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

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Basic information

Entry
Database: PDB / ID: 7unb
TitleCrystal structure of malaria transmission-blocking antigen Pfs48/45-6C variant in complex with human antibodies RUPA-117 and RUPA-47
Components
  • (RUPA-117 Fab ...) x 2
  • Gametocyte surface protein P45/48
  • RUPA-47 Fab heavy chain
  • RUPA-47 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: 2.18 Å
AuthorsHailemariam, S. / McLeod, B. / Julien, J.-P.
Funding support United States, Canada, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI148557-01A1 United States
Bill & Melinda Gates FoundationOPP1156262 United States
Canadian Institutes of Health Research (CIHR)428410 Canada
Bill & Melinda Gates FoundationOPP1179906 United States
CIFAR Azrieli Global Scholars Canada
Ontario Early Researcher Awards Canada
Canada Research Chairs Canada
CitationJournal: Immunity / Year: 2022
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
DepositionApr 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 28, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 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
L: RUPA-47 Fab kappa chain
R: Gametocyte surface protein P45/48
E: RUPA-117 Fab kappa chain
H: RUPA-47 Fab heavy chain
F: RUPA-117 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,7296
Polymers111,5085
Non-polymers2211
Water10,701594
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)73.669, 127.160, 132.706
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 4 types, 4 molecules LEHF

#1: Antibody RUPA-47 Fab kappa chain


Mass: 23490.184 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
#3: Antibody RUPA-117 Fab kappa chain


Mass: 23523.211 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-47 Fab heavy chain


Mass: 23725.613 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-117 Fab heavy chain


Mass: 24253.268 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

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Protein / Sugars / Non-polymers , 3 types, 596 molecules R

#2: Protein Gametocyte surface protein P45/48


Mass: 16515.447 Da / Num. of mol.: 1 / Mutation: G397L, H308Y, and 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: isolated from a genetically manipulated source
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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 594 / Source method: isolated from a natural source / Formula: H2O

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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: 2.83 Å3/Da / Density % sol: 56.5 %
Crystal growTemperature: 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

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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: Jul 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
PHENIXv1.17.1-3660refinement
XDSdata reduction
PHASERphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GHG for RUPA-47; unpublished in-house structure for other components

6ghg


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
RfactorNum. reflection% reflection
Rfree0.228 2006 3.05 %
Rwork0.178 63715 -
obs0.1798 65721 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.08 Å2 / Biso mean: 33.1884 Å2 / Biso min: 6.15 Å2
Refinement stepCycle: final / Resolution: 2.18→29.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7730 0 14 594 8338
Biso mean--63.25 36.42 -
Num. residues----1017
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
2.18-2.230.3411420.265445134655
2.23-2.290.28521420.249344874629
2.29-2.360.2891340.229544784612
2.36-2.440.31351510.2244884639
2.44-2.530.25661370.211345184655
2.53-2.630.28481430.210745154658
2.63-2.750.26871440.207244934637
2.75-2.890.25851410.204645264667
2.89-3.070.23031450.18745494694
3.07-3.310.20721350.175345484683
3.31-3.640.22591440.164645564700
3.64-4.170.21421500.149945944744
4.17-5.240.16761460.126946494795
5.25-29.430.19071520.168948014953
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)
10.9781.0945-0.19552.8748-0.07730.18820.03080.08530.22140.1490.04440.0865-0.09210.032-0.07230.22290.00530.00870.28190.00750.2536-7.35827.31519.712
20.29520.263-0.27730.4189-0.26950.5236-0.05660.04350.0301-0.05810.052-0.02230.0651-0.00450.01260.20640.0089-0.00960.2306-0.00710.22065.7133.193-36.189
30.62570.387-0.11562.11620.45070.80790.0407-0.14140.11260.04850.0131-0.1356-0.13150.0892-0.06080.1875-0.00110.01020.2933-0.02360.256410.48725.78418.684
41.64680.1187-0.65512.3335-0.13072.5983-0.0245-0.0456-0.08120.12570.00470.03990.13050.06470.02630.1752-0.0182-0.0260.1856-0.01740.166-5.286-14.8154.174
50.64930.4136-0.79670.7998-0.89971.96110.08330.02780.16930.09260.01670.1767-0.2004-0.0027-0.12610.2288-0.00070.00740.2352-0.00220.30725.49720.714-31.267
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 1:214 )H1 - 214
2X-RAY DIFFRACTION2( CHAIN F AND ( RESID 1:216 OR RESID 301:301 ) )F1 - 216
3X-RAY DIFFRACTION2( CHAIN F AND ( RESID 1:216 OR RESID 301:301 ) )F301
4X-RAY DIFFRACTION3( CHAIN L AND RESID 1:213 )L1 - 213
5X-RAY DIFFRACTION4( CHAIN R AND RESID 292:429 )R292 - 429
6X-RAY DIFFRACTION5( CHAIN E AND RESID 1:214 )E1 - 214

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