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- PDB-9e7o: Pfs230 D13D14 in complex with nanobody W2810 -

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Basic information

Entry
Database: PDB / ID: 9e7o
TitlePfs230 D13D14 in complex with nanobody W2810
Components
  • Gametocyte surface protein P230
  • Nanobody W2810
KeywordsPROTEIN BINDING / 6-cysteine protein / Plasmodium falciparum / malaria transmission / nanobody
Function / homology: / 6-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 / Gametocyte surface protein P230
Function and homology information
Biological speciesVicugna pacos (alpaca)
Plasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsDietrich, M.H. / Tan, L.L. / Tham, W.H.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP2001385 Australia
National Health and Medical Research Council (NHMRC, Australia)APP2016908 Australia
CitationJournal: To Be Published
Title: Cryo-EM structure of the native Pfs230 and Pfs48/45 fertilisation complex from Plasmodium falciparum
Authors: Dietrich, M.H. / Chan, L.J. / Chmielewski, J. / Tan, L.L. / Adair, A. / Lyons, F.M.T. / Gabriela, M. / Lopaticki, S. / Dite, T.A. / Dagley, L.F. / Longley, R. / Mueller, I. / Glukhova, A. / ...Authors: Dietrich, M.H. / Chan, L.J. / Chmielewski, J. / Tan, L.L. / Adair, A. / Lyons, F.M.T. / Gabriela, M. / Lopaticki, S. / Dite, T.A. / Dagley, L.F. / Longley, R. / Mueller, I. / Glukhova, A. / Shakeel, S. / Tham, W.H.
History
DepositionNov 3, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nanobody W2810
B: Gametocyte surface protein P230
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1589
Polymers47,0432
Non-polymers1,1157
Water2,306128
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)135.494, 62.824, 56.481
Angle α, β, γ (deg.)90.00, 98.92, 90.00
Int Tables number5
Space group name H-MC121
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
Components on special symmetry positions
IDModelComponents
11A-303-

HOH

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Components

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Antibody / Protein , 2 types, 2 molecules AB

#1: Antibody Nanobody W2810


Mass: 13666.928 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#2: Protein Gametocyte surface protein P230


Mass: 33375.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PFS230, PF230, S230, PF3D7_0209000 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P68874

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Sugars , 2 types, 3 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 132 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.52 Å3/Da / Density % sol: 51.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.4 M sodium malonate dibasic monohydrate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953647 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953647 Å / Relative weight: 1
ReflectionResolution: 1.93→39.92 Å / Num. obs: 35422 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 43.98 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.088 / Net I/σ(I): 13.83
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.93-2.050.64256080.7041.3641
2.05-2.190.34253950.8310.8681
2.19-2.360.22749660.9230.5211
2.36-2.590.16146210.9680.3331
2.59-2.890.09641680.9870.1831
2.89-3.330.05336930.9970.0921
3.33-4.080.0331230.9990.0521
4.08-5.750.01924580.9990.0371

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→39.92 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.254 1767 4.99 %
Rwork0.2138 --
obs0.2158 35377 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.93→39.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3104 0 72 128 3304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093288
X-RAY DIFFRACTIONf_angle_d1.0284475
X-RAY DIFFRACTIONf_dihedral_angle_d17.0081208
X-RAY DIFFRACTIONf_chiral_restr0.064504
X-RAY DIFFRACTIONf_plane_restr0.007570
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.980.40361340.35282567X-RAY DIFFRACTION100
1.98-2.040.34061320.29282543X-RAY DIFFRACTION100
2.04-2.110.33081370.27192589X-RAY DIFFRACTION100
2.11-2.180.34161360.2672592X-RAY DIFFRACTION100
2.18-2.270.31351350.25292561X-RAY DIFFRACTION100
2.27-2.370.31831350.23832565X-RAY DIFFRACTION100
2.37-2.50.28091360.24422582X-RAY DIFFRACTION100
2.5-2.650.32511350.24152571X-RAY DIFFRACTION100
2.65-2.860.31841360.23992582X-RAY DIFFRACTION100
2.86-3.150.29581370.23382605X-RAY DIFFRACTION100
3.15-3.60.2381360.21032581X-RAY DIFFRACTION100
3.6-4.530.20391370.18312605X-RAY DIFFRACTION100
4.54-39.920.20391410.17852667X-RAY DIFFRACTION100

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