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- PDB-7phu: PfRH5 bound to monoclonal antibody R5.015 and R5.016 Fab fragments -

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Basic information

Entry
Database: PDB / ID: 7phu
TitlePfRH5 bound to monoclonal antibody R5.015 and R5.016 Fab fragments
Components
  • (Monoclonal antibody R5.015 ...) x 2
  • (Monoclonal antibody R5.016 ...) x 2
  • Reticulocyte-binding protein homolog 5
KeywordsIMMUNE SYSTEM / malaria / Plasmodium falciparum / monoclonal antibody / vaccine
Function / homology
Function and homology information


rhoptry lumen / rhoptry / symbiont entry into host / host cell membrane / bicellular tight junction / apical part of cell / heparin binding / cytoplasmic vesicle / host extracellular space / host cell surface receptor binding ...rhoptry lumen / rhoptry / symbiont entry into host / host cell membrane / bicellular tight junction / apical part of cell / heparin binding / cytoplasmic vesicle / host extracellular space / host cell surface receptor binding / host cell plasma membrane / protein-containing complex / extracellular region / membrane
Similarity search - Function
Rh5 coiled-coil domain / Rh5 coiled-coil domain
Similarity search - Domain/homology
Reticulocyte-binding protein homolog 5
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsRagotte, R.J. / Higgins, M.K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Nat Commun / Year: 2022
Title: Heterotypic interactions drive antibody synergy against a malaria vaccine candidate.
Authors: Ragotte, R.J. / Pulido, D. / Lias, A.M. / Quinkert, D. / Alanine, D.G.W. / Jamwal, A. / Davies, H. / Nacer, A. / Lowe, E.D. / Grime, G.W. / Illingworth, J.J. / Donat, R.F. / Garman, E.F. / ...Authors: Ragotte, R.J. / Pulido, D. / Lias, A.M. / Quinkert, D. / Alanine, D.G.W. / Jamwal, A. / Davies, H. / Nacer, A. / Lowe, E.D. / Grime, G.W. / Illingworth, J.J. / Donat, R.F. / Garman, E.F. / Bowyer, P.W. / Higgins, M.K. / Draper, S.J.
History
DepositionAug 18, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: 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 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Reticulocyte-binding protein homolog 5
B: Monoclonal antibody R5.015 heavy chain
C: Monoclonal antibody R5.015 light chain
D: Monoclonal antibody R5.016 heavy chain
E: Monoclonal antibody R5.016 light chain


Theoretical massNumber of molelcules
Total (without water)183,5745
Polymers183,5745
Non-polymers00
Water2,288127
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11360 Å2
ΔGint-67 kcal/mol
Surface area52660 Å2
Unit cell
Length a, b, c (Å)97.740, 163.300, 176.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Antibody , 4 types, 4 molecules BCDE

#2: Antibody Monoclonal antibody R5.015 heavy chain


Mass: 25478.518 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: Antibody Monoclonal antibody R5.015 light chain


Mass: 23184.594 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 Monoclonal antibody R5.016 heavy chain


Mass: 50902.977 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: Antibody Monoclonal antibody R5.016 light chain


Mass: 23953.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Protein / Non-polymers , 2 types, 128 molecules A

#1: Protein Reticulocyte-binding protein homolog 5 / PfRH5


Mass: 60053.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: RH5, PFD1145c, PF3D7_0424100 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q8IFM5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O

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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

Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium formate, 0.1 M bis-tris propane pH 6.5, 20 % PEG 3350 with an additive containing 0.08 % w/v Ellipticine, 0.20 % w/v Protamine sulfate salt, 0.20 % w/v D-(+)-Trehalose ...Details: 0.2 M sodium formate, 0.1 M bis-tris propane pH 6.5, 20 % PEG 3350 with an additive containing 0.08 % w/v Ellipticine, 0.20 % w/v Protamine sulfate salt, 0.20 % w/v D-(+)-Trehalose dihydrate, 0.20 % w/v 6-Phosphogluconic acid trisodium salt, 0.20 % w/v D-(+)-Glucose, 0.02 M HEPES sodium pH 6.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.53→48.22 Å / Num. obs: 316074 / % possible obs: 99.6 % / Redundancy: 6.7 % / CC1/2: 0.999 / Net I/σ(I): 13.1
Reflection shellResolution: 2.53→2.57 Å / Num. unique obs: 16521 / CC1/2: 0.575

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (24-FEB-2021)refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U0R

4u0r


Resolution: 2.53→47.79 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.885 / SU R Cruickshank DPI: 0.571 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.547 / SU Rfree Blow DPI: 0.302 / SU Rfree Cruickshank DPI: 0.309
RfactorNum. reflection% reflectionSelection details
Rfree0.2759 2354 4.98 %RANDOM
Rwork0.2358 ---
obs0.2379 47308 99.5 %-
Displacement parametersBiso max: 119.53 Å2 / Biso mean: 63.66 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-18.8574 Å20 Å20 Å2
2---28.9184 Å20 Å2
3---10.0609 Å2
Refine analyzeLuzzati coordinate error obs: 0.42 Å
Refinement stepCycle: final / Resolution: 2.53→47.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9167 0 0 127 9294
Biso mean---58.89 -
Num. residues----1172
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3165SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1557HARMONIC5
X-RAY DIFFRACTIONt_it9399HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1247SEMIHARMONIC5
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_contact7090SEMIHARMONIC0
X-RAY DIFFRACTIONt_bond_d9399HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg12767HARMONIC21.04
X-RAY DIFFRACTIONt_omega_torsion3.15
X-RAY DIFFRACTIONt_other_torsion19.66
LS refinement shellResolution: 2.53→2.55 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.4472 42 4.44 %
Rwork0.3704 905 -
all-947 -
obs--99.79 %
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)
10.5786-0.3398-0.13331.01430.85690.6137-0.02470.00850.10770.1214-0.0426-0.06740.13570.0150.0673-0.17580.0173-0.0289-0.06140.0128-0.24361.118161.410511.2587
21.4196-0.02620.992200.21160.7166-0.1666-0.09370.02920.01580.1172-0.0219-0.1649-0.20930.0493-0.14560.04660.0388-0.01710.0064-0.273-19.216447.3698-38.5947
30.8550.14331.41440.31020.37792.14390.069-0.0523-0.14650.03080.091-0.0120.0858-0.1386-0.1601-0.1919-0.00860.0508-0.07340.0316-0.2266-16.757629.3893-39.2606
42.71950.43230.15390.10320.09220.384-0.19420.4140.4627-0.01690.14640.13020.03510.09030.0478-0.2547-0.0267-0.1461-0.18450.0029-0.069735.471892.805314.2148
53.89740.8530.39820.0397-0.03060.06490.2025-0.49450.0887-0.017-0.19610.0101-0.00530.0325-0.0064-0.2502-0.0477-0.1389-0.1398-0.152-0.108842.26189.669630.2253
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A160 - 506
2X-RAY DIFFRACTION2{ B|* }B7 - 232
3X-RAY DIFFRACTION3{ C|* }C2 - 213
4X-RAY DIFFRACTION4{ D|* }D6 - 237
5X-RAY DIFFRACTION5{ E|* }E7 - 217

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