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- PDB-7zwf: Pfs48/45 bound to scFv fragment of monoclonal antibody 32F3 -

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Basic information

Entry
Database: PDB / ID: 7zwf
TitlePfs48/45 bound to scFv fragment of monoclonal antibody 32F3
Components
  • 32F3scFv
  • Gametocyte surface protein P45/48
KeywordsCELL ADHESION / Pfs48/45 / malaria / transmission-blocking / Plasmodium falciparum / gamete / antibody
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 / side of membrane / cell surface / plasma membrane / Gametocyte surface protein P45/48
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.132 Å
AuthorsKo, K.T. / Lennartz, F.L. / Higgins, M.K.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/R001138/1 United Kingdom
Wellcome Trust218482/Z/19/Z United Kingdom
Wellcome Trust101020/Z/13/Z United Kingdom
CitationJournal: Nat Commun / Year: 2022
Title: Structure of the malaria vaccine candidate Pfs48/45 and its recognition by transmission blocking antibodies.
Authors: Ko, K.T. / Lennartz, F. / Mekhaiel, D. / Guloglu, B. / Marini, A. / Deuker, D.J. / Long, C.A. / Jore, M.M. / Miura, K. / Biswas, S. / Higgins, M.K.
History
DepositionMay 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gametocyte surface protein P45/48
B: 32F3scFv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,5603
Polymers79,1932
Non-polymers3671
Water1,69394
1
A: Gametocyte surface protein P45/48
B: 32F3scFv
hetero molecules

A: Gametocyte surface protein P45/48
B: 32F3scFv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,1206
Polymers158,3854
Non-polymers7352
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area6760 Å2
ΔGint-7 kcal/mol
Surface area46000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.826, 126.115, 146.787
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Gametocyte surface protein P45/48 / Pfs48/45


Mass: 49180.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PF45/48, PFS45-48, PFS45/48, PF13_0247, PF3D7_1346700 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q8I6T1
#2: Antibody 32F3scFv / monoclonal antibody 32F3


Mass: 30011.615 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
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: 3.18 Å3/Da / Density % sol: 61.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M MES pH6.0, 0.2M CaCl2, 20% PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.13→73.39 Å / Num. obs: 586552 / % possible obs: 99.8 % / Redundancy: 13.8 % / CC1/2: 0.999 / Rpim(I) all: 0.037 / Net I/σ(I): 11.2
Reflection shellResolution: 2.13→2.17 Å / Num. unique obs: 28745 / CC1/2: 0.384 / Rpim(I) all: 2.26

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (20-OCT-2021)refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H5N

6h5n


Resolution: 2.132→40.91 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.933 / SU R Cruickshank DPI: 0.238 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.234 / SU Rfree Blow DPI: 0.19 / SU Rfree Cruickshank DPI: 0.193
RfactorNum. reflection% reflectionSelection details
Rfree0.2864 1964 4.81 %RANDOM
Rwork0.2757 ---
obs0.2762 40794 95.6 %-
Displacement parametersBiso max: 212.13 Å2 / Biso mean: 98.74 Å2 / Biso min: 35.44 Å2
Baniso -1Baniso -2Baniso -3
1-6.1299 Å20 Å20 Å2
2---1.7024 Å20 Å2
3----4.4275 Å2
Refine analyzeLuzzati coordinate error obs: 0.44 Å
Refinement stepCycle: final / Resolution: 2.132→40.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3865 0 24 94 3983
Biso mean--116.96 67.28 -
Num. residues----497
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1351SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes658HARMONIC5
X-RAY DIFFRACTIONt_it3981HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion536SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2876SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3981HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg5393HARMONIC20.99
X-RAY DIFFRACTIONt_omega_torsion3.14
X-RAY DIFFRACTIONt_other_torsion18.93
LS refinement shellResolution: 2.132→2.17 Å
RfactorNum. reflection% reflection
Rfree0.5075 33 4.04 %
Rwork0.4896 783 -
obs--42.03 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10-0.5824-0.50781.35731.03492.88940.10350.0310.1173-0.2217-0.1705-0.09070.5476-0.33780.067-0.1633-0.1260.05350.495-0.061-0.242214.842-5.759316.7619
24.30840.1830.54810.5059-0.25521.8349-0.1829-0.43520.6942-0.0686-0.1162-0.1199-0.0955-0.17330.299-0.3670.0248-0.05750.3827-0.1813-0.068125.227723.214241.3535
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A71 - 427
2X-RAY DIFFRACTION2{ B|* }B30 - 274

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