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- PDB-6h5n: Plasmodium falciparum Pfs48/45 C-terminal domain bound to monoclo... -

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Basic information

Entry
Database: PDB / ID: 6h5n
TitlePlasmodium falciparum Pfs48/45 C-terminal domain bound to monoclonal antibody 85RF45.1
Components
  • Antibody 85RF45.1 heavy chain
  • Antibody 85RF45.1 light chain
  • Gametocyte surface protein P45/48
KeywordsCELL INVASION / Pfs48/45 Gamete Fusion Plasmodium falciparum Transmission blocking Monoclonal 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
Gametocyte surface protein P45/48
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.23 Å
AuthorsLennartz, F. / Higgins, M.K.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/R001138/1 United Kingdom
Wellcome Trust101020/Z/13/Z United Kingdom
CitationJournal: Nat Commun / Year: 2018
Title: Structural basis for recognition of the malaria vaccine candidate Pfs48/45 by a transmission blocking antibody.
Authors: Lennartz, F. / Brod, F. / Dabbs, R. / Miura, K. / Mekhaiel, D. / Marini, A. / Jore, M.M. / Sogaard, M.M. / Jorgensen, T. / de Jongh, W.A. / Sauerwein, R.W. / Long, C.A. / Biswas, S. / Higgins, M.K.
History
DepositionJul 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
A: Gametocyte surface protein P45/48
B: Antibody 85RF45.1 light chain
C: Antibody 85RF45.1 heavy chain
D: Gametocyte surface protein P45/48
E: Antibody 85RF45.1 light chain
F: Antibody 85RF45.1 heavy chain


Theoretical massNumber of molelcules
Total (without water)124,2716
Polymers124,2716
Non-polymers00
Water0
1
A: Gametocyte surface protein P45/48
B: Antibody 85RF45.1 light chain
C: Antibody 85RF45.1 heavy chain


Theoretical massNumber of molelcules
Total (without water)62,1353
Polymers62,1353
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-28 kcal/mol
Surface area25420 Å2
MethodPISA
2
D: Gametocyte surface protein P45/48
E: Antibody 85RF45.1 light chain
F: Antibody 85RF45.1 heavy chain


Theoretical massNumber of molelcules
Total (without water)62,1353
Polymers62,1353
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-31 kcal/mol
Surface area25480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.690, 165.390, 189.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Gametocyte surface protein P45/48


Mass: 15073.829 Da / Num. of mol.: 2
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 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q8I6T1
#2: Antibody Antibody 85RF45.1 light chain


Mass: 23205.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Rattus norvegicus (Norway rat)
#3: Antibody Antibody 85RF45.1 heavy chain


Mass: 23855.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Rattus norvegicus (Norway rat)

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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: 3.79 Å3/Da / Density % sol: 67.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2M ammonium dihydrogen phosphate, 0.1M Tris 8.5 Buffer, 50 % v/v 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97624 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 3.23→41.98 Å / Num. obs: 30979 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 64.17 Å2 / Net I/σ(I): 5.4
Reflection shellResolution: 3.23→3.29 Å

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4k2u

4k2u


Resolution: 3.23→41.98 Å / Cor.coef. Fo:Fc: 0.841 / Cor.coef. Fo:Fc free: 0.809 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.465
RfactorNum. reflection% reflectionSelection details
Rfree0.282 1564 5.05 %RANDOM
Rwork0.261 ---
obs0.262 30979 99.8 %-
Displacement parametersBiso mean: 91.7 Å2
Baniso -1Baniso -2Baniso -3
1--7.022 Å20 Å20 Å2
2--17.6255 Å20 Å2
3----10.6035 Å2
Refine analyzeLuzzati coordinate error obs: 0.61 Å
Refinement stepCycle: 1 / Resolution: 3.23→41.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8407 0 0 0 8407
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0058622HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8511752HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2834SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1439HARMONIC5
X-RAY DIFFRACTIONt_it8622HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.83
X-RAY DIFFRACTIONt_other_torsion16.08
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1172SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9372SEMIHARMONIC0
LS refinement shellResolution: 3.23→3.34 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2886 145 5.14 %
Rwork0.2539 2678 -
all0.2556 2823 -
obs--99.68 %
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)
10.08430.82810.02241.06850.70610.0903-0.005-0.0218-0.01140.02890.02510.0121-0.0172-0.0312-0.0202-0.01310.0622-0.0112-0.16660.00380.035-17.2667-34.396958.1371
200.5413-0.85120.02840.75670.48960.00990.0367-0.0318-0.04340.02460.02180.00780.0661-0.0345-0.01730.0035-0.0416-0.0564-0.0572-0.0235-12.0832-7.637217.8876
30-0.1243-0.41160-0.08650.42610.0044-0.0748-0.0525-0.111-0.02870.0392-0.0845-0.07040.0243-0.0845-0.0670.0715-0.0105-0.02360.009-14.3862.461233.0517
40-1.00851.05511.9347-1.27220.8714-0.0083-0.01570.01780.00010.01760.02670.01030.0096-0.00930.01320.057-0.0401-0.12360.05870.0453-12.721-56.376355.2976
50.43340.59430.83440.09261.19411.6165-0.007-0.0510.0201-0.00380.02250.0046-0.01120.0019-0.0155-0.0293-0.05490.0483-0.052-0.0142-0.0748-16.9928-83.903514.979
600.7636-0.14370.00550.28430.5354-0.015-0.0870.0979-0.0694-0.0085-0.03770.04410.01570.0235-0.08430.0028-0.0014-0.0752-0.10070.0505-15.376-93.716230.5697
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }

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