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- PDB-7pi3: PfCyRPA bound to Fab fragments from monoclonal antibodies Cy.003,... -

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Basic information

Entry
Database: PDB / ID: 7pi3
TitlePfCyRPA bound to Fab fragments from monoclonal antibodies Cy.003, Cy.004 and Cy.007
Components
  • (Monoclonal antibody Cy.003 ...) x 2
  • (Monoclonal antibody Cy.004 ...) x 2
  • (Monoclonal antibody Cy.007 ...) x 2
  • Cysteine-rich protective antigen
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
Cysteine-rich protective antigen
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.269 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 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

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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.003 heavy chain
C: Monoclonal antibody Cy.003 light chain
D: Monoclonal antibody Cy.007 heavy chain
E: Monoclonal antibody Cy.007 light chain
F: Monoclonal antibody Cy.004 heavy chain
G: Monoclonal antibody Cy.004 light chain
H: Cysteine-rich protective antigen
I: Monoclonal antibody Cy.003 heavy chain
J: Monoclonal antibody Cy.003 light chain
K: Monoclonal antibody Cy.007 heavy chain
L: Monoclonal antibody Cy.007 light chain
M: Monoclonal antibody Cy.004 heavy chain
N: Monoclonal antibody Cy.004 light chain
O: Cysteine-rich protective antigen
P: Monoclonal antibody Cy.003 heavy chain
Q: Monoclonal antibody Cy.003 light chain
R: Monoclonal antibody Cy.007 heavy chain
S: Monoclonal antibody Cy.007 light chain
T: Monoclonal antibody Cy.004 heavy chain
U: Monoclonal antibody Cy.004 light chain
V: Cysteine-rich protective antigen
W: Monoclonal antibody Cy.003 heavy chain
X: Monoclonal antibody Cy.003 light chain
Y: Monoclonal antibody Cy.007 heavy chain
Z: Monoclonal antibody Cy.007 light chain
a: Monoclonal antibody Cy.004 heavy chain
b: Monoclonal antibody Cy.004 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)758,09436
Polymers757,77328
Non-polymers3218
Water00
1
A: Cysteine-rich protective antigen
B: Monoclonal antibody Cy.003 heavy chain
C: Monoclonal antibody Cy.003 light chain
D: Monoclonal antibody Cy.007 heavy chain
E: Monoclonal antibody Cy.007 light chain
F: Monoclonal antibody Cy.004 heavy chain
G: Monoclonal antibody Cy.004 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,5239
Polymers189,4437
Non-polymers802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: Cysteine-rich protective antigen
I: Monoclonal antibody Cy.003 heavy chain
J: Monoclonal antibody Cy.003 light chain
K: Monoclonal antibody Cy.007 heavy chain
L: Monoclonal antibody Cy.007 light chain
M: Monoclonal antibody Cy.004 heavy chain
N: Monoclonal antibody Cy.004 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,5239
Polymers189,4437
Non-polymers802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
O: Cysteine-rich protective antigen
P: Monoclonal antibody Cy.003 heavy chain
Q: Monoclonal antibody Cy.003 light chain
R: Monoclonal antibody Cy.007 heavy chain
S: Monoclonal antibody Cy.007 light chain
T: Monoclonal antibody Cy.004 heavy chain
U: Monoclonal antibody Cy.004 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,5239
Polymers189,4437
Non-polymers802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
V: Cysteine-rich protective antigen
W: Monoclonal antibody Cy.003 heavy chain
X: Monoclonal antibody Cy.003 light chain
Y: Monoclonal antibody Cy.007 heavy chain
Z: Monoclonal antibody Cy.007 light chain
a: Monoclonal antibody Cy.004 heavy chain
b: Monoclonal antibody Cy.004 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,5239
Polymers189,4437
Non-polymers802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)164.842, 164.842, 382.311
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

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Antibody , 6 types, 24 molecules BIPWCJQXDKRYELSZFMTaGNUb

#2: Antibody
Monoclonal antibody Cy.003 heavy chain


Mass: 23855.576 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Homo sapiens (human)
#3: Antibody
Monoclonal antibody Cy.003 light chain


Mass: 22372.590 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Homo sapiens (human)
#4: Antibody
Monoclonal antibody Cy.007 heavy chain


Mass: 24030.791 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Homo sapiens (human)
#5: Antibody
Monoclonal antibody Cy.007 light chain


Mass: 22380.545 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Homo sapiens (human)
#6: Antibody
Monoclonal antibody Cy.004 heavy chain


Mass: 34168.133 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Homo sapiens (human)
#7: Antibody
Monoclonal antibody Cy.004 light chain


Mass: 22451.641 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Homo sapiens (human)

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Protein / Non-polymers , 2 types, 12 molecules AHOV

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


Mass: 40184.039 Da / Num. of mol.: 4
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
#8: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca

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Details

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: 3.74 Å3/Da / Density % sol: 67.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.25 % 1,5-Naphthalenedisulfonic acid disodium salt, 0.25 % 2,7-naphthalenedisulfonic acid disodium salt, 0.25 % 5-Sulfoisophthalic acid monosodium salt, 0.25 % sulfanilic acid, 0.02 M HEPES sodium pH 6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.269→164.84 Å / Num. obs: 1115594 / % possible obs: 99.9 % / Redundancy: 7.1 % / CC1/2: 0.998 / Net I/σ(I): 9.4
Reflection shellResolution: 3.27→3.28 Å / Num. unique obs: 1589 / CC1/2: 0.586

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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: 3.269→47.64 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.883 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.516
RfactorNum. reflection% reflectionSelection details
Rfree0.2976 7806 4.99 %RANDOM
Rwork0.2846 ---
obs0.2852 156578 99.9 %-
Displacement parametersBiso max: 299.06 Å2 / Biso mean: 187.19 Å2 / Biso min: 68.7 Å2
Baniso -1Baniso -2Baniso -3
1-27.1911 Å20 Å20 Å2
2--27.1911 Å20 Å2
3----54.3822 Å2
Refine analyzeLuzzati coordinate error obs: 0.59 Å
Refinement stepCycle: final / Resolution: 3.269→47.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms48839 0 0 0 48839
Num. residues----4918
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d16569SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes8457HARMONIC5
X-RAY DIFFRACTIONt_it49984HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion6630SEMIHARMONIC5
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_contact31219SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d49984HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg67958HARMONIC20.9
X-RAY DIFFRACTIONt_omega_torsion2.39
X-RAY DIFFRACTIONt_other_torsion21.72
LS refinement shellResolution: 3.27→3.29 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3764 171 5.46 %
Rwork0.3857 2961 -
all-3132 -
obs--99.65 %
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)
10-5.8208-0.82956.5354-3.71413.1105-0.09440.43611.0885-0.3856-0.46681.08850.66660.73290.56120.19790.14340.304-0.25430.0473-0.424151.7257-39.8979-27.4164
20.1971-0.42351.44993.949-3.06612.23920.2578-0.260.0817-0.24910.028-0.20640.2499-0.3101-0.28590.17720.0770.304-0.33880.14640.607951.8511-80.8685.7957
30.9451-0.53671.03623.7455-1.2691.99460.4704-0.20320.18940.246-0.2285-0.5250.0787-0.0903-0.2419-0.03260.05760.1868-0.31340.19250.607963.2576-74.322118.7016
43.53882.57581.78640.97551.04735.56650.0304-0.7403-0.01960.4075-0.15260.3447-0.18050.66830.12230.00530.27930.2391-0.05070.02270.607990.0411-36.51989.4584
57.2772-0.88615.54721.9489-0.97064.1360.0949-0.30510.1390.747-0.0559-0.2529-0.2040.6495-0.03890.01580.25470.3040.06160.11790.6079102.728-49.58674.5671
64.6259-5.8208-4.21774.952.07793.44690.06890.50790.05780.0783-0.1889-0.0116-0.00740.11720.12-0.17230.3040.304-0.23350.11320.352593.1178-74.0142-39.4531
77.7572-5.8208-1.1523.910.83612.0138-0.04660.2251-0.04850.11070.19070.4720.23460.5531-0.1441-0.02170.29530.304-0.48050.02530.607994.7517-83.6168-23.9578
84.79631.03620.29845.78980.77311.65820.1128-0.43270.25990.0992-0.2650.0692-0.1050.11030.1522-0.2446-0.14860.304-0.3633-0.02120.607932.5801-40.587938.3339
90.66130.61291.4613.49422.74461.46930.10040.02090.0268-0.3045-0.02310.26770.20850.2073-0.07730.3178-0.03130.2918-0.43870.04140.607929.656-80.29973.653
101.14940.77761.2522.27570.69321.03510.2680.33460.2245-0.4653-0.170.35810.0239-0.1018-0.0980.11660.00060.1373-0.2365-0.05180.607918.7634-72.3801-9.081
115.8831-3.56713.6292.4858-2.2425.8168-0.06670.702-0.2075-0.6901-0.0489-0.4571-0.1274-0.74820.1156-0.0228-0.1710.0646-0.11990.06860.6079-6.6557-34.55062.4923
128.18571.91415.82081.70050.92383.85880.07360.15460.2755-0.61030.0338-0.01920.0029-0.7678-0.1074-0.279-0.13690.11870.0922-0.14520.6079-19.4938-47.43137.3378
137.02944.2618-2.76797.5902-1.27392.4457-0.0553-0.4633-0.41020.004-0.19760.09840.7083-0.04510.2529-0.1026-0.3040.2945-0.3073-0.20170.6079-7.6599-74.752551.8205
149.53455.8208-0.942810.30650.81221.626-0.12560.0956-0.4897-0.4816-0.15770.15090.4532-0.30330.2833-0.2468-0.3040.304-0.5798-0.3040.6079-10.6548-84.382436.3926
153.6014-1.2385-1.14386.32930.692.9470.04860.3229-0.08720.085-0.14550.0270.0837-0.34090.0969-0.25970.1440.1218-0.49620.15540.607928.36155.6711-24.8343
162.0110.6824-0.03615.12474.57893.719-0.0955-0.6427-0.2932-0.0314-0.05280.2024-0.6381-0.2040.14830.41890.28530.0822-0.50370.11720.607932.892145.71239.5983
170.2098-1.4721-1.33484.64913.29364.49360.0695-0.7453-0.31850.2043-0.11820.0164-0.5216-0.42390.04870.11040.26840.14880.0716-0.24960.607923.60638.395123.8532
183.56042.0998-4.62061.0807-1.46756.13940.0354-0.65120.29820.5702-0.1427-0.63410.158-0.25960.10720.03290.3040.3040.0459-0.00170.6079-4.53440.701116.7912
196.2686-1.318-5.82082.20990.51074.46170.1112-0.2043-0.06630.6089-0.1563-0.40820.2804-0.44510.0451-0.210.19440.19790.2493-0.12760.6079-18.836213.525914.018
2011.5175-5.82080.0195.41280.06321.7647-0.03260.1886-0.2382-0.0422-0.2132-0.01140.003-0.29250.2458-0.49650.304-0.0594-0.2033-0.04680.6079-16.072537.4455-28.1313
217.5551-5.8208-0.86899.46270.68371.15990.0746-0.23770.28430.5889-0.1584-0.3706-0.2277-0.22870.0838-0.27380.3040.1073-0.5062-0.13460.6079-16.062846.3427-11.6431
225.15772.1836-1.54157.7989-0.46633.16770.2139-0.6184-0.38180.441-0.45-0.4217-0.02960.34310.2361-0.2153-0.2938-0.1478-0.52150.16460.607957.31814.334337.1647
230.46392.74-1.759910.9018-4.50531.10870.0052-0.0926-0.2605-0.68720.32890.33870.1575-0.408-0.33410.2936-0.08990.0858-0.6079-0.02640.607954.574745.16764.0284
240.88580.5426-1.01815.6728-1.52982.4090.49340.1526-0.5967-0.9501-0.1644-0.2259-0.2929-0.0515-0.3290.24640.04570.304-0.49560.02060.607963.201637.5295-11.1247
253.8566-2.3151-4.19092.02822.65487.4880.05030.66560.0694-0.6944-0.17460.63560.12130.47950.1244-0.0202-0.3040.2378-0.11250.02650.607989.2443-1.4297-5.4567
267.28172.7622-5.82083.9481-1.42933.9840.15670.4089-0.2885-0.8511-0.17650.41450.30410.48450.0197-0.1989-0.1769-0.01380.34370.09170.6079103.47911.1085-2.536
2710.03775.82081.83095.73670.83373.0134-0.0846-0.3431-0.36640.04680.0313-0.02710.2997-0.0760.0533-0.532-0.304-0.1801-0.45820.06790.6079102.08134.988241.9018
289.57165.8208-0.754216.0235-3.61751.93570.0559-0.23890.1777-0.4902-0.01680.43250.0910.2545-0.0391-0.3511-0.3040.0101-0.6001-0.04620.6079102.89843.931625.5106
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A31 - 361
2X-RAY DIFFRACTION2{ B|* }B21 - 246
3X-RAY DIFFRACTION3{ C|* }C23 - 229
4X-RAY DIFFRACTION4{ D|* }D20 - 244
5X-RAY DIFFRACTION5{ E|* }E23 - 229
6X-RAY DIFFRACTION6{ F|* }F20 - 246
7X-RAY DIFFRACTION7{ G|* }G23 - 231
8X-RAY DIFFRACTION8{ H|* }H31 - 361
9X-RAY DIFFRACTION9{ I|* }I21 - 246
10X-RAY DIFFRACTION10{ J|* }J23 - 229
11X-RAY DIFFRACTION11{ K|* }K21 - 244
12X-RAY DIFFRACTION12{ L|* }L24 - 229
13X-RAY DIFFRACTION13{ M|* }M20 - 246
14X-RAY DIFFRACTION14{ N|* }N23 - 231
15X-RAY DIFFRACTION15{ O|* }O31 - 361
16X-RAY DIFFRACTION16{ P|* }P21 - 246
17X-RAY DIFFRACTION17{ Q|* }Q23 - 229
18X-RAY DIFFRACTION18{ R|* }R20 - 244
19X-RAY DIFFRACTION19{ S|* }S26 - 229
20X-RAY DIFFRACTION20{ T|* }T21 - 245
21X-RAY DIFFRACTION21{ U|* }U24 - 231
22X-RAY DIFFRACTION22{ V|* }V31 - 361
23X-RAY DIFFRACTION23{ W|* }W21 - 246
24X-RAY DIFFRACTION24{ X|* }X24 - 229
25X-RAY DIFFRACTION25{ Y|* }Y20 - 244
26X-RAY DIFFRACTION26{ Z|* }Z23 - 229
27X-RAY DIFFRACTION27{ a|* }a21 - 243
28X-RAY DIFFRACTION28{ b|* }b23 - 230

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