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- PDB-6e63: Crystal structure of malaria transmission-blocking antigen Pfs48/... -

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Basic information

Entry
Database: PDB / ID: 6.0E+63
TitleCrystal structure of malaria transmission-blocking antigen Pfs48/45 6C in complex with antibody TB31F
Components
  • Pf48/45
  • TB31F Fab heavy chain
  • TB31F Fab light chain
KeywordsIMMUNE SYSTEM / malaria / transmission-blocking / antigen / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Pf48/45 / Gametocyte surface protein P45/48
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsKundu, P. / Semesi, A. / Julien, J.P.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1108403 United States
CitationJournal: Nat Commun / Year: 2018
Title: Structural delineation of potent transmission-blocking epitope I on malaria antigen Pfs48/45.
Authors: Kundu, P. / Semesi, A. / Jore, M.M. / Morin, M.J. / Price, V.L. / Liang, A. / Li, J. / Miura, K. / Sauerwein, R.W. / King, C.R. / Julien, J.P.
History
DepositionJul 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: Pf48/45
H: TB31F Fab heavy chain
L: TB31F Fab light chain
A: Pf48/45
B: TB31F Fab heavy chain
C: TB31F Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,8718
Polymers124,6876
Non-polymers1842
Water3,405189
1
P: Pf48/45
H: TB31F Fab heavy chain
L: TB31F Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4364
Polymers62,3433
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-31 kcal/mol
Surface area24550 Å2
MethodPISA
2
A: Pf48/45
B: TB31F Fab heavy chain
C: TB31F Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4364
Polymers62,3433
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-29 kcal/mol
Surface area24120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.994, 120.907, 177.562
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11C-328-

HOH

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Components

#1: Protein Pf48/45


Mass: 15332.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Production host: Homo sapiens (human) / References: UniProt: A8QVT1, UniProt: Q8I6T1*PLUS
#2: Antibody TB31F Fab heavy chain


Mass: 23841.736 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody TB31F Fab light chain


Mass: 23169.549 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O
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: 2.24 Å3/Da / Density % sol: 45.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris, pH 6.0, 22% (w/v) PEG 3350, 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.6→49.9 Å / Num. obs: 35359 / % possible obs: 99.9 % / Redundancy: 13.2 % / Net I/σ(I): 8.9
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3678 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 2.6→49.899 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.49
RfactorNum. reflection% reflection
Rfree0.2398 1765 5 %
Rwork0.2018 --
obs0.2037 35294 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→49.899 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8447 0 12 189 8648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058670
X-RAY DIFFRACTIONf_angle_d0.7611802
X-RAY DIFFRACTIONf_dihedral_angle_d18.9913135
X-RAY DIFFRACTIONf_chiral_restr0.0491330
X-RAY DIFFRACTIONf_plane_restr0.0051501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.67030.3791310.31872479X-RAY DIFFRACTION100
2.6703-2.74890.32731350.28022569X-RAY DIFFRACTION100
2.7489-2.83760.26961320.25812502X-RAY DIFFRACTION100
2.8376-2.9390.32941350.25172559X-RAY DIFFRACTION100
2.939-3.05660.28521350.24772561X-RAY DIFFRACTION100
3.0566-3.19570.23951330.21442529X-RAY DIFFRACTION100
3.1957-3.36420.24541350.20882556X-RAY DIFFRACTION100
3.3642-3.57490.22571350.19672558X-RAY DIFFRACTION100
3.5749-3.85080.2191350.20172576X-RAY DIFFRACTION100
3.8508-4.23820.24011360.17192595X-RAY DIFFRACTION100
4.2382-4.8510.18361380.15282615X-RAY DIFFRACTION100
4.851-6.110.22441400.17782647X-RAY DIFFRACTION100
6.11-49.90790.22011450.19332783X-RAY DIFFRACTION100

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