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- PDB-7phw: PfCyRPA bound to monoclonal antibody Cy.004 Fab fragment -

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Basic information

Entry
Database: PDB / ID: 7phw
TitlePfCyRPA bound to monoclonal antibody Cy.004 Fab fragment
Components
  • Cysteine-rich protective antigen
  • Monoclonal antibody Cy.004 heavy chain
  • Monoclonal antibody Cy.004 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: 2.793 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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.004 heavy chain
C: Monoclonal antibody Cy.004 light chain
D: Cysteine-rich protective antigen
E: Monoclonal antibody Cy.004 heavy chain
F: Monoclonal antibody Cy.004 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,76810
Polymers193,6086
Non-polymers1604
Water00
1
A: Cysteine-rich protective antigen
B: Monoclonal antibody Cy.004 heavy chain
C: Monoclonal antibody Cy.004 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8845
Polymers96,8043
Non-polymers802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Cysteine-rich protective antigen
E: Monoclonal antibody Cy.004 heavy chain
F: Monoclonal antibody Cy.004 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8845
Polymers96,8043
Non-polymers802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.057, 80.316, 114.910
Angle α, β, γ (deg.)90.000, 115.230, 90.000
Int Tables number4
Space group name H-MP1211

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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.004 heavy chain


Mass: 34168.133 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.004 light chain


Mass: 22451.641 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: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: 2.22 Å3/Da / Density % sol: 44.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 20 % PEG 6000, 0.1 M Tris pH 8.5

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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: 2.79→47.11 Å / Num. obs: 284862 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.992 / Net I/σ(I): 6.8
Reflection shellResolution: 2.79→2.87 Å / Num. unique obs: 13827 / CC1/2: 0.757

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (24-FEB-2021)refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TIH

5tih


Resolution: 2.793→47.11 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.86 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.392
RfactorNum. reflection% reflectionSelection details
Rfree0.2769 2164 5.15 %RANDOM
Rwork0.2391 ---
obs0.2411 42008 99 %-
Displacement parametersBiso max: 176.5 Å2 / Biso mean: 90.11 Å2 / Biso min: 43.84 Å2
Baniso -1Baniso -2Baniso -3
1--15.5246 Å20 Å29.2231 Å2
2---11.0269 Å20 Å2
3---26.5515 Å2
Refine analyzeLuzzati coordinate error obs: 0.44 Å
Refinement stepCycle: final / Resolution: 2.793→47.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11676 0 4 0 11680
Biso mean--82.54 --
Num. residues----1494
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4033SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2025HARMONIC5
X-RAY DIFFRACTIONt_it11956HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1574SEMIHARMONIC5
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_contact8649SEMIHARMONIC0
X-RAY DIFFRACTIONt_bond_d11956HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg16224HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion3.09
X-RAY DIFFRACTIONt_other_torsion20.45
LS refinement shellResolution: 2.793→2.82 Å
RfactorNum. reflection% reflection
Rfree0.434 49 5.83 %
Rwork0.4146 792 -
obs--77.47 %
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)
10.30920.59510.04670.8794-0.28693.23850.02940.03710.02720.041-0.0146-0.0415-0.14110.0606-0.01480.21350.060.0263-0.08190.02560.096686.9602-27.9585-14.2793
20.0907-0.2744-0.66610.43530.35284.4920.0303-0.05080.012-0.1224-0.0132-0.04-0.1233-0.2661-0.01710.0821-0.0333-0.04740.05470.01080.139569.4627-16.660635.703
30.3921-0.2216-0.257800.05952.74270.108-0.03150.09610.05440.0122-0.02640.42130.0337-0.12020.284-0.0962-0.0008-0.03030.00460.053177.4601-29.678646.0787
40.28720.29920.19650.14930.35496.7827-0.06870.24520.1320.2415-0.1052-0.19640.5535-0.20320.17390.2661-0.0698-0.0126-0.0565-0.0644-0.107276.221811.8057-39.4784
5-0.0142-0.2106-0.45130.753-0.60224.3143-0.1167-0.04640.1374-0.12250.2898-0.067-0.1632-0.4319-0.1731-0.0404-0.0071-0.07850.17230.02120.131360.332125.451811.8071
6-0.0079-0.08680.03880-0.02933.5303-0.0329-0.1320.0768-0.15270.2013-0.15550.4287-0.4744-0.16840.2760.007-0.03280.05070.04510.006866.85611.325521.656
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A31 - 362
2X-RAY DIFFRACTION2{ B|* }B20 - 246
3X-RAY DIFFRACTION3{ C|* }C23 - 231
4X-RAY DIFFRACTION4{ D|* }D31 - 362
5X-RAY DIFFRACTION5{ E|* }E20 - 245
6X-RAY DIFFRACTION6{ F|* }F24 - 230

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