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- PDB-7pi7: PfCyRPA bound to monoclonal antibody Cy.002 Fab fragment -

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Basic information

Entry
Database: PDB / ID: 7pi7
TitlePfCyRPA bound to monoclonal antibody Cy.002 Fab fragment
Components
  • Cysteine-rich protective antigen
  • Monoclonal antibody Cy.002 heavy chain
  • Monoclonal antibody Cy.002 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cysteine-rich protective antigen
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å
AuthorsRagotte, R.J. / Higgins, M.K.
Funding support1items
OrganizationGrant numberCountry
Wellcome Trust
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 19, 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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.002 heavy chain
C: Monoclonal antibody Cy.002 light chain
D: Cysteine-rich protective antigen
E: Monoclonal antibody Cy.002 heavy chain
F: Monoclonal antibody Cy.002 light chain


Theoretical massNumber of molelcules
Total (without water)174,7996
Polymers174,7996
Non-polymers00
Water1,36976
1
A: Cysteine-rich protective antigen
B: Monoclonal antibody Cy.002 heavy chain
C: Monoclonal antibody Cy.002 light chain


Theoretical massNumber of molelcules
Total (without water)87,3993
Polymers87,3993
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-30 kcal/mol
Surface area32600 Å2
MethodPISA
2
D: Cysteine-rich protective antigen
E: Monoclonal antibody Cy.002 heavy chain
F: Monoclonal antibody Cy.002 light chain


Theoretical massNumber of molelcules
Total (without water)87,3993
Polymers87,3993
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-29 kcal/mol
Surface area33110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)205.050, 80.690, 117.360
Angle α, β, γ (deg.)90.000, 108.730, 90.000
Int Tables number5
Space group name H-MC121

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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 (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: CyRPA, pfd1130w, PF3D7_0423800 / Production host: Homo sapiens (human) / References: UniProt: Q8IFM8
#2: Antibody Monoclonal antibody Cy.002 heavy chain


Mass: 23525.227 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.002 light chain


Mass: 23690.127 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.63 Å3/Da / Density % sol: 53.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M lithium sulfate, 30 % polyvinylpyrrolidone K15, 0.1 M HEPES pH7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.72→48.55 Å / Num. obs: 169805 / % possible obs: 99.6 % / Redundancy: 3.5 % / CC1/2: 0.999 / Net I/σ(I): 13.3
Reflection shellResolution: 2.72→2.81 Å / Num. unique obs: 15709 / CC1/2: 0.864

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Processing

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

5tih


Resolution: 2.72→37.92 Å / Cor.coef. Fo:Fc: 0.869 / Cor.coef. Fo:Fc free: 0.841 / SU R Cruickshank DPI: 2.35 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.453 / SU Rfree Blow DPI: 0.389 / SU Rfree Cruickshank DPI: 0.403
RfactorNum. reflection% reflectionSelection details
Rfree0.3005 2096 4.28 %RANDOM
Rwork0.2728 ---
obs0.274 48960 99.8 %-
Displacement parametersBiso max: 229.92 Å2 / Biso mean: 100.55 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-21.2625 Å20 Å28.8946 Å2
2---38.2103 Å20 Å2
3---16.9478 Å2
Refine analyzeLuzzati coordinate error obs: 0.51 Å
Refinement stepCycle: final / Resolution: 2.72→37.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11867 0 0 76 11943
Biso mean---67.93 -
Num. residues----1377
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4142SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2054HARMONIC5
X-RAY DIFFRACTIONt_it12146HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1608SEMIHARMONIC5
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_contact8244SEMIHARMONIC0
X-RAY DIFFRACTIONt_bond_d12146HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg16479HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion3.32
X-RAY DIFFRACTIONt_other_torsion19.61
LS refinement shellResolution: 2.72→2.74 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3385 42 4.29 %
Rwork0.3862 938 -
all-980 -
obs--99.7 %
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)
11.34970.3930.36240-0.27950.7409-0.06660.1144-0.04950.05440.02270.0494-0.03450.08590.0439-0.016-0.00670.0191-0.1167-0.0807-0.026319.7768-29.158141.8119
20.1776-0.3064-0.31430-0.46383.03440.1949-0.03490.0453-0.07910.13060.22120.02810.5628-0.3254-0.3040.0016-0.01230.304-0.16-0.23090.4216-29.786789.9358
30.6153-0.5402-1.30950.47081.08112.37240.0186-0.02740.12120.11480.1928-0.08050.190.1698-0.2114-0.01060.076-0.0006-0.001-0.1347-0.106-16.2608-23.725187.1643
41.98150.04930.88630.23040.21430.7780.0856-0.113-0.0497-0.1125-0.0552-0.07330.0301-0.1252-0.0305-0.03250.0197-0.0263-0.0982-0.0877-0.0262.747510.134741.0613
52.47040.2562-1.676801.92591.5955-0.1473-0.3650.50640.05850.41370.12330.23290.4509-0.2665-0.24750.1379-0.10370.304-0.1137-0.183239.195210.88684.5511
60.5406-0.4752-1.29510.01570.64742.9372-0.0111-0.07380.35720.16810.19850.04540.22970.5497-0.1874-0.16250.0939-0.07740.2169-0.1241-0.103330.37074.7591-9.7882
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|31 - A|361 }A31 - 361
2X-RAY DIFFRACTION2{ B|20 - B|238 }B20 - 238
3X-RAY DIFFRACTION3{ C|21 - C|236 }C21 - 236
4X-RAY DIFFRACTION4{ D|31 - D|362 }D31 - 362
5X-RAY DIFFRACTION5{ E|20 - E|238 }E20 - 238
6X-RAY DIFFRACTION6{ F|21 - F|236 }F21 - 236

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