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- PDB-7zwi: Pfs48/45 C-terminal domain bound to fab fragment of monoclonal an... -

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Basic information

Entry
Database: PDB / ID: 7zwi
TitlePfs48/45 C-terminal domain bound to fab fragment of monoclonal antibody 32F3
Components
  • 32F3 heavy chain
  • 32F3 light chain
  • 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: 1.9 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 1.1Jun 29, 2022Group: Derived calculations / Category: pdbx_struct_assembly / pdbx_struct_assembly_gen
Revision 1.2Oct 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 1.3Jan 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: 32F3 heavy chain
C: 32F3 light chain
D: Gametocyte surface protein P45/48
E: 32F3 heavy chain
F: 32F3 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,7167
Polymers243,1466
Non-polymers5711
Water17,348963
1
A: Gametocyte surface protein P45/48
B: 32F3 heavy chain
C: 32F3 light chain


Theoretical massNumber of molelcules
Total (without water)121,5733
Polymers121,5733
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Gametocyte surface protein P45/48
E: 32F3 heavy chain
F: 32F3 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,1444
Polymers121,5733
Non-polymers5711
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.659, 87.104, 110.620
Angle α, β, γ (deg.)90.000, 99.540, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 49278.094 Da / Num. of mol.: 2
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 32F3 heavy chain


Mass: 49105.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Antibody 32F3 light chain


Mass: 23189.568 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 963 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.04M potassium dihydrogen phosphate, 16% (w/v) polyethylene glycol (PEG) 8000 and 20 % (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→77.57 Å / Num. obs: 781771 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rpim(I) all: 0.037 / Net I/σ(I): 11.6
Reflection shellResolution: 1.9→1.93 Å / Num. unique obs: 36476 / CC1/2: 0.78 / Rpim(I) all: 0.282

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (20-APR-2021)refinement
PDB_EXTRACT3.22data extraction
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H5N

6h5n


Resolution: 1.9→77.57 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.937 / SU R Cruickshank DPI: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.131 / SU Rfree Blow DPI: 0.12 / SU Rfree Cruickshank DPI: 0.118
RfactorNum. reflection% reflectionSelection details
Rfree0.2166 5743 4.95 %RANDOM
Rwork0.1889 ---
obs0.1903 115991 99.8 %-
Displacement parametersBiso max: 107.46 Å2 / Biso mean: 42.85 Å2 / Biso min: 17.27 Å2
Baniso -1Baniso -2Baniso -3
1-6.4488 Å20 Å24.3757 Å2
2---1.354 Å20 Å2
3----5.0948 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: final / Resolution: 1.9→77.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8590 0 38 963 9591
Biso mean--53.15 47.44 -
Num. residues----1123
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2919SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1465HARMONIC5
X-RAY DIFFRACTIONt_it8852HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1214SEMIHARMONIC5
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_contact7571SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8852HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg12068HARMONIC21.02
X-RAY DIFFRACTIONt_omega_torsion3.83
X-RAY DIFFRACTIONt_other_torsion14.58
LS refinement shellResolution: 1.9→1.91 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3223 126 5.43 %
Rwork0.2935 2194 -
all-2320 -
obs--94.9 %
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)
11.27630.17930.35140.43440.68971.1981-0.00160.2431-0.0183-0.03110.0503-0.0581-0.09340.0266-0.0487-0.0680.01980.0042-0.00870.0047-0.003128.0791-8.718-19.348
20.71090.03020.26660.1448-0.1491.14130.1198-0.1877-0.07610.0654-0.0361-0.09480.0016-0.0939-0.0836-0.0179-0.0415-0.0476-0.02770.01950.019433.9869-3.586824.1001
31.2983-0.01150.25820.0866-0.14480.72330.0593-0.45250.04530.0284-0.0365-0.0516-0.0454-0.1827-0.0228-0.0308-0.0275-0.03390.0922-0.01230.026715.9401-5.229424.2881
41.19830.12750.56340.8983-0.03470.79020.0817-0.0966-0.04960.1333-0.05-0.07540.0366-0.0862-0.0317-0.051-0.02650.0028-0.05970.01250.020652.3756-21.3188112.6631
50.19010.1356-0.05720.1619-0.09511.47140.00050.1514-0.0276-0.0515-0.02690.1477-0.1252-0.0310.0264-0.05740.0444-0.08050.05320.01360.030341.5415-7.526872.4573
60.34580.21390.1490.12260.11121.2987-0.10820.24970.0677-0.03210.04030.1278-0.26220.18810.0679-0.0268-0.0501-0.0630.12050.06370.024558.6375-0.979172.2879
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A293 - 429
2X-RAY DIFFRACTION2{ B|* }B1 - 220
3X-RAY DIFFRACTION3{ C|* }C1 - 210
4X-RAY DIFFRACTION4{ D|* }D293 - 428
5X-RAY DIFFRACTION5{ E|* }E1 - 220
6X-RAY DIFFRACTION6{ F|* }F1 - 211

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