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- PDB-8pwx: PfRH5 bound to monoclonal antibody R5.008 -

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Basic information

Entry
Database: PDB / ID: 8pwx
TitlePfRH5 bound to monoclonal antibody R5.008
Components
  • Reticulocyte-binding protein homolog 5
  • scFv fragment for antibody R5.008
KeywordsCELL ADHESION / Plasmodium falciparum / malaria / monoclonal antibody / growth-inhibition / blood stage / erythrocyte invasion
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 / symbiont entry into host cell / 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 speciesHomo sapiens (human)
Plasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsFarrell, B. / Higgins, M.K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust220797/Z/20/Z United Kingdom
CitationJournal: Cell / Year: 2024
Title: Natural malaria infection elicits rare but potent neutralizing antibodies to the blood-stage antigen RH5.
Authors: Wang, L.T. / Cooper, A.J.R. / Farrell, B. / Miura, K. / Diouf, A. / Muller-Sienerth, N. / Crosnier, C. / Purser, L. / Kirtley, P.J. / Maciuszek, M. / Barrett, J.R. / McHugh, K. / Ogwang, R. ...Authors: Wang, L.T. / Cooper, A.J.R. / Farrell, B. / Miura, K. / Diouf, A. / Muller-Sienerth, N. / Crosnier, C. / Purser, L. / Kirtley, P.J. / Maciuszek, M. / Barrett, J.R. / McHugh, K. / Ogwang, R. / Tucker, C. / Li, S. / Doumbo, S. / Doumtabe, D. / Pyo, C.W. / Skinner, J. / Nielsen, C.M. / Silk, S.E. / Kayentao, K. / Ongoiba, A. / Zhao, M. / Nguyen, D.C. / Lee, F.E. / Minassian, A.M. / Geraghty, D.E. / Traore, B. / Seder, R.A. / Wilder, B.K. / Crompton, P.D. / Wright, G.J. / Long, C.A. / Draper, S.J. / Higgins, M.K. / Tan, J.
History
DepositionJul 21, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Dec 18, 2024Group: Database references / Category: citation / citation_author / struct_ref_seq_dif
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: scFv fragment for antibody R5.008
B: Reticulocyte-binding protein homolog 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7873
Polymers70,6952
Non-polymers921
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint1 kcal/mol
Surface area24720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.990, 114.990, 147.494
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Antibody scFv fragment for antibody R5.008


Mass: 29732.141 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: Protein Reticulocyte-binding protein homolog 5 / PfRH5


Mass: 40962.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: RH5, PFD1145c, PF3D7_0424100 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q8IFM5
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.98 Å3/Da / Density % sol: 69.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.12 M Ethylene Glycol Mix (di-, tri-, tetra- and pentaethylene glycols) 0.1 M Buffer System 3 pH 8.5 (BICINE, Trizma base) 30% v/v Precipitant Mix 3 (glycerol, PEG 4000)

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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 PILATUS3 6M / Detector: PIXEL / Date: Aug 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 3.2→57.49 Å / Num. obs: 19138 / % possible obs: 100 % / Redundancy: 5.2 % / Biso Wilson estimate: 75.45 Å2 / CC1/2: 0.986 / Net I/σ(I): 5.2
Reflection shellResolution: 3.2→3.42 Å / Num. unique obs: 3408 / CC1/2: 1

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Processing

Software
NameVersionClassification
BUSTER1.20.1_4487refinement
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→49.79 Å / SU ML: 0.4561 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.8308
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2935 974 5.11 %
Rwork0.2402 18079 -
obs0.2429 19053 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 90.32 Å2
Refinement stepCycle: LAST / Resolution: 3.2→49.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4229 0 6 6 4241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01154326
X-RAY DIFFRACTIONf_angle_d1.49315824
X-RAY DIFFRACTIONf_chiral_restr0.0823631
X-RAY DIFFRACTIONf_plane_restr0.0096728
X-RAY DIFFRACTIONf_dihedral_angle_d4.7565572
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.370.45891570.40362515X-RAY DIFFRACTION99.4
3.37-3.580.36941470.3392525X-RAY DIFFRACTION99.52
3.58-3.860.34961060.28012574X-RAY DIFFRACTION99.81
3.86-4.240.30631300.22162582X-RAY DIFFRACTION99.78
4.24-4.860.23311490.20332551X-RAY DIFFRACTION99.89
4.86-6.120.28011470.21742596X-RAY DIFFRACTION99.82
6.12-49.790.23981380.19722736X-RAY DIFFRACTION99.79

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