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- PDB-5f3j: Crystal structure of DBP in complex with inhibitory monoclonal an... -

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Basic information

Entry
Database: PDB / ID: 5f3j
TitleCrystal structure of DBP in complex with inhibitory monoclonal antibody 2D10
Components
  • Antibody 2D10 single chain variable fragment
  • Duffy receptor
KeywordsIMMUNE SYSTEM / Plasmodium / vivax / duffy binding protein / DBP / antibody / malaria / scfv / neutralizing / interaction / immune / blocking / invasion / vaccine / therapeutic
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 speciesPlasmodium vivax (malaria parasite P. vivax)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.001 Å
AuthorsChen, E. / Salinas, N.D. / Tolia, N.H.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI080792 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R56 AI080792 United States
Burroughs Wellcome FundPATH award United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI064478 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)BAA-NIAID-DAIT-NIHAI2013164 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Broadly neutralizing epitopes in the Plasmodium vivax vaccine candidate Duffy Binding Protein.
Authors: Chen, E. / Salinas, N.D. / Huang, Y. / Ntumngia, F. / Plasencia, M.D. / Gross, M.L. / Adams, J.H. / Tolia, N.H.
History
DepositionDec 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Jun 15, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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: Duffy receptor
B: Duffy receptor
C: Antibody 2D10 single chain variable fragment
D: Antibody 2D10 single chain variable fragment


Theoretical massNumber of molelcules
Total (without water)139,6764
Polymers139,6764
Non-polymers00
Water0
1
A: Duffy receptor
C: Antibody 2D10 single chain variable fragment


Theoretical massNumber of molelcules
Total (without water)69,8382
Polymers69,8382
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Duffy receptor
D: Antibody 2D10 single chain variable fragment


Theoretical massNumber of molelcules
Total (without water)69,8382
Polymers69,8382
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.940, 63.940, 108.880
Angle α, β, γ (deg.)90.00, 100.09, 90.00
Int Tables number4
Space group name H-MP1211

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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 (strain Salvador I) (eukaryote)
Strain: Salvador I / Gene: PVDR / Production host: Escherichia coli (E. coli) / References: UniProt: P22290
#2: Antibody Antibody 2D10 single chain variable fragment


Mass: 32227.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)

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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: 2.08 Å3/Da / Density % sol: 40.98 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1% w/v tryptone, 50 mM HEPES sodium salt pH 7.0, 12% w/v PEG 3,350

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00482 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Feb 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00482 Å / Relative weight: 1
ReflectionResolution: 4→20 Å / Num. obs: 9271 / % possible obs: 92.9 % / Redundancy: 2.73 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 6.74
Reflection shellResolution: 4→4.1 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 3.29 / % possible all: 91

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NUV

4nuv


Resolution: 4.001→19.944 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2997 487 5.3 %
Rwork0.2669 --
obs0.2686 9188 93.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.001→19.944 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7721 0 0 0 7721
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047883
X-RAY DIFFRACTIONf_angle_d0.67810617
X-RAY DIFFRACTIONf_dihedral_angle_d17.2734765
X-RAY DIFFRACTIONf_chiral_restr0.0421122
X-RAY DIFFRACTIONf_plane_restr0.0041344
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.001-4.57390.32581520.28752913X-RAY DIFFRACTION94
4.5739-5.73970.3211780.26022886X-RAY DIFFRACTION94
5.7397-19.9440.26881570.25852902X-RAY DIFFRACTION92
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)
10.3967-0.16650.06163.00050.64640.7978-0.1839-0.15160.14020.39470.2419-0.60350.04030.6211-0.00020.69-0.1024-0.10151.21510.01521.062427.6601-10.8176.5036
20.2947-1.9062-1.00051.69521.79411.1298-0.0954-0.1985-0.07520.08970.2868-0.70340.34360.543101.34950.10520.04361.1950.02121.137318.952130.133456.7842
32.62780.3391-1.11713.78410.22292.87290.29140.0938-0.3506-0.1299-0.2434-0.0036-0.124-0.11580.00010.6011-0.0436-0.06890.7643-0.05060.83318.8161-42.7491-11.5852
41.8481-1.09590.91282.56061.17492.2068-0.07880.05140.38410.0308-0.0589-0.26440.09030.0154-0.00031.012-0.0990.04610.7638-0.01230.8833-5.06761.34367.4339
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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