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- PDB-7zxf: Pfs48/45 bound to monoclonal antibodies 10D8 and 85RF45.1 -

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Basic information

Entry
Database: PDB / ID: 7zxf
TitlePfs48/45 bound to monoclonal antibodies 10D8 and 85RF45.1
Components
  • 10D8 heavy chain
  • 10D8 light chain
  • 85RF45.1 heavy chain
  • 85RF45.1 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)
Rattus norvegicus (Norway rat)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.72 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 20, 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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: 85RF45.1 heavy chain
C: 85RF45.1 light chain
D: 10D8 heavy chain
E: 10D8 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,0437
Polymers202,5455
Non-polymers1,4972
Water00
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)156.880, 156.880, 148.761
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
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

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Antibody , 4 types, 4 molecules BCDE

#2: Antibody 85RF45.1 heavy chain


Mass: 49338.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Rattus norvegicus (Norway rat)
#3: Antibody 85RF45.1 light chain


Mass: 23638.053 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Rattus norvegicus (Norway rat)
#4: Antibody 10D8 heavy chain


Mass: 51485.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#5: Antibody 10D8 light chain


Mass: 26537.549 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)

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Protein / Sugars , 2 types, 3 molecules A

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


Mass: 51545.887 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: Homo sapiens (human) / References: UniProt: Q8I6T1
#6: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE

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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: 2.63 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1M Lithium sulfate, 0.1M HEPES pH 7.0 and 20 % w/v Polyvinylpyrrolidone

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.99998 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 3.72→108 Å / Num. obs: 456518 / % possible obs: 94.9 % / Redundancy: 26.8 % / Biso Wilson estimate: 189.87 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.027 / Net I/σ(I): 15.7
Reflection shellResolution: 3.72→4.06 Å / Num. unique obs: 56247 / CC1/2: 0.377 / Rpim(I) all: 0.875

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Processing

Software
NameVersionClassification
BUSTER1.19_4092refinement
PHENIX1.19_4092refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H5N

6h5n


Resolution: 3.72→70.16 Å / SU ML: 0.5504 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.7104
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2976 869 5.13 %RANDOM
Rwork0.2809 16068 --
obs0.2817 16937 84.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 216.24 Å2
Refinement stepCycle: LAST / Resolution: 3.72→70.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9284 0 100 0 9384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00289606
X-RAY DIFFRACTIONf_angle_d0.599613061
X-RAY DIFFRACTIONf_chiral_restr0.0611498
X-RAY DIFFRACTIONf_plane_restr0.00471645
X-RAY DIFFRACTIONf_dihedral_angle_d13.60413486
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.72-3.960.4436650.3899919X-RAY DIFFRACTION30.22
3.96-4.260.38151130.37612487X-RAY DIFFRACTION79.1
4.26-4.690.3211430.31513025X-RAY DIFFRACTION96.56
4.69-5.370.32221630.29943147X-RAY DIFFRACTION100
5.37-6.760.31552130.32283150X-RAY DIFFRACTION99.97
6.76-70.160.26841720.24413340X-RAY DIFFRACTION99.69
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)
15.01200235145-1.1758339509-0.3498470177860.6651927230741.004157296275.54582380696-0.4141201760490.3612382622320.2747907983420.491772026372-0.289061437958-0.266612580064-0.510780268947-0.5299551852820.6793705820882.066091036750.1337669173890.02368782070211.47102212475-0.4640957484971.95950896312-5.0553665463929.450962806135.7111288642
21.54640512445-0.9276467102270.7093982968013.000815157610.7699527369161.65476551118-0.147972484464-1.501828281310.3353960705810.5544095203330.558599376807-0.0538069690323-0.519007273820.524647101774-0.4704428316972.528965904150.345460758886-0.3496838822361.72261818514-0.4834324367731.83531453499-0.35086934379342.538754223147.8201401173
34.959029051881.80158753395-0.2391922082340.6157697152880.2444600700841.356193160980.116387818490.4600761484280.2330928508280.156377039389-0.0794542482052-0.421819551581-0.2178877528210.1727854949150.02685041826221.772977588940.319464761794-0.1647970843761.47398910391-0.1513751848252.0079769245727.23230944944.096307677929.93827476635
40.675677699856-1.32044304408-0.5899432074067.88739862244-2.400825902182.62095669524-0.20195124878-0.275393098996-0.1833944982540.014964984501-0.00126631090511-0.7393457179790.643645441893-0.1910560013750.2297435766451.67046057097-0.0535563305125-0.3030449843991.6672012835-0.3827252224871.9230755323714.8930133351-48.272195288616.2136976087
51.36562630509-0.337345698480.1732619674823.21652913105-2.655271136732.200599355-0.0877570492244-0.266666527088-0.510029762604-0.8258311454630.4127641195060.5548052530350.818206113016-1.19401499852-0.3243004311711.79572159784-0.40271063453-0.3637617701982.82818276344-0.3106591872211.57318532377-2.30948864869-52.17738699711.3480571072
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ D|1-220 }D1 - 220
2X-RAY DIFFRACTION2{ E|1-217 }E1 - 217
3X-RAY DIFFRACTION3{ A|43-428 }A43 - 428
4X-RAY DIFFRACTION4{ B|2-218 }B2 - 218
5X-RAY DIFFRACTION5{ C|1-216 }C1 - 216

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