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- PDB-9n8n: Tandem antigen chimera of Pfs230 and Pfs48/45 bound by potent mAbs -

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Basic information

Entry
Database: PDB / ID: 9n8n
TitleTandem antigen chimera of Pfs230 and Pfs48/45 bound by potent mAbs
Components
  • Gametocyte surface protein P230,Gametocyte surface protein P45/48
  • RUPA-39 Kappa chain
  • RUPA-39 heavy chain
  • RUPA-44 Kappa chain
  • RUPA-44 heavy chain
KeywordsIMMUNE SYSTEM / Malaria vaccine / 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
Similarity search - Domain/homology
ACETATE ION / CACODYLATE ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Gametocyte surface protein P230 / Gametocyte surface protein P45/48
Similarity search - Component
Biological speciesHomo sapiens (human)
Plasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsIvanochko, D. / Semesi, A. / Julien, J.P.
Funding support United States, Canada, 3items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-008866 and OPP1156262 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI148557-01A1 United States
Canadian Institutes of Health Research (CIHR)428410 Canada
CitationJournal: Nat Commun / Year: 2026
Title: A stabilized tandem antigen chimera that elicits potent malaria transmission-reducing activity.
Authors: Danton Ivanochko / Kazutoyo Miura / Sophia Hailemariam / Rashmi Ravichandran / Yiting Song / Wei-Chiao Huang / Rianne Stoter / Karina Teelen / Geert-Jan van Gemert / Elizabeth M Leaf / ...Authors: Danton Ivanochko / Kazutoyo Miura / Sophia Hailemariam / Rashmi Ravichandran / Yiting Song / Wei-Chiao Huang / Rianne Stoter / Karina Teelen / Geert-Jan van Gemert / Elizabeth M Leaf / Sidney Chan / Christine Men / Anthony Semesi / Carol Shiu / Randall S MacGill / Carole A Long / Matthijs M Jore / Neil P King / Jonathan F Lovell / Jean-Philippe Julien /
Abstract: Malaria parasite transmission remains a barrier to elimination since asymptomatic individuals sustain the infectious reservoir. Transmission-blocking vaccine (TBV) candidates targeting Plasmodium ...Malaria parasite transmission remains a barrier to elimination since asymptomatic individuals sustain the infectious reservoir. Transmission-blocking vaccine (TBV) candidates targeting Plasmodium falciparum (Pf) gametocyte surface proteins Pfs230 and Pfs48/45 have shown promise in clinical trials. Several vaccine candidates have been developed for these antigens, yet it is unclear which elicit the most robust and durable transmission-blocking responses. From structure-function relationships of monoclonal antibodies in complex with both antigens, we report the development of a stabilized tandem antigen chimera (STAC), which presents the most potent epitopes from Pfs230 domain 1 (Pfs230-D1) and Pfs48/45 domain 3 (Pfs48/45-D3) in a single construct, while masking non-functional epitopes using an engineered pseudo-native domain disposition. Iterative structure-guided optimization improved antigen yields and stability, while nanoparticle-based multimerization enhanced the functional transmission-reducing activity elicited by the immunogen in female mice. Immunizations with STAC genetically conjugated to self-assembling protein nanoparticles elicited antibodies with potent transmission-reducing activity comparable or superior to the multimerized Pfs230-D1 and Pfs48/45-D3. These findings establish STAC as a promising next-generation TBV candidate to disrupt malaria transmission and accelerate elimination efforts. More broadly, our results support the engineering of highly ordered and stable multi-domain antigens in a single protein as a strategy for the cost-efficient development of multi-component vaccines.
History
DepositionFeb 9, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2026Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RUPA-39 heavy chain
B: RUPA-39 Kappa chain
E: RUPA-44 Kappa chain
F: RUPA-44 heavy chain
I: Gametocyte surface protein P230,Gametocyte surface protein P45/48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,13045
Polymers131,8045
Non-polymers3,32640
Water8,125451
1
A: RUPA-39 heavy chain
B: RUPA-39 Kappa chain
E: RUPA-44 Kappa chain
F: RUPA-44 heavy chain
I: Gametocyte surface protein P230,Gametocyte surface protein P45/48
hetero molecules

A: RUPA-39 heavy chain
B: RUPA-39 Kappa chain
E: RUPA-44 Kappa chain
F: RUPA-44 heavy chain
I: Gametocyte surface protein P230,Gametocyte surface protein P45/48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)270,26090
Polymers263,60710
Non-polymers6,65380
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation2_656-x+1,y,-z+11
Buried area37150 Å2
ΔGint-70 kcal/mol
Surface area102920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)227.990, 80.490, 137.730
Angle α, β, γ (deg.)90.000, 111.460, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Components on special symmetry positions
IDModelComponents
11E-455-

HOH

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Components

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Antibody , 4 types, 4 molecules ABEF

#1: Antibody RUPA-39 heavy chain


Mass: 24054.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody RUPA-39 Kappa chain


Mass: 23420.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody RUPA-44 Kappa chain


Mass: 23483.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody RUPA-44 heavy chain


Mass: 24277.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 2 molecules I

#5: Protein Gametocyte surface protein P230,Gametocyte surface protein P45/48


Mass: 36568.180 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, PF45/48, PFS45-48, PFS45/48, PF13_0247, PF3D7_1346700
Production host: Homo sapiens (human) / References: UniProt: P68874, UniProt: Q8I6T1
#6: 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

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Non-polymers , 9 types, 490 molecules

#7: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#10: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#11: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H12NO3 / Comment: pH buffer*YM
#12: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#13: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#14: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#15: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 451 / Source method: isolated from a natural source / Formula: H2O

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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: 4.46 Å3/Da / Density % sol: 72.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Na Cacodylate pH 6.5, 40% PEG 300, 0.2 M Ca acetate, 15% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.03322 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03322 Å / Relative weight: 1
ReflectionResolution: 2.22→75.26 Å / Num. obs: 81183 / % possible obs: 93.6 % / Redundancy: 16.1 % / CC1/2: 0.998 / Rpim(I) all: 0.051 / Net I/σ(I): 12.2
Reflection shellResolution: 2.22→2.45 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4058 / CC1/2: 0.637 / Rpim(I) all: 0.499

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→70.1 Å / SU ML: 0.231 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.3355
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2097 1999 2.46 %
Rwork0.1744 79137 -
obs0.1753 81136 70.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.03 Å2
Refinement stepCycle: LAST / Resolution: 2.22→70.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8977 0 203 451 9631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01089349
X-RAY DIFFRACTIONf_angle_d1.244612647
X-RAY DIFFRACTIONf_chiral_restr0.07371434
X-RAY DIFFRACTIONf_plane_restr0.0091597
X-RAY DIFFRACTIONf_dihedral_angle_d7.69741308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.270.375430.351120X-RAY DIFFRACTION1.51
2.27-2.340.4074160.2899646X-RAY DIFFRACTION8.13
2.34-2.40.3646410.291577X-RAY DIFFRACTION19.81
2.4-2.480.2706660.28232640X-RAY DIFFRACTION33.17
2.48-2.570.35951070.27244244X-RAY DIFFRACTION53.02
2.57-2.670.28141500.28035932X-RAY DIFFRACTION74.19
2.67-2.80.30371910.26597574X-RAY DIFFRACTION95.02
2.8-2.940.28112020.24527994X-RAY DIFFRACTION99.98
2.94-3.130.32040.22668035X-RAY DIFFRACTION100
3.13-3.370.23552010.19468013X-RAY DIFFRACTION100
3.37-3.710.19242030.15998018X-RAY DIFFRACTION99.99
3.71-4.240.19082030.13378045X-RAY DIFFRACTION100
4.24-5.350.1372050.11388107X-RAY DIFFRACTION100
5.35-70.10.17372070.16228192X-RAY DIFFRACTION99.47
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)
12.440388856140.1586884950361.181161591011.33656426304-2.0931154085.10412915740.0821961727324-0.009548639137440.2599404660050.3294367622690.07904907609970.000704329819683-0.6561606386660.0324997455935-0.1601484238870.3775725641-0.02632508806770.06731702383970.33966204979-0.1521707029630.30884030819434.127531509817.5407283773-5.02776528024
27.048647595362.59270494904-2.976599837954.48530663005-1.463387001874.967286778580.289757241073-0.4549986911010.7761191337250.505718333456-0.2216173106741.08731960711-0.648948043656-0.674285066974-0.0616347538310.4029126304320.04074439657650.1288989176930.713387163392-0.1304600757540.5326456236455.3604141069321.5999056839-24.330724671
34.41620932734-0.6503649241563.237401388873.683484362450.8631925535034.152672976650.1348603700230.00703627603569-1.092657376650.01374815768480.154308411446-0.2636827724510.220407643146-0.371616757803-0.3455718632270.255839535838-0.05215923203220.03329745903520.419896065308-0.04266296533340.54387291112821.5809592348-4.58786063301-1.54560530401
46.511255076271.715298951362.785207038971.021613755610.2315185349532.287397872440.0366326033206-0.130713353595-0.3301831538570.1405417042710.09528326217680.0258989477209-0.109097773068-0.649710810693-0.1384967228180.2687235208210.05691798940340.08410687222930.489065723073-0.02663327166370.32082948619719.20011022233.051573566470.962561895651
53.306337505332.11491038021-2.024858145054.46510888453-3.428818494645.50475684677-0.3643023240080.464992863137-0.0711442522915-0.8113326932350.3141413739590.1504202332280.632761831425-0.3552070321270.03556775529170.417851706226-0.1215555838160.04238787640750.845826799209-0.1259168714460.3849481209763.192902875796.39119084405-30.9331429165
66.624635857592.889663996833.457765443622.535770003951.700730816332.9272561980.08008846810460.0224182320377-0.1612761660050.0914170111655-0.0136758701712-0.05056657839090.2440089247590.124318528456-0.06785717164420.3403275825050.0437505346561-0.001845952514030.1572441550120.02603286935690.17445339681284.859524188347.852024595853.2744196669
72.65544683045-0.7573487459090.2048122906669.91478849805-2.566369198462.00590801951-0.171376618499-0.1866430559790.9804015503371.039951852270.04739764099870.016010641385-0.8566622822930.2220588349410.1066034797710.630947778379-0.106422511546-0.1023753500870.284012098896-0.009211591446830.64629651679694.592130292383.576299323554.219333218
85.27950094246-1.81044491601-2.358804093068.217962995493.539831045977.69877248829-0.1365009464640.1553326982171.10109645801-0.2935278865970.3746717849270.0543853052023-0.376950056592-0.096042649488-0.2524685365060.2727338109-0.0299676579364-0.05859540572240.3046738271290.1096287669440.35920979969871.552013190262.583297713834.8956170537
95.26920282710.214118978455-0.08469279035325.85949939027-1.439101499762.60471932593-0.007449361264250.3081101432030.368333621520.09398568846960.04133027597450.297370982578-0.179575479255-0.279823142467-0.02297024903750.2024048678860.0154527616145-0.05635103435070.190630503050.07567183098330.20719292317571.864579641352.038197099937.3730287215
102.218713863720.3056240339950.896781249725.850268352071.860417305782.088377692950.008739600701810.2223645622610.305304724774-0.070405383092-0.1028924734850.508791445749-0.180423893425-0.2647827352160.1074374777740.225860648752-0.0071366016332-0.002582828951240.243500518510.05599914211830.24771208777168.287705758251.505986561338.0504046567
115.77456016390.847092394261-0.3852614528396.02881156279-1.058773745072.86059707009-0.417793210540.5734879016081.35352997954-0.1663045134560.106042525670.466613448804-0.4992264171410.1526004184630.2535066380070.4936007761910.0359599677261-0.06905147049760.2043366975310.06958284517780.41285221331283.213148696581.47215309940.7174926198
126.44126420693-0.933507047050.3351072119363.38711115155-1.037815928112.69604953909-0.0581448104890.1925192907780.797431196940.0121121238341-0.00882073029810.0508273554976-0.5248767730970.11417227460.02856825982110.426458186191-0.0482039972615-0.07713482220840.1986376066560.07259511614320.3786688684288.756429604176.384683972342.0048705965
138.51697989548-2.628046533360.7788291835455.26123084250.02773933376943.908952597150.04954288515440.9253384889031.28401751409-0.714936863328-0.0742878400635-0.309692093594-0.513508512390.4104845400560.05861499958230.522873939893-0.0198228231637-0.02210423495460.3249502468960.1300354368020.50756288678594.551490138879.478438231336.5281555967
145.26094208682-1.153277095822.77310249744.94840274149-0.07015992199015.694351711630.4183224175110.768341570015-1.26124246843-0.2946561936930.0596214558451-0.2290041194920.5615412536781.07196224425-0.461954910070.3659782479920.0884591840996-0.1086326953020.656170504347-0.2656704998540.70378389826754.2564675386-1.714243580769.68491951148
153.682584051083.77558240633.604542046785.479951716365.828041445023.37303762101-0.1626418417960.485850601526-0.472324939568-0.2673031104160.452102453598-0.174062583724-0.03798765441820.386146756431-0.2263009086260.4952198464150.0163442357928-0.1499844889840.368880280184-0.06344196676250.42126932907968.409082280620.488433988429.8027581185
165.02376503605-5.007148954181.426247425255.990977191390.3879328186549.539292436920.52924779901-1.0500689540.3364658753152.16071469996-0.171268842649-0.1265205635740.730511119473-0.63193877961-0.4313087475431.19530608781-0.133737830571-0.2239905192730.5966485455210.09704304735780.76260229506971.117286642216.148727247347.9653288503
174.953163104232.704812907330.784947925387.46300579291.102155617735.178543612950.3366081435780.242401654875-0.8487785665490.2662992212150.0523751857759-0.4650980508230.8853697960960.101399651051-0.3973627717730.5431490668860.0560425257293-0.2328774027810.252451062685-0.07058798495420.49595022554370.49860610317.79621357436.8587225695
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 111 )AA1 - 1111 - 122
22chain 'A' and (resid 112 through 213 )AA112 - 213123 - 217
33chain 'B' and (resid 1 through 32 )BF1 - 321 - 32
44chain 'B' and (resid 33 through 113 )BF33 - 11333 - 114
55chain 'B' and (resid 114 through 213 )BF114 - 213115 - 214
66chain 'E' and (resid 1 through 113 )ER1 - 1131 - 113
77chain 'E' and (resid 114 through 213 )ER114 - 213114 - 209
88chain 'F' and (resid 1 through 17 )FAA1 - 171 - 17
99chain 'F' and (resid 18 through 51 )FAA18 - 5118 - 53
1010chain 'F' and (resid 52 through 109 )FAA52 - 10954 - 123
1111chain 'F' and (resid 110 through 134 )FAA110 - 134124 - 142
1212chain 'F' and (resid 135 through 175 )FAA135 - 175143 - 183
1313chain 'F' and (resid 176 through 214 )FAA176 - 214184 - 222
1414chain 'I' and (resid 8 through 168 )IE8 - 1681 - 161
1515chain 'I' and (resid 169 through 244 )IE169 - 244162 - 237
1616chain 'I' and (resid 245 through 267 )IE245 - 267238 - 260
1717chain 'I' and (resid 268 through 315 )IE268 - 315261 - 308

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