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- PDB-9e7n: Pfs230 D13D14 in complex with nanobody W2809 -

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Basic information

Entry
Database: PDB / ID: 9e7n
TitlePfs230 D13D14 in complex with nanobody W2809
Components
  • Gametocyte surface protein P230
  • Nanobody W2809
KeywordsPROTEIN BINDING / 6-cysteine protein / Plasmodium falciparum / malaria transmission / nanobody
Function / homology
Function and homology information


cell surface / plasma membrane
Similarity search - Function
: / 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
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Gametocyte surface protein P230
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsTan, L.L. / Dietrich, M.H. / 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
B: Gametocyte surface protein P230
A: Gametocyte surface protein P230
C: Nanobody W2809
D: Nanobody W2809
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,05114
Polymers96,1164
Non-polymers2,93510
Water1,11762
1
B: Gametocyte surface protein P230
D: Nanobody W2809
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7076
Polymers48,0582
Non-polymers1,6494
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint15 kcal/mol
Surface area19720 Å2
MethodPISA
2
A: Gametocyte surface protein P230
C: Nanobody W2809
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3448
Polymers48,0582
Non-polymers1,2866
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint13 kcal/mol
Surface area19810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.919, 79.919, 342.703
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein / Antibody , 2 types, 4 molecules BACD

#1: Protein Gametocyte surface protein P230


Mass: 33375.906 Da / Num. of mol.: 2
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
#2: Antibody Nanobody W2809


Mass: 14682.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)

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Sugars , 3 types, 7 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#4: 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.: 2 / Source method: isolated from a natural 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
#6: 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.: 4 / 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 , 3 types, 65 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.85 Å3/Da / Density % sol: 56.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 12% (w/v) polyethylene glycol (PEG) 8000, 4% (v/v) glycerol 0.2 M sodium acetate, 0.1 M imidazole pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953732 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 28, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953732 Å / Relative weight: 1
ReflectionResolution: 2.49→47.17 Å / Num. obs: 39958 / % possible obs: 99.9 % / Redundancy: 26.6 % / Biso Wilson estimate: 68.299 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.104 / Rrim(I) all: 0.164 / Net I/σ(I): 16.1
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.49-2.641.15862220.6932.3241
2.64-2.830.71459600.8581.3611
2.83-3.050.39955630.960.7621
3.05-3.340.20251590.9870.3871
3.34-3.730.11146800.9960.2031
3.73-4.310.07541770.9980.1251
4.31-5.260.05636010.9990.0881
5.26-7.40.05528510.9990.0841

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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: 2.49→47.17 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2643 1997 5 %
Rwork0.2237 --
obs0.2257 39948 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.49→47.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6470 0 192 62 6724
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046863
X-RAY DIFFRACTIONf_angle_d0.6729318
X-RAY DIFFRACTIONf_dihedral_angle_d14.9432622
X-RAY DIFFRACTIONf_chiral_restr0.0491045
X-RAY DIFFRACTIONf_plane_restr0.0051164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.560.43951350.39262570X-RAY DIFFRACTION97
2.56-2.620.35811390.32872644X-RAY DIFFRACTION100
2.63-2.70.34271410.29362666X-RAY DIFFRACTION100
2.7-2.790.36171390.28182645X-RAY DIFFRACTION100
2.79-2.890.3121410.27742681X-RAY DIFFRACTION100
2.89-30.33491400.29072672X-RAY DIFFRACTION100
3-3.140.36851420.30072685X-RAY DIFFRACTION100
3.14-3.310.34711410.27682689X-RAY DIFFRACTION100
3.31-3.510.29941410.24832699X-RAY DIFFRACTION100
3.51-3.790.27561440.22282724X-RAY DIFFRACTION100
3.79-4.170.22241430.21272719X-RAY DIFFRACTION100
4.17-4.770.22741450.16952758X-RAY DIFFRACTION100
4.77-60.231480.17862802X-RAY DIFFRACTION100
6.01-47.170.20771580.2022997X-RAY DIFFRACTION100

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