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- PDB-7zwm: Pfs48/45 central and C-terminal domains bound to Fab fragments of... -

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Basic information

Entry
Database: PDB / ID: 7zwm
TitlePfs48/45 central and C-terminal domains bound to Fab fragments of monoclonal antibody 10D8 and 32F3
Components
  • 10D8 heavy chain
  • 10D8 light chain
  • 32F3 heavy chain
  • 32F3 light chain
  • Gametocyte surface protein P45/48
KeywordsCELL ADHESION / Pfs48/45 / malaria / transmission-blocking / Plasmodium falciparum / gamete / antibody
Function / homology
Function and homology information


side of membrane / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Gametocyte surface protein P45/48
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.69 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
Revision 1.3Nov 20, 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: 32F3 heavy chain
C: 32F3 light chain
D: 10D8 heavy chain
E: 10D8 light chain
F: Gametocyte surface protein P45/48
G: 32F3 heavy chain
H: 32F3 light chain
I: 10D8 heavy chain
J: 10D8 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)400,98015
Polymers398,99710
Non-polymers1,9835
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)108.583, 158.451, 186.163
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "D" and (resid 2 or resid 4 through 88...
d_2ens_1(chain "I" and (resid 2 or resid 4 through 88...
d_1ens_2(chain "E" and (resid 2 through 30 or resid 32...
d_2ens_2(chain "J" and (resid 2 through 30 or resid 32...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1VALVALH1
d_12ens_1LEUSERH3 - 87
d_13ens_1ASPALAH89 - 123
d_14ens_1THRSERH125 - 159
d_15ens_1SERGLNH161 - 172
d_16ens_1LEUTHRH175 - 205
d_17ens_1VALPROH207 - 213
d_21ens_1VALVALH1
d_22ens_1LEUSERH3 - 87
d_23ens_1ASPALAH89 - 123
d_24ens_1THRPROH125 - 135
d_25ens_1METSERH138 - 161
d_26ens_1SERGLNH163 - 174
d_27ens_1LEUTHRH177 - 207
d_28ens_1VALPROH209 - 215
d_11ens_2ILEPHEI2 - 30
d_12ens_2SERTHRI32 - 108
d_13ens_2LEULEUI110
d_14ens_2ILEILEI112
d_15ens_2ARGPROI114 - 147
d_16ens_2ASPARGI149 - 161
d_17ens_2ASNSERI163 - 174
d_18ens_2ASPHISI176 - 204
d_19ens_2THRARGI206 - 217
d_21ens_2ILEPHEJ1 - 29
d_22ens_2SERTHRJ31 - 107
d_23ens_2LEULEUJ109
d_24ens_2ILEILEJ111
d_25ens_2ARGPROJ113 - 146
d_26ens_2ASPARGJ148 - 160
d_27ens_2ASNSERJ162 - 173
d_28ens_2ASPHISJ175 - 203
d_29ens_2THRARGJ205 - 216

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.99170684398, 0.0399090139083, 0.122167124104), (0.0863966694305, 0.910751750739, 0.403815383607), (-0.0951480483994, 0.411021312264, -0.906646750257)-64.29399236, 4.71393512275, -2.52143646167
2given(-0.979840701231, 0.113290570507, 0.164552261748), (0.172756268932, 0.894156453695, 0.413085351787), (-0.10033679164, 0.433185275547, -0.895702542864)-67.2630055362, 7.91098870871, -2.76304161899

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Components

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Protein , 1 types, 2 molecules AF

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


Mass: 49180.977 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

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Antibody , 4 types, 8 molecules BGCHDIEJ

#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: Antibody 10D8 heavy chain


Mass: 51485.203 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)
#5: Antibody 10D8 light chain


Mass: 26537.549 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)

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Sugars , 3 types, 5 molecules

#6: 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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#7: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#8: 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.: 3 / 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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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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10 % (w/v) PEG monomethyl ether 5000, 0.1M 2-(N-morpholino) ethanesulfonic acid pH 6.5 and 12% (v/v) 1-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 3.69→108.58 Å / Num. obs: 230227 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 138.73 Å2 / CC1/2: 0.971 / Rpim(I) all: 0.065 / Net I/σ(I): 7.2
Reflection shellResolution: 3.69→3.75 Å / Num. unique obs: 11072 / CC1/2: 0.438 / Rpim(I) all: 0.338

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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: 3.69→93.79 Å / SU ML: 0.5723 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 30.4429
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2798 1806 5.12 %
Rwork0.2552 33480 -
obs0.2565 35286 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 161.43 Å2
Refinement stepCycle: LAST / Resolution: 3.69→93.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16839 0 130 0 16969
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003617374
X-RAY DIFFRACTIONf_angle_d0.67223629
X-RAY DIFFRACTIONf_chiral_restr0.04412697
X-RAY DIFFRACTIONf_plane_restr0.00442980
X-RAY DIFFRACTIONf_dihedral_angle_d13.7156282
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2HX-RAY DIFFRACTIONTorsion NCS1.6563238316
ens_2d_2IX-RAY DIFFRACTIONTorsion NCS1.85773726862
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.69-3.790.36511240.36692534X-RAY DIFFRACTION98.7
3.79-3.90.37751080.34322561X-RAY DIFFRACTION100
3.9-4.030.3591290.3172558X-RAY DIFFRACTION100
4.03-4.170.37531420.2872530X-RAY DIFFRACTION100
4.17-4.340.30911300.24972555X-RAY DIFFRACTION99.96
4.34-4.530.27841160.23922581X-RAY DIFFRACTION100
4.53-4.770.25291430.24832539X-RAY DIFFRACTION100
4.77-5.070.28141460.24052547X-RAY DIFFRACTION100
5.07-5.460.26951490.23492573X-RAY DIFFRACTION100
5.46-6.010.31331450.26272570X-RAY DIFFRACTION100
6.01-6.880.31471620.27422580X-RAY DIFFRACTION100
6.88-8.670.27831270.24482643X-RAY DIFFRACTION100
8.67-93.790.2331850.23092709X-RAY DIFFRACTION99.59
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)
11.97537836588-1.54171718522-0.0003511963013193.24122126324-1.1051733673-0.4796864534410.1011884807110.07943930051840.575078803053-0.6328800061430.06806361694130.3944691259120.428158386764-0.189455153205-0.05228809444771.466069030480.0692567365556-0.234816578911.343695006890.1846981223391.23034805707-21.656214609730.4210917590.0583832730754
20.772483459536-0.243610286261-0.7811082036443.309879039790.102073191697-0.14207736588-0.27141932881-0.264861102692-0.05655253343990.789885532946-0.0933474777-0.4589058726970.03765063505470.07497261789770.3559837644051.253106307240.0551820897559-0.1291953310911.480371178760.4550568544061.45243564793-2.7088650994-19.844722493418.236233276
30.9249569068040.0888355477003-1.198668961244.38798889172-0.8338105923930.584811651204-0.247613740104-0.405286171831-0.570506650660.8491387686780.07744585074561.056216284520.04733800361640.1837201877770.3616225609931.295863134620.05965583581020.09175776830381.464176984470.4763645374391.49494651905-20.1042894378-19.458633326425.1961107998
42.54114277927-0.1388259917220.1535705097632.06227681466-2.380460073114.582584735150.4303687224140.259952720554-0.0673821221019-0.7172556939940.1060251594680.08560574399381.268994123891.45472207556-0.04295553135321.344729968750.250373749096-0.3213465261311.24445421845-0.3018086734171.47845153274-17.519933886354.9928552441-40.3829444161
51.212506692770.0367234438105-0.04668002078690.876636260066-3.771313484735.522291997630.6282329316180.258258410745-0.2137041513920.01162979122830.3487275451850.727600976544-0.322789406919-0.0737371234171-0.2038167440181.209054269240.0882962854486-0.3009306245171.22942666622-0.1339069406391.67026996734-27.363347817370.0896884377-43.2247710782
62.399342664332.392402471352.201069006153.26150306391.8327172584-1.36045830486-0.2068200574230.05917078595670.5277913872510.6136304432710.08199262389190.8141017451140.2164680627150.0963138119368-0.2810778052861.3847341991-0.1373122179490.1746734652931.138621489210.2366814688151.090647088-42.541338589127.959264432514.2118702612
71.62753413369-0.225335868878-2.440553088014.297602635982.077990177050.682168405554-0.280111276529-0.1179202919850.129724938478-0.01525510593640.1528743805861.087028428050.234245922470.05580887682190.04726300061141.17892183016-0.138238686161-0.386371815841.622063332210.2655570440671.31723818415-52.9334407319-15.0507163269-15.7361849975
8-0.623805953719-2.2462388268-2.825388177843.704977960992.509451131460.718294130611-0.268522025807-0.1529152021150.225547171813-0.5811958657650.5517807718460.28056381420.04189648038730.299815430542-0.06593885484351.39026109339-0.187000992616-0.4515035913581.729564179010.1188371494251.3474893384-34.6617107083-12.6280296511-18.5819863453
91.93410156-0.442396942542-2.234006406933.06866167072-2.060482284064.56893876551-0.307592628172-0.2690050452270.836405928370.440346206190.7262128203560.5009500096130.0768791860614-0.445412463149-0.357160321021.46663262068-0.2181670057610.08778024445141.39546550429-0.5242575003531.86097442885-49.694745458837.092859732158.6890661795
102.115814924141.248134257410.916542893660.8243795765082.719136544232.820121729990.0172045355911-0.8515129398751.319410587171.28885697320.0332799558517-0.7890755206920.171246472730.421931917805-0.1317883896532.464862369570.03841861474940.2206274500921.10323553735-0.9652045238511.66681682604-39.62985621148.05463473569.1286861343
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|182-428 }
2X-RAY DIFFRACTION2{ B|1-220 }
3X-RAY DIFFRACTION3{ C|1-211 }
4X-RAY DIFFRACTION4{ D|2-222 }
5X-RAY DIFFRACTION5{ E|1-217 }
6X-RAY DIFFRACTION6{ F|183-428 }
7X-RAY DIFFRACTION7{ G|1-221 }
8X-RAY DIFFRACTION8{ H|1-211 }
9X-RAY DIFFRACTION9{ I|2-222 }
10X-RAY DIFFRACTION10{ J|2-217 }

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