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- PDB-7uvo: Pfs230 domain 1 bound by RUPA-38 Fab -

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Basic information

Entry
Database: PDB / ID: 7uvo
TitlePfs230 domain 1 bound by RUPA-38 Fab
Components
  • Gametocyte surface protein P230
  • RUPA-38 Fab heavy chain
  • RUPA-38 Fab light chain
KeywordsCELL INVASION/IMMUNE SYSTEM / Antibody-fragment / malaria transmission / CELL INVASION / CELL INVASION-IMMUNE SYSTEM complex
Function / homology6-Cysteine (6-Cys) domain / 6-Cysteine (6-Cys) domain superfamily / Sexual stage antigen s48/45 domain / 6-Cysteine (6-Cys) domain profile. / Sexual stage antigen s48/45 domain / cell surface / plasma membrane / ISOPROPYL ALCOHOL / Gametocyte surface protein P230
Function and homology information
Biological speciesHomo sapiens (human)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsIvanochko, D. / Newton, J. / Julien, J.P.
Funding support Canada, United States, 4items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)428410 Canada
Ontario Early Researcher Awards Canada
Bill & Melinda Gates FoundationOPP1170236 United States
Canada Research Chairs Canada
CitationJournal: Immunity / Year: 2023
Title: Potent transmission-blocking monoclonal antibodies from naturally exposed individuals target a conserved epitope on Plasmodium falciparum Pfs230.
Authors: Ivanochko, D. / Fabra-Garcia, A. / Teelen, K. / van de Vegte-Bolmer, M. / van Gemert, G.J. / Newton, J. / Semesi, A. / de Bruijni, M. / Bolscher, J. / Ramjith, J. / Szabat, M. / Vogt, S. / ...Authors: Ivanochko, D. / Fabra-Garcia, A. / Teelen, K. / van de Vegte-Bolmer, M. / van Gemert, G.J. / Newton, J. / Semesi, A. / de Bruijni, M. / Bolscher, J. / Ramjith, J. / Szabat, M. / Vogt, S. / Kraft, L. / Duncan, S. / Lee, S.M. / Kamya, M.R. / Feeney, M.E. / Jagannathan, P. / Greenhouse, B. / Sauerwein, R.W. / Richter King, C. / MacGill, R.S. / Bousema, T. / Jore, M.M. / Julien, J.P.
History
DepositionMay 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.2Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RUPA-38 Fab heavy chain
B: RUPA-38 Fab light chain
C: Gametocyte surface protein P230
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2256
Polymers70,0943
Non-polymers1313
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)163.710, 42.850, 95.300
Angle α, β, γ (deg.)90.000, 102.492, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 1 types, 1 molecules C

#3: Protein Gametocyte surface protein P230


Mass: 22694.705 Da / Num. of mol.: 1 / Fragment: domain 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PFS230, PF230, S230, PF3D7_0209000 / Production host: Homo sapiens (human) / References: UniProt: P68874

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Antibody , 2 types, 2 molecules AB

#1: Antibody RUPA-38 Fab heavy chain


Mass: 24135.170 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 RUPA-38 Fab light chain


Mass: 23263.891 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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Non-polymers , 3 types, 145 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.33 Å3/Da / Density % sol: 47.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 19% v/v isopropanol, 20% w/v PEG 4000, 0.1 M sodium citrate ph 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033192 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033192 Å / Relative weight: 1
ReflectionResolution: 2.09→29.06 Å / Num. obs: 38731 / % possible obs: 99.8 % / Redundancy: 12 % / Biso Wilson estimate: 39.55 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.218 / Rpim(I) all: 0.064 / Rrim(I) all: 0.232 / Net I/σ(I): 7.7
Reflection shellResolution: 2.09→2.15 Å / Rmerge(I) obs: 1.407 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3171 / CC1/2: 0.629 / Rpim(I) all: 0.482 / Rrim(I) all: 1.523

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XPREPdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OHG

6ohg


Resolution: 2.09→29.06 Å / SU ML: 0.2662 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.5836
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2346 1937 5 %
Rwork0.2169 36785 -
obs0.2178 38722 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.15 Å2
Refinement stepCycle: LAST / Resolution: 2.09→29.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4743 0 6 142 4891
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00684857
X-RAY DIFFRACTIONf_angle_d1.00076607
X-RAY DIFFRACTIONf_chiral_restr0.0579745
X-RAY DIFFRACTIONf_plane_restr0.0076844
X-RAY DIFFRACTIONf_dihedral_angle_d16.17871769
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.140.33911390.3062644X-RAY DIFFRACTION99.5
2.14-2.20.31811330.29222533X-RAY DIFFRACTION99.4
2.2-2.260.30861370.28432602X-RAY DIFFRACTION98.7
2.26-2.340.30241370.25652594X-RAY DIFFRACTION99.93
2.34-2.420.26961390.24462642X-RAY DIFFRACTION100
2.42-2.520.2641380.24282608X-RAY DIFFRACTION100
2.52-2.630.26271360.23392599X-RAY DIFFRACTION99.89
2.63-2.770.25051370.22612593X-RAY DIFFRACTION99.96
2.77-2.950.23561380.22312624X-RAY DIFFRACTION99.93
2.95-3.170.23621380.21572629X-RAY DIFFRACTION99.82
3.17-3.490.23911400.21282648X-RAY DIFFRACTION99.79
3.49-3.990.22671400.20162652X-RAY DIFFRACTION99.86
4-5.030.18291390.18012655X-RAY DIFFRACTION99.89
5.03-29.060.22251460.21342762X-RAY DIFFRACTION99.97

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