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- PDB-9e7p: Pfs230 D13D14 in complex with nanobody W2812 -

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Basic information

Entry
Database: PDB / ID: 9e7p
TitlePfs230 D13D14 in complex with nanobody W2812
Components
  • Gametocyte surface protein P230
  • Nanobody W2812
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
CITRIC ACID / Gametocyte surface protein P230
Similarity search - Component
Biological speciesVicugna pacos (alpaca)
Plasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.22 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 W2812
B: Gametocyte surface protein P230
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8274
Polymers48,0482
Non-polymers7792
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint1 kcal/mol
Surface area18410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.647, 134.647, 75.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Antibody Nanobody W2812


Mass: 14672.247 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
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
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: 3.57 Å3/Da / Density % sol: 65.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 5% (w/v) PEG8000, 5% (w/v) PEG10000, 5% (w/v) PEG 6000, 0.15M ammonium acetate, 0.1 M sodium citrate pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953728 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953728 Å / Relative weight: 1
ReflectionResolution: 3.22→47.6 Å / Num. obs: 11793 / % possible obs: 99.9 % / Redundancy: 13.3 % / Biso Wilson estimate: 95.457 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.131 / Net I/av σ(I): 16.44 / Net I/σ(I): 6
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
3.22-3.410.79618410.7181.471
3.41-3.640.4617400.9110.7411
3.64-3.930.23816450.970.4241
3.93-4.310.14415200.9910.2211
4.31-4.810.07913800.9970.1221
4.81-5.540.05612340.9980.0991
5.54-6.770.05410650.9980.091
6.77-9.470.0358430.9990.0541

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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: 3.22→47.6 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3197 1058 9.01 %
Rwork0.2858 --
obs0.2889 11747 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.22→47.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3095 0 52 0 3147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033226
X-RAY DIFFRACTIONf_angle_d0.6024412
X-RAY DIFFRACTIONf_dihedral_angle_d16.081143
X-RAY DIFFRACTIONf_chiral_restr0.048507
X-RAY DIFFRACTIONf_plane_restr0.004567
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.22-3.370.41071300.411308X-RAY DIFFRACTION100
3.37-3.540.44081280.36781293X-RAY DIFFRACTION100
3.54-3.770.37041300.35521317X-RAY DIFFRACTION100
3.77-4.060.4161300.35881315X-RAY DIFFRACTION100
4.06-4.460.28531300.27421317X-RAY DIFFRACTION100
4.46-5.110.30571320.25511338X-RAY DIFFRACTION100
5.11-6.440.31041350.28081360X-RAY DIFFRACTION100
6.44-47.60.2781430.24491441X-RAY DIFFRACTION100

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