso -3
1-16.9122 Å20 Å20 Å2
2--16.9122 Å20 Å2
3----33.8244 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: 1 / Resolution: 3.04→42.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5752 0 0 0 5752
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0155890HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.367993HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2035SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes980HARMONIC5
X-RAY DIFFRACTIONt_it5890HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.89
X-RAY DIFFRACTIONt_other_torsion20.5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion770SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6482SEMIHARMONIC0
LS refinement shellResolution: 3→3.02 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3246 -4.39 %
Rwork0.2725 588 -
all0.2747 615 -
obs--99.84 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1125-0.70470.26870.9988-0.38950.1150.0653-0.28050.2479-0.0951-0.157-0.13360.0164-0.22120.09160.1220.0072-0.10740.2292-0.10930.014120.2963-81.3279-16.305
21.1419-0.51680.54951.1574-0.62680.74780.2097-0.0258-0.315-0.1926-0.33930.00870.0046-0.05720.12960.0465-0.0051-0.0120.1944-0.13250.097519.5987-98.7124-20.3072
32.2910.27060.01130.2263-0.41280.35310.22240.0108-0.2408-0.03440.0567-0.10750.0233-0.0634-0.27910.0757-0.007-0.09840.08190.02710.19766.0176-104.9066-9.3304
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

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