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- PDB-6z2l: Structure of Plasmodium falciparum P113 bound to antibody P3.2 -

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Basic information

Entry
Database: PDB / ID: 6z2l
TitleStructure of Plasmodium falciparum P113 bound to antibody P3.2
Components
  • FAb fragment - VH chain
  • FAb fragment - VL chain
  • Surface protein P113
KeywordsCELL INVASION / protein complex / Fab-antigen / invasion
Function / homology: / symbiont-containing vacuole membrane / plasma membrane / Surface protein P113
Function and homology information
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsCampeotto, I. / Higgins, K.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
Citation
Journal: Mbio / Year: 2020
Title: The Structure of the Cysteine-Rich Domain of Plasmodium falciparum P113 Identifies the Location of the RH5 Binding Site.
Authors: Campeotto, I. / Galaway, F. / Mehmood, S. / Barfod, L.K. / Quinkert, D. / Kotraiah, V. / Phares, T.W. / Wright, K.E. / Snijders, A.P. / Draper, S.J. / Higgins, M.K. / Wright, G.J.
#1: Journal: Biorxiv / Year: 2020
Title: Structure of the cysteine-rich domain of Plasmodium falciparum P113 identifies the location of the RH5 binding site
Authors: Campeotto, I. / Galaway, F. / Mehmood, S. / Barfod, L.K. / Quinkert, D. / Kotraiah, V. / Phares, T.W. / Wright, K.E. / Snijders, A.P. / Draper, S.J. / Higgins, K.M. / Wright, G.J.
History
DepositionMay 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Data collection / Refinement description / Category: refine / reflns / reflns_shell
Item: _refine.ls_d_res_low / _reflns.d_resolution_low ..._refine.ls_d_res_low / _reflns.d_resolution_low / _reflns.number_all / _reflns.number_obs / _reflns.pdbx_CC_half / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rpim_I_all / _reflns.pdbx_netI_over_sigmaI / _reflns.pdbx_redundancy / _reflns.percent_possible_obs / _reflns_shell.Rmerge_I_obs / _reflns_shell.d_res_low / _reflns_shell.meanI_over_sigI_obs / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_CC_half / _reflns_shell.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rrim_I_all / _reflns_shell.pdbx_redundancy / _reflns_shell.percent_possible_all
Revision 1.2Sep 30, 2020Group: Database references / Category: citation / citation_author
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI ..._citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Surface protein P113
B: FAb fragment - VL chain
C: FAb fragment - VH chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6664
Polymers73,5703
Non-polymers961
Water7,116395
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-38 kcal/mol
Surface area28710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.921, 96.921, 177.898
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Surface protein P113 /


Mass: 23057.244 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Lys methylation method was used resulting on methylation of some Lys residues
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: P113, PF3D7_1420700 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q8ILP3
#2: Antibody FAb fragment - VL chain


Mass: 24827.506 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Antibody FAb fragment - VH chain


Mass: 25684.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 395 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2M NH4SO4, 0.1M MES pH=6.5, 20% w/v PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.95→96.92 Å / Num. all: 1636680 / Num. obs: 62581 / % possible obs: 100 % / Redundancy: 26.2 % / CC1/2: 0.994 / Rpim(I) all: 0.042 / Net I/σ(I): 16.6
Reflection shellResolution: 1.95→2 Å / Redundancy: 26.2 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4310 / CC1/2: 0.571 / Rpim(I) all: 1.422 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (19-MAR-2020)refinement
PDB_EXTRACT3.22data extraction
autoPROCdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U0R

4u0r


Resolution: 1.95→96.92 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.938 / SU R Cruickshank DPI: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.15 / SU Rfree Blow DPI: 0.131 / SU Rfree Cruickshank DPI: 0.128
RfactorNum. reflection% reflectionSelection details
Rfree0.2257 3110 4.98 %RANDOM
Rwork0.2047 ---
obs0.2058 62481 100 %-
Displacement parametersBiso max: 138.89 Å2 / Biso mean: 43.14 Å2 / Biso min: 13.86 Å2
Baniso -1Baniso -2Baniso -3
1-4.2067 Å20 Å20 Å2
2--4.2067 Å20 Å2
3----8.4135 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: final / Resolution: 1.95→96.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4929 0 5 395 5329
Biso mean--79.98 50.3 -
Num. residues----631
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1713SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes854HARMONIC5
X-RAY DIFFRACTIONt_it5039HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion674SEMIHARMONIC5
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_contact4475SEMIHARMONIC0
X-RAY DIFFRACTIONt_bond_d5043HARMONIC20.013
X-RAY DIFFRACTIONt_angle_deg6848HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion6.33
X-RAY DIFFRACTIONt_other_torsion18.15
LS refinement shellResolution: 1.95→1.96 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2673 60 4.8 %
Rwork0.2353 1190 -
all-1250 -
obs--99.77 %
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)
10.65070.2665-0.066900.12850.41150.0881-0.02680.1974-0.0689-0.11420.10640.15790.0070.0261-0.04820.0037-0.0461-0.0913-0.0508-0.058610.517951.055-17.6815
20.06690.40010.3620.5160.13830.31650.094-0.1442-0.06120.062-0.1315-0.01170.0015-0.00980.0374-0.0803-0.00620.0121-0.0654-0.0162-0.05120.44260.2223-14.9419
30.0220.31750.09690.40170.02870.191-0.0415-0.0423-0.1155-0.0236-0.0022-0.0784-0.0949-0.04590.0437-0.07750.03730.004-0.0868-0.0292-0.03927.5246.8685-29.5479
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 197
2X-RAY DIFFRACTION2{ B|* }B11 - 223
3X-RAY DIFFRACTION3{ C|* }C20 - 240

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