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- PDB-7uxl: Crystal structure of malaria transmission-blocking antigen Pfs48/... -

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Basic information

Entry
Database: PDB / ID: 7uxl
TitleCrystal structure of malaria transmission-blocking antigen Pfs48/45-6C variant in complex with human antibodies RUPA-44 and RUPA-29
Components
  • Gametocyte surface protein P45/48
  • RUPA-29 Fab Heavy chain
  • RUPA-29 Fab Lambda chain
  • RUPA-44 Fab Heavy chain
  • RUPA-44 Fab Kappa chain
KeywordsIMMUNE SYSTEM / Pfs48/45 / human transmission-blocking antibodies / Plasmodium falciparum / Malaria
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 speciesHomo sapiens (human)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 Å
AuthorsHailemariam, S. / Ivanochko, D. / Julien, J.P.
Funding support Canada, United States, 4items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)428410 Canada
Ontario Early Researcher Awards Canada
Bill & Melinda Gates FoundationOPP1170236 United States
Canada Research Chairs Canada
CitationJournal: Immunity / Year: 2023
Title: Highly potent, naturally acquired human monoclonal antibodies against Pfs48/45 block Plasmodium falciparum transmission to mosquitoes.
Authors: Fabra-Garcia, A. / Hailemariam, S. / de Jong, R.M. / Janssen, K. / Teelen, K. / van de Vegte-Bolmer, M. / van Gemert, G.J. / Ivanochko, D. / Semesi, A. / McLeod, B. / Vos, M.W. / de Bruijni, ...Authors: Fabra-Garcia, A. / Hailemariam, S. / de Jong, R.M. / Janssen, K. / Teelen, K. / van de Vegte-Bolmer, M. / van Gemert, G.J. / Ivanochko, D. / Semesi, A. / McLeod, B. / Vos, M.W. / de Bruijni, M.H.C. / Bolscher, J.M. / Szabat, M. / Vogt, S. / Kraft, L. / Duncan, S. / Kamya, M.R. / Feeney, M.E. / Jagannathan, P. / Greenhouse, B. / Dechering, K.J. / Sauerwein, R.W. / King, C.R. / MacGill, R.S. / Bousema, T. / Julien, J.P. / Jore, M.M.
History
DepositionMay 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 25, 2023Group: 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
E: RUPA-44 Fab Kappa chain
F: RUPA-44 Fab Heavy chain
R: Gametocyte surface protein P45/48
A: RUPA-29 Fab Heavy chain
B: RUPA-29 Fab Lambda chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,4716
Polymers111,2495
Non-polymers2211
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)223.081, 223.081, 223.081
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23

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Components

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Antibody , 4 types, 4 molecules EFAB

#1: Antibody RUPA-44 Fab Kappa chain


Mass: 23483.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): epithelial / Cell line (production host): 293S / Production host: Homo sapiens (human) / Tissue (production host): embryonic kidney
#2: Antibody RUPA-44 Fab Heavy chain


Mass: 24277.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): epithelial / Cell line (production host): 293S / Production host: Homo sapiens (human) / Tissue (production host): embryonic kidney
#4: Antibody RUPA-29 Fab Heavy chain


Mass: 23912.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): epithelial / Cell line (production host): 293F / Production host: Homo sapiens (human) / Tissue (production host): embryonic kidney
#5: Antibody RUPA-29 Fab Lambda chain


Mass: 23061.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): epithelial / Cell line (production host): 293F / Production host: Homo sapiens (human) / Tissue (production host): embryonic kidney

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Protein / Sugars , 2 types, 2 molecules R

#3: Protein Gametocyte surface protein P45/48


Mass: 16515.447 Da / Num. of mol.: 1 / Mutation: G397L, H308Y, I402V
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 / Cell (production host): epithelial / Cell line (production host): 293S / Production host: Homo sapiens (human) / Tissue (production host): embryonic kidney / References: UniProt: Q8I6T1
#6: 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.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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 interestY

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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: 4.16 Å3/Da / Density % sol: 70.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2 M calcium acetate, 0.1 M MES, and 20 % (w/v) polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03319 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 2.86→29.81 Å / Num. obs: 42583 / % possible obs: 99.9 % / Redundancy: 40.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.025 / Net I/σ(I): 23.2
Reflection shellResolution: 2.86→2.91 Å / Redundancy: 41 % / Rmerge(I) obs: 0.927 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2126 / CC1/2: 0.612 / Rpim(I) all: 0.146 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QF1, 7K8P, 6E63

4qf1

7k8p

6e63


Resolution: 2.86→29.81 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.54 / Stereochemistry target values: ML
Details: Poor electron density for the RUPA-29 Fab constant domain may in part be attributed to two extra VL residues introduced aberrantly during cloning in the hinge of the lambda chain. To more ...Details: Poor electron density for the RUPA-29 Fab constant domain may in part be attributed to two extra VL residues introduced aberrantly during cloning in the hinge of the lambda chain. To more accurately account for the experimental density in this region, two conformations of the RUPA-29 constant domain were built with partial occupancies of 0.60 and 0.40.
RfactorNum. reflection% reflection
Rfree0.2218 1997 4.69 %
Rwork0.1834 40578 -
obs0.1852 42575 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 427.66 Å2 / Biso mean: 93.4031 Å2 / Biso min: 46.19 Å2
Refinement stepCycle: final / Resolution: 2.86→29.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7691 0 14 0 7705
Biso mean--156.38 --
Num. residues----1014
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.86-2.930.34611400.292928833023
2.93-3.010.36821400.277428472987
3.01-3.10.31400.256829163056
3.1-3.20.28831410.251728512992
3.2-3.310.28471410.235128913032
3.31-3.450.24061400.21628773017
3.45-3.60.26881420.207228673009
3.6-3.790.23111440.19629213065
3.79-4.030.23241450.17528773022
4.03-4.340.20051410.147428923033
4.34-4.770.17051450.129929023047
4.78-5.460.18011400.137929253065
5.46-6.860.20471530.184729273080
6.87-29.810.21581450.196330023147
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)
12.36352.4055-0.71542.96120.21040.0669-0.08640.1814-0.302-0.15150.00390.30860.0092-0.1480.10560.60320.152-0.06150.68360.15831.0402-78.929-112.69917.846
23.56294.5304-1.17553.9148-0.22160.29970.02040.11410.16820.2352-0.05280.3568-0.0769-0.18290.01450.54330.1373-0.01030.69780.22911.2151-91.582-105.48727.503
35.9799-1.4567-0.20350.77630.80121.74920.0613-0.6448-0.3416-0.2105-0.24260.139-0.2371-0.21140.18710.69450.035-0.15860.53550.04650.6386-90.947-50.69521.36
43.7866-1.4824-0.37462.20921.48582.6276-0.0351-0.64690.2871-0.1592-0.1207-0.2846-0.4233-0.09510.13930.7446-0.0878-0.18720.54510.08990.5723-75.36-42.13326.547
54.5983-1.1611-2.11777.27882.64838.7614-0.09010.19880.0971-0.281-0.0012-0.93050.06761.02810.04130.41920.05050.04880.76210.29250.8032-46.55-74.75711.143
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:214 )A1 - 214
2X-RAY DIFFRACTION2( CHAIN B AND RESID 1:211 )B1 - 211
3X-RAY DIFFRACTION3( CHAIN E AND RESID 1:212 )E1 - 212
4X-RAY DIFFRACTION4( CHAIN F AND RESID 1:215 )F1 - 215
5X-RAY DIFFRACTION5( CHAIN R AND RESID 292:429 )R292 - 429

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