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- PDB-7unb: Crystal structure of malaria transmission-blocking antigen Pfs48/... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7unb | ||||||||||||||||||||||||
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Title | Crystal structure of malaria transmission-blocking antigen Pfs48/45-6C variant in complex with human antibodies RUPA-117 and RUPA-47 | ||||||||||||||||||||||||
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![]() | IMMUNE SYSTEM / Pfs48/45 / human transmission-blocking antibodies / Plasmodium falciparum / Malaria | ||||||||||||||||||||||||
Function / homology | 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 / side of membrane / cell surface / plasma membrane / Gametocyte surface protein P45/48![]() | ||||||||||||||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||||||||
![]() | Hailemariam, S. / McLeod, B. / Julien, J.-P. | ||||||||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Vaccination with a structure-based stabilized version of malarial antigen Pfs48/45 elicits ultra-potent transmission-blocking antibody responses. Authors: McLeod, B. / Mabrouk, M.T. / Miura, K. / Ravichandran, R. / Kephart, S. / Hailemariam, S. / Pham, T.P. / Semesi, A. / Kucharska, I. / Kundu, P. / Huang, W.C. / Johnson, M. / Blackstone, A. / ...Authors: McLeod, B. / Mabrouk, M.T. / Miura, K. / Ravichandran, R. / Kephart, S. / Hailemariam, S. / Pham, T.P. / Semesi, A. / Kucharska, I. / Kundu, P. / Huang, W.C. / Johnson, M. / Blackstone, A. / Pettie, D. / Murphy, M. / Kraft, J.C. / Leaf, E.M. / Jiao, Y. / van de Vegte-Bolmer, M. / van Gemert, G.J. / Ramjith, J. / King, C.R. / MacGill, R.S. / Wu, Y. / Lee, K.K. / Jore, M.M. / King, N.P. / Lovell, J.F. / Julien, J.P. | ||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 411 KB | Display | ![]() |
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PDB format | ![]() | 329 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6ghgS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Antibody , 4 types, 4 molecules LEHF
#1: Antibody | Mass: 23490.184 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#3: Antibody | Mass: 23523.211 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#4: Antibody | Mass: 23725.613 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#5: Antibody | Mass: 24253.268 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Protein / Sugars / Non-polymers , 3 types, 596 molecules R![](data/chem/img/NAG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NAG.gif)
![](data/chem/img/HOH.gif)
#2: Protein | Mass: 16515.447 Da / Num. of mol.: 1 / Mutation: G397L, H308Y, and I402V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: PF45/48, PFS45-48, PFS45/48, PF13_0247, PF3D7_1346700 / Cell (production host): epithelial / Cell line (production host): 293S / Production host: ![]() |
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#6: Sugar | ChemComp-NAG / |
#7: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M magnesium chloride, 25 % (w/v) polyethylene glycol 3350, and 0.1 M Tris |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 24, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03319 Å / Relative weight: 1 |
Reflection | Resolution: 2.18→29.43 Å / Num. obs: 65804 / % possible obs: 99.9 % / Redundancy: 12.6 % / Biso Wilson estimate: 31 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.205 / Rpim(I) all: 0.059 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.18→2.21 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.733 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2596 / CC1/2: 0.603 / Rpim(I) all: 0.281 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6GHG for RUPA-47; unpublished in-house structure for other components Resolution: 2.18→29.43 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.13 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 102.08 Å2 / Biso mean: 33.1884 Å2 / Biso min: 6.15 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.18→29.43 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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