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- PDB-9n7k: Crystal structure of human anti-Pfs48/45 transmission-blocking an... -

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Basic information

Entry
Database: PDB / ID: 9n7k
TitleCrystal structure of human anti-Pfs48/45 transmission-blocking antibody RUPA-71
Components
  • RUPA-71 Fab heavy chain
  • RUPA-71 Fab kappa chain
KeywordsIMMUNE SYSTEM / Pfs48/45 / human transmission-blocking antibodies / Malaria
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsHailemariam, S. / Ivanochko, D. / Liu, X. / Julien, J.P.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Immunity / Year: 2025
Title: Cryo-EM structure of endogenous Pfs230:Pfs48/45 complex with six antibodies reveals mechanisms of malaria transmission-blocking activity
Authors: Bekkering, E. / Yoo, R. / Hailemariam, S. / Heide, F. / Ivanochko, D. / Jackman, M. / Proellochs, N.I. / Stoter, R. / van Gemert, G. / Maeda, A. / Yuguchi, T. / Wanders, O.T. / van Daalen, R. ...Authors: Bekkering, E. / Yoo, R. / Hailemariam, S. / Heide, F. / Ivanochko, D. / Jackman, M. / Proellochs, N.I. / Stoter, R. / van Gemert, G. / Maeda, A. / Yuguchi, T. / Wanders, O.T. / van Daalen, R.C. / Inklaar, M.R. / Andrade, C.M. / Jansen, P.W.T.C. / Vermeulen, M. / Bousema, T. / Takashima, E. / Rubinstein, J.L. / Kooij, T.W.A. / Jore, M.M. / Julien, J.P.
History
DepositionFeb 6, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RUPA-71 Fab heavy chain
B: RUPA-71 Fab kappa chain
H: RUPA-71 Fab heavy chain
L: RUPA-71 Fab kappa chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,42315
Polymers96,6204
Non-polymers80311
Water3,765209
1
A: RUPA-71 Fab heavy chain
B: RUPA-71 Fab kappa chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6807
Polymers48,3102
Non-polymers3705
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-26 kcal/mol
Surface area19310 Å2
MethodPISA
2
H: RUPA-71 Fab heavy chain
L: RUPA-71 Fab kappa chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7428
Polymers48,3102
Non-polymers4326
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-13 kcal/mol
Surface area20670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.660, 74.550, 204.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody RUPA-71 Fab heavy chain


Mass: 24711.725 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 F / Production host: Homo sapiens (human)
#2: Antibody RUPA-71 Fab kappa chain


Mass: 23598.248 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 F / Production host: Homo sapiens (human)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.56 Å3/Da / Density % sol: 51.94 %
Crystal growTemperature: 100 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Ammonium Sulfate, 0.1 M MES, 30 %w/v PEG MME 5K

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.95357 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95357 Å / Relative weight: 1
ReflectionResolution: 2.28→48.85 Å / Num. obs: 46105 / % possible obs: 100 % / Redundancy: 15.4 % / CC1/2: 0.991 / Rpim(I) all: 0.099 / Net I/σ(I): 7.5
Reflection shellResolution: 2.28→2.36 Å / Redundancy: 15.2 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4434 / CC1/2: 0.561 / Rpim(I) all: 0.562 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
Aimlessdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→48.85 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2407 2000 4.34 %
Rwork0.1906 --
obs0.1932 46103 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.37 Å2
Refinement stepCycle: LAST / Resolution: 2.28→48.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6776 0 52 209 7037
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d0.991
X-RAY DIFFRACTIONf_dihedral_angle_d15.9972507
X-RAY DIFFRACTIONf_chiral_restr0.0581055
X-RAY DIFFRACTIONf_plane_restr0.0071207
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.340.32271400.27383103X-RAY DIFFRACTION100
2.34-2.40.35561430.26283121X-RAY DIFFRACTION100
2.4-2.470.31151400.2533096X-RAY DIFFRACTION100
2.47-2.550.30761390.24413070X-RAY DIFFRACTION100
2.55-2.640.30641420.2423117X-RAY DIFFRACTION100
2.64-2.750.28671410.23573131X-RAY DIFFRACTION100
2.75-2.870.27291420.2263126X-RAY DIFFRACTION100
2.87-3.020.29091410.21033111X-RAY DIFFRACTION100
3.02-3.210.27081420.19863139X-RAY DIFFRACTION100
3.21-3.460.25591430.18933148X-RAY DIFFRACTION100
3.46-3.810.21311430.17793158X-RAY DIFFRACTION100
3.81-4.360.20531450.1593196X-RAY DIFFRACTION100
4.36-5.490.17111460.14683214X-RAY DIFFRACTION100
5.49-48.850.21941530.173373X-RAY DIFFRACTION100
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)
16.8922-2.8183-2.82287.36865.97214.8145-0.2651-0.157-0.20880.69760.4082-0.41460.3180.288-0.17120.38440.0485-0.04630.32420.07230.3538-36.5003-45.6339-29.3447
23.762-0.6376-0.3450.64490.05280.5135-0.07820.0557-0.1820.00090.02380.067-0.0297-0.00140.06130.22770.00470.01910.16810.01720.1988-30.3016-40.6686-32.4147
36.2485-0.24210.83512.86880.4993.6054-0.63870.97520.5275-0.57330.2944-0.0635-0.3188-0.16070.31790.41830.02160.05960.47360.18350.5257-38.3561-18.1639-44.7229
45.21420.8681-1.60494.4449-0.79992.00530.06670.20470.6990.0270.069-0.0828-0.3533-0.0135-0.10220.26090.02940.00950.21960.04530.3447-40.5929-20.7075-35.3295
57.37740.9012-3.02210.1132-0.32431.30730.07710.65050.20760.54410.2630.19590.1017-0.4924-0.28770.34320.00020.10380.35340.13760.581-20.8088-20.1605-45.7542
63.0666-1.25190.26226.60890.8361.66640.1750.26510.1038-0.7967-0.06630.0051-0.12790.1219-0.10920.2552-0.02120.01050.29920.03360.2723-7.6206-38.2187-50.2555
77.2425-3.6741-4.50388.69176.41895.1444-0.3380.2976-0.58880.0576-0.45830.54940.2217-1.24870.74230.2845-0.04030.05940.26620.11460.3412-12.2256-14.1052-4.5487
83.11330.766-0.17645.04371.51435.9714-0.1097-0.0645-0.37680.3574-0.05790.0430.54110.05390.17950.21850.05050.04590.25750.01610.3247-0.9815-17.6078-9.0756
91.8373-1.7746-1.01932.20891.30431.1968-0.1722-0.1305-0.18580.30450.1720.08210.24570.12710.01370.260.00960.0170.24270.0140.2578-4.4648-12.3575-6.2947
104.8709-1.4573-0.64385.24661.88934.75240.22410.34340.3642-0.1638-0.17350.4736-0.8679-0.2552-0.05580.26050.03320.03240.3425-0.00290.3157-26.287522.1441-8.9763
112.711-1.11310.41562.3622-0.97424.10450.02020.0175-0.01620.0190.12360.27970.089-0.288-0.14050.22450.01940.02150.2235-0.00210.2651-27.97211.8574-7.8951
126.3672-2.1476-0.81797.05560.45943.06970.1530.21970.2721-0.7694-0.0572-0.7993-0.36710.0113-0.06610.40320.01260.12840.2714-0.0240.3282.8759-3.0362-26.2191
133.3898-4.92370.67618.4376-1.02970.030.22270.27810.0032-0.4489-0.1868-0.137-0.04180.0591-0.01120.29920.02010.0490.30270.0160.2822-1.30170.5971-22.4251
141.38830.0366-0.68862.33541.49316.9179-0.05-0.03390.09730.2054-0.0201-0.0383-0.1499-0.03320.06040.23720.0442-0.03940.20710.02640.2751-14.751723.4717-6.9663
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 216 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 25 )
4X-RAY DIFFRACTION4chain 'B' and (resid 26 through 101 )
5X-RAY DIFFRACTION5chain 'B' and (resid 102 through 113 )
6X-RAY DIFFRACTION6chain 'B' and (resid 114 through 214 )
7X-RAY DIFFRACTION7chain 'H' and (resid 1 through 17 )
8X-RAY DIFFRACTION8chain 'H' and (resid 18 through 59 )
9X-RAY DIFFRACTION9chain 'H' and (resid 60 through 124 )
10X-RAY DIFFRACTION10chain 'H' and (resid 125 through 145 )
11X-RAY DIFFRACTION11chain 'H' and (resid 146 through 214 )
12X-RAY DIFFRACTION12chain 'L' and (resid 1 through 75 )
13X-RAY DIFFRACTION13chain 'L' and (resid 76 through 113 )
14X-RAY DIFFRACTION14chain 'L' and (resid 114 through 213 )

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