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- PDB-5ezn: Crystal Structure of PfCyRPA -

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Basic information

Entry
Database: PDB / ID: 5ezn
TitleCrystal Structure of PfCyRPA
Components(Cysteine-rich protective antigen) x 4
KeywordsIMMUNE SYSTEM / MALARIA INHIBITORY ANTIBODY / FAB / cyrpa
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 (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsFavuzza, P. / Pluschke, G. / Rudolph, M.G.
CitationJournal: Elife / Year: 2017
Title: Structure of the malaria vaccine candidate antigen CyRPA and its complex with a parasite invasion inhibitory antibody.
Authors: Favuzza, P. / Guffart, E. / Tamborrini, M. / Scherer, B. / Dreyer, A.M. / Rufer, A.C. / Erny, J. / Hoernschemeyer, J. / Thoma, R. / Schmid, G. / Gsell, B. / Lamelas, A. / Benz, J. / Joseph, ...Authors: Favuzza, P. / Guffart, E. / Tamborrini, M. / Scherer, B. / Dreyer, A.M. / Rufer, A.C. / Erny, J. / Hoernschemeyer, J. / Thoma, R. / Schmid, G. / Gsell, B. / Lamelas, A. / Benz, J. / Joseph, C. / Matile, H. / Pluschke, G. / Rudolph, M.G.
History
DepositionNov 26, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Structure summary
Revision 1.2Apr 26, 2017Group: Other / Structure summary
Revision 1.3Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 13, 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
E: Cysteine-rich protective antigen
B: Cysteine-rich protective antigen
G: Cysteine-rich protective antigen


Theoretical massNumber of molelcules
Total (without water)78,6874
Polymers78,6874
Non-polymers00
Water905
1
A: Cysteine-rich protective antigen
E: Cysteine-rich protective antigen


Theoretical massNumber of molelcules
Total (without water)39,4952
Polymers39,4952
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-35 kcal/mol
Surface area17150 Å2
MethodPISA
2
B: Cysteine-rich protective antigen
G: Cysteine-rich protective antigen


Theoretical massNumber of molelcules
Total (without water)39,1912
Polymers39,1912
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-32 kcal/mol
Surface area17050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.240, 78.500, 97.040
Angle α, β, γ (deg.)90.000, 94.850, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cysteine-rich protective antigen


Mass: 18845.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PF3D7_0423800 / Production host: Homo sapiens (human) / References: UniProt: Q8IFM8
#2: Protein Cysteine-rich protective antigen


Mass: 20649.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PF3D7_0423800 / Production host: Homo sapiens (human) / References: UniProt: Q8IFM8
#3: Protein Cysteine-rich protective antigen


Mass: 19305.014 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: isolate 3D7 / Gene: PF3D7_0423800 / Production host: Homo sapiens (human) / References: UniProt: Q8IFM8
#4: Protein Cysteine-rich protective antigen


Mass: 19886.123 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PF3D7_0423800 / Production host: Homo sapiens (human) / References: UniProt: Q8IFM8
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.33 Å3/Da / Density % sol: 47.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0-0.5 M MgCl2, 20-25 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99998 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 2.51→43 Å / Num. obs: 23448 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 80.6 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rrim(I) all: 0.055 / Χ2: 1.046 / Net I/σ(I): 15.57 / Num. measured all: 77219
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.51-2.587.21.6310.685900175317410.2941.93499.3
2.58-2.651.2880.895696167216670.4141.52699.7
2.65-2.720.8451.345474165616410.5861.00699.1
2.72-2.810.6211.825055157215670.7430.74599.7
2.81-2.90.4362.655118158115750.8380.52399.6
2.9-30.3213.694978147814760.9070.38199.9
3-3.110.2215.184963145314560.950.263100
3.11-3.240.1467.954646139313870.9770.17499.6
3.24-3.380.10111.134285132613170.9880.12199.3
3.38-3.550.07514.44089130712990.9920.09199.4
3.55-3.740.06517.583904120111900.9950.07899.1
3.74-3.970.04822.913846115211470.9970.05799.6
3.97-4.240.03331.293541108210680.9990.03998.7
4.24-4.580.02538.843201102210120.9990.03199
4.58-5.020.02342.7729519219130.9990.02799.1
5.02-5.610.02243.0528398528480.9990.02799.5
5.61-6.480.02539.723917577510.9990.0399.2
6.48-7.940.02143.2619396296230.9990.02699
7.94-11.230.01554.93158450349310.01798
11.230.01459.281928527710.01797.2

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
PHENIXrefinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ezo, 5ezi

5ezo

5ezi


Resolution: 2.51→43 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2501 1178 4.9 %
Rwork0.1833 --
obs0.1866 24032 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 237.15 Å2 / Biso mean: 103.2297 Å2 / Biso min: 46.15 Å2
Refinement stepCycle: final / Resolution: 2.51→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5313 0 0 5 5318
Biso mean---73.61 -
Num. residues----637
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)
17.33220.3469-5.99543.6321-1.43345.6071-0.86790.1856-1.4248-0.37280.4028-0.32261.22590.48880.80150.7228-0.0504-0.02040.9224-0.26930.9847-23.374226.8829-27.1611
23.3762.0372-1.54243.9822-1.74925.0492-0.95121.8247-2.4217-1.67420.26550.39720.4686-0.62690.50690.9256-0.20280.08431.158-0.56151.1108-19.344525.8272-39.9675
35.3199-0.4449-1.72561.9107-0.89751.1094-0.06962.0227-0.3515-0.79680.667-0.23641.1693-0.45081.04931.2026-0.30070.28451.9483-0.91021.1158-15.36423.5568-45.1544
48.52052.1624-1.03124.80731.01664.933-0.66362.7591-0.0148-1.14490.6809-0.1450.2212-0.12880.13271.0619-0.10670.00951.6187-0.04590.6613-10.140638.5973-45.8244
53.01950.6875-1.23488.48870.9543.2636-0.21761.0421.1276-1.17270.3185-0.8537-0.26190.0801-0.3340.6972-0.09630.16411.20010.10910.3441-2.137143.1478-39.9982
68.73552.6384-0.60785.45270.02674.65880.17130.72780.28390.0101-0.0945-0.44540.02890.4828-0.16410.45130.02630.06660.5387-0.0140.432-3.702543.1501-27.192
78.66955.1731-4.90985.4872-2.64998.1120.2011-0.0305-0.0370.258-0.3452-0.6897-0.31730.59030.1040.51010.0743-0.0170.47040.04820.5337-14.063940.5276-19.1201
82.36281.84432.59862.34933.0914.08530.49630.3997-1.59623.30490.8168-0.14391.57-0.7467-1.12461.74920.1188-0.11620.81350.16531.1876-16.477418.684-18.3376
98.91062.98720.53122.8179-3.02587.5849-0.10050.444-0.7593-1.0330.1631.06940.751-0.2454-0.03350.6366-0.12430.01130.5968-0.0590.5951-24.490433.1613-24.6178
105.63061.3328-4.39262.239-2.02846.77710.27720.23570.7968-0.03990.17140.2767-0.93480.4131-0.36240.7607-0.1325-0.05840.50770.02540.726-4.06569.1119-7.3402
114.43930.37614.62451.90790.16426.25520.3247-0.21380.9258-0.21560.1321-0.8703-1.15291.0834-0.06540.7935-0.22960.1690.7341-0.02460.96163.193712.0046-8.3551
127.15720.4527-0.07488.3050.04422.8137-0.27510.41490.4125-1.03490.3892-0.4967-0.26630.3803-0.0110.8139-0.08110.12550.76260.07310.78811.41482.6428-20.3102
137.70043.1005-0.63216.43621.53695.8821-0.29440.8750.1594-0.76490.262-0.28480.03340.3232-0.04450.7003-0.01730.13310.60960.02240.5427-3.4236-5.1971-24.4188
144.4271-1.7916-1.5388.5650.74618.3193-0.36590.0833-0.5844-0.60420.3360.88920.3805-1.0435-0.09980.5654-0.1206-0.01020.57180.02180.6795-18.2625-8.7389-19.054
155.6769-2.9546-1.3332.91862.49182.7395-0.30450.63611.46690.44920.405-0.3462-1.2888-0.5884-0.57020.6906-0.03420.09450.78750.160.8026-21.0946-0.2108-16.807
164.10640.951-0.12633.22482.40087.9097-0.0832-0.16810.08950.09570.1016-0.0608-0.1758-0.1381-0.02450.48640.03180.07370.4010.0290.591-16.988-1.5709-2.4932
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 52 )A32 - 52
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 83 )A53 - 83
3X-RAY DIFFRACTION3chain 'A' and (resid 84 through 103 )A84 - 103
4X-RAY DIFFRACTION4chain 'A' and (resid 104 through 176 )A104 - 176
5X-RAY DIFFRACTION5chain 'A' and (resid 177 through 209 )A177 - 209
6X-RAY DIFFRACTION6chain 'A' and (resid 210 through 260 )A210 - 260
7X-RAY DIFFRACTION7chain 'A' and (resid 261 through 315 )A261 - 315
8X-RAY DIFFRACTION8chain 'A' and (resid 316 through 330 )A316 - 330
9X-RAY DIFFRACTION9chain 'A' and (resid 331 through 362 )A331 - 362
10X-RAY DIFFRACTION10chain 'B' and (resid 32 through 75 )B32 - 75
11X-RAY DIFFRACTION11chain 'B' and (resid 76 through 92 )B76 - 92
12X-RAY DIFFRACTION12chain 'B' and (resid 93 through 119 )B93 - 119
13X-RAY DIFFRACTION13chain 'B' and (resid 120 through 209 )B120 - 209
14X-RAY DIFFRACTION14chain 'B' and (resid 210 through 235 )B210 - 235
15X-RAY DIFFRACTION15chain 'B' and (resid 236 through 251 )B236 - 251
16X-RAY DIFFRACTION16chain 'B' and (resid 252 through 362 )B252 - 362

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