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- PDB-7phv: PfCyRPA bound to monoclonal antibody Cy.007 Fab fragment -

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Basic information

Entry
Database: PDB / ID: 7phv
TitlePfCyRPA bound to monoclonal antibody Cy.007 Fab fragment
Components
  • Cysteine-rich protective antigen
  • Monoclonal antibody Cy.007 heavy chain
  • Monoclonal antibody Cy.007 light chain
KeywordsIMMUNE SYSTEM / malaria / Plasmodium falciparum / monoclonal antibody / vaccine
Function / homology
Function and homology information


microneme lumen / microneme / symbiont entry into host / apical part of cell / cytoplasmic vesicle / host extracellular space / host cell plasma membrane / protein-containing complex / extracellular region / plasma membrane
Similarity search - Function
Cysteine-rich protective antigen 6 bladed domain / Cysteine-Rich Protective Antigen 6 bladed domain
Similarity search - Domain/homology
AMMONIUM ION / Cysteine-rich protective antigen
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.091 Å
AuthorsRagotte, R.J. / Higgins, M.K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Nat Commun / Year: 2022
Title: Heterotypic interactions drive antibody synergy against a malaria vaccine candidate.
Authors: Ragotte, R.J. / Pulido, D. / Lias, A.M. / Quinkert, D. / Alanine, D.G.W. / Jamwal, A. / Davies, H. / Nacer, A. / Lowe, E.D. / Grime, G.W. / Illingworth, J.J. / Donat, R.F. / Garman, E.F. / ...Authors: Ragotte, R.J. / Pulido, D. / Lias, A.M. / Quinkert, D. / Alanine, D.G.W. / Jamwal, A. / Davies, H. / Nacer, A. / Lowe, E.D. / Grime, G.W. / Illingworth, J.J. / Donat, R.F. / Garman, E.F. / Bowyer, P.W. / Higgins, M.K. / Draper, S.J.
History
DepositionAug 18, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: 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 31, 2024Group: 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
A: Cysteine-rich protective antigen
B: Monoclonal antibody Cy.007 heavy chain
C: Monoclonal antibody Cy.007 light chain
D: Cysteine-rich protective antigen
E: Monoclonal antibody Cy.007 heavy chain
F: Monoclonal antibody Cy.007 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,9628
Polymers173,9266
Non-polymers362
Water0
1
A: Cysteine-rich protective antigen
B: Monoclonal antibody Cy.007 heavy chain
C: Monoclonal antibody Cy.007 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9814
Polymers86,9633
Non-polymers181
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Cysteine-rich protective antigen
E: Monoclonal antibody Cy.007 heavy chain
F: Monoclonal antibody Cy.007 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9814
Polymers86,9633
Non-polymers181
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.097, 87.000, 342.774
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cysteine-rich protective antigen / Inactive sialidase CyRPA / PfCyRPA


Mass: 40184.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Strain: isolate 3D7 / Gene: CyRPA, pfd1130w, PF3D7_0423800 / Production host: Homo sapiens (human) / References: UniProt: Q8IFM8
#2: Antibody Monoclonal antibody Cy.007 heavy chain


Mass: 24398.260 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Homo sapiens (human)
#3: Antibody Monoclonal antibody Cy.007 light chain


Mass: 22380.545 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Gallus gallus (chicken)
#4: Chemical ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N
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: 3.37 Å3/Da / Density % sol: 63.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M zinc acetate, 10 % PEG 3000, 0.1 M sodium acetate pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.09→48.97 Å / Num. obs: 564609 / % possible obs: 99.9 % / Redundancy: 13.5 % / CC1/2: 0.969 / Net I/σ(I): 5.1
Reflection shellResolution: 3.09→3.22 Å / Num. unique obs: 62331 / CC1/2: 0.733

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (20-OCT-2021)refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TIH

5tih


Resolution: 3.091→45.24 Å / Cor.coef. Fo:Fc: 0.811 / Cor.coef. Fo:Fc free: 0.725 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.527
RfactorNum. reflection% reflectionSelection details
Rfree0.3321 2060 4.95 %RANDOM
Rwork0.287 ---
obs0.2892 41616 100 %-
Displacement parametersBiso max: 255.34 Å2 / Biso mean: 176.04 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-30.7741 Å20 Å20 Å2
2---75.201 Å20 Å2
3---44.427 Å2
Refine analyzeLuzzati coordinate error obs: 0.61 Å
Refinement stepCycle: final / Resolution: 3.091→45.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11519 0 2 0 11521
Biso mean--95.53 --
Num. residues----1180
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3964SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1996HARMONIC5
X-RAY DIFFRACTIONt_it11792HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1560SEMIHARMONIC5
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_contact7350SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d11792HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg16010HARMONIC20.95
X-RAY DIFFRACTIONt_omega_torsion2.54
X-RAY DIFFRACTIONt_other_torsion19.84
LS refinement shellResolution: 3.091→3.11 Å
RfactorNum. reflection% reflection
Rfree0.492 48 5.76 %
Rwork0.4072 785 -
obs--97.96 %
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)
11.10340.48990.56112.3312-1.00081.6977-0.20870.13630.0553-0.0540.1030.01930.04130.12590.1058-0.2189-0.0382-0.0037-0.35310.23110.129410.5564-19.8706-9.6937
26.10850.44733.1750.85961.36374.8252-0.01521.0885-0.1882-0.2098-0.07960.290.129-0.1220.09470.02-0.304-0.304-0.00760.21650.0279-24.7208-39.5267-44.418
36.864805.82083.4930.886915.02440.14861.0885-0.6673-0.7853-0.14590.26270.144-1.0885-0.00270.4588-0.304-0.25530.5950.1634-0.428-21.0051-30.5994-60.4478
41.58010.59211.09513.1056-1.94853.5016-0.39560.4236-0.0009-0.03840.1021-0.0577-0.18790.29120.2935-0.1175-0.2239-0.2045-0.33490.3040.0452-23.0419-74.0152-26.427
57.60560.30915.82081.78440.32487.53250.24050.55910.0407-0.0979-0.44560.261-0.0706-0.82470.2052-0.4334-0.0528-0.3040.60790.1939-0.3295-65.7219-81.4229-57.6873
65.665-1.16815.82085.6417-0.727713.42430.13320.6518-0.5422-0.6749-0.29090.55040.0097-0.95560.15770.2127-0.0508-0.3040.60790.1686-0.6079-60.5808-73.6721-74.1791
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A32 - 361
2X-RAY DIFFRACTION2{ B|* }B20 - 244
3X-RAY DIFFRACTION3{ C|* }C23 - 229
4X-RAY DIFFRACTION4{ D|* }D32 - 361
5X-RAY DIFFRACTION5{ E|* }E21 - 244
6X-RAY DIFFRACTION6{ F|* }F23 - 229

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