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Basic information

Entry
Database: PDB / ID: 5tik
TitleStructural basis for inhibition of erythrocyte invasion by antibodies to Plasmodium falciparum protein CyRPA
ComponentsCysteine-rich protective antigen
KeywordsIMMUNE SYSTEM / Plasmodium falciparum CyRPA Inhibitory antibody
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 / molecular replacement / Resolution: 3.09 Å
AuthorsChen, L. / Xu, Y. / Wang, W. / Thompson, J.K. / Goddard-Borger, E. / Lawrence, M.C. / Cowman, A.F.
CitationJournal: Elife / Year: 2017
Title: Structural basis for inhibition of erythrocyte invasion by antibodies toPlasmodium falciparumprotein CyRPA.
Authors: Chen, L. / Xu, Y. / Wong, W. / Thompson, J.K. / Healer, J. / Goddard-Borger, E.D. / Lawrence, M.C. / Cowman, A.F.
History
DepositionOct 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.title / _citation_author.name / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Mar 28, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.3Oct 4, 2023Group: 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 1.4Nov 6, 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: Cysteine-rich protective antigen
C: Cysteine-rich protective antigen
D: Cysteine-rich protective antigen


Theoretical massNumber of molelcules
Total (without water)157,9424
Polymers157,9424
Non-polymers00
Water23413
1
A: Cysteine-rich protective antigen


Theoretical massNumber of molelcules
Total (without water)39,4851
Polymers39,4851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cysteine-rich protective antigen


Theoretical massNumber of molelcules
Total (without water)39,4851
Polymers39,4851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cysteine-rich protective antigen


Theoretical massNumber of molelcules
Total (without water)39,4851
Polymers39,4851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cysteine-rich protective antigen


Theoretical massNumber of molelcules
Total (without water)39,4851
Polymers39,4851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.700, 83.560, 95.320
Angle α, β, γ (deg.)96.770, 104.110, 115.210
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Cysteine-rich protective antigen


Mass: 39485.402 Da / Num. of mol.: 4 / Fragment: UNP residues 30-362
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: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8IFM8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.96 Å3/Da / Density % sol: 58.4 %
Crystal growTemperature: 298 K / Method: evaporation
Details: 9% PEG1000 9% PEG8000 0.25M potassium iodide 50 mM potassium thiocynate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 3.09→48.262 Å / Num. obs: 32256 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 3.753 % / Biso Wilson estimate: 71.06 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.12 / Rrim(I) all: 0.14 / Χ2: 0.961 / Net I/σ(I): 10.84 / Num. measured all: 121060 / Scaling rejects: 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.09-3.273.6640.7392.1117464517647670.7610.86392.1
3.27-3.53.8220.433.9719218510350280.9030.598.5
3.5-3.783.8040.2616.6817592469546240.9470.30498.5
3.78-4.133.7750.179.3515655421841470.9780.19898.3
4.13-4.623.6470.08614.5114182395238890.9930.10198.4
4.62-5.333.7840.06618.2912921344234150.9950.07799.2
5.33-6.53.820.07117.0110998289328790.9940.08399.5
6.5-9.113.7680.05520.48466226222470.9970.06499.3
9.11-48.2623.6220.03628.724564129212600.9970.04297.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TIH

5tih


Resolution: 3.09→48.262 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 25.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2287 1585 4.91 %
Rwork0.1874 30671 -
obs0.1895 32256 97.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 198.26 Å2 / Biso mean: 82.8684 Å2 / Biso min: 21.12 Å2
Refinement stepCycle: final / Resolution: 3.09→48.262 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10614 0 0 13 10627
Biso mean---45.2 -
Num. residues----1273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210871
X-RAY DIFFRACTIONf_angle_d0.47214680
X-RAY DIFFRACTIONf_chiral_restr0.0451573
X-RAY DIFFRACTIONf_plane_restr0.0031867
X-RAY DIFFRACTIONf_dihedral_angle_d11.6036494
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0903-3.190.41431280.36692486261488
3.19-3.3040.3091610.2712825298699
3.304-3.43620.28251440.2312840298499
3.4362-3.59260.24651230.212804292799
3.5926-3.78190.24471560.20082793294999
3.7819-4.01880.23961320.19182804293699
4.0188-4.32890.21691680.15892819298798
4.3289-4.76420.18761350.13372788292399
4.7642-5.45270.18521410.147628572998100
5.4527-6.86670.22261450.198228512996100
6.8667-48.26770.21191520.18392804295699
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)
15.614-1.79112.82154.1535-0.20655.1946-0.47170.49041.00620.0654-0.1859-1.1089-0.45640.840.32780.5768-0.12760.05680.5890.09920.6394-141.0998-5.5377-33.752
24.886-0.2172-0.13944.49170.08614.338-0.4078-0.43490.94781.42070.1563-1.3257-0.62260.73470.30210.8446-0.1306-0.38880.7005-0.08030.9895-133.8429-7.6811-17.3234
34.8911-2.972-1.09572.58960.2971.8299-0.26-0.59850.26032.11470.25690.0186-0.55340.05650.08840.98160.08290.00370.5648-0.02530.3969-147.7385-15.9363-11.6431
43.3099-1.96122.29564.3129-3.06895.0550.00390.2242-0.1103-0.0995-0.01870.20090.41810.25050.06640.4983-0.02880.02470.4021-0.0380.3146-151.2418-17.8954-30.2827
54.57271.04283.18892.00931.22064.2611-0.4147-0.62771.0787-0.4356-0.380.6879-0.7658-0.81590.50720.97230.2176-0.14090.6055-0.19290.5029-177.5362-6.894-58.4998
64.9181-0.26341.29961.92440.39076.1895-0.40140.24750.2509-0.4151-0.15170.6414-0.6993-0.78710.53211.1940.2301-0.28370.656-0.06990.6189-185.094-7.8959-73.5952
74.13841.02121.083.90260.48954.9509-0.2490.61210.1808-0.66220.0116-0.4347-0.58980.1330.20370.8696-0.1261-0.03450.5121-0.01380.3756-169.521-20.2082-77.5344
84.47950.59530.54242.61281.41966.7104-0.049-0.0877-0.0991-0.1256-0.0862-0.07-0.5251-0.03120.09040.7430.0006-0.10910.42060.01180.3057-165.5226-15.9355-57.9862
94.8320.6015-4.1120.96950.68937.4782-0.3937-0.8011-0.7778-0.0915-0.2944-0.26550.69350.90250.56440.84730.17590.05640.47910.26870.5964-140.250510.9351-59.5885
101.35161.6785-0.35323.1508-0.02457.4192-0.2298-0.0019-0.49450.5822-0.0133-0.33210.56971.62420.64760.65970.59520.0171.1070.70060.6788-131.41997.0086-62.5197
115.2434-1.0195-0.88095.8548-0.27867.4715-0.13340.0621-0.2767-1.0273-0.2607-1.02850.80810.84450.37710.72760.13380.2740.54470.01390.5183-135.629315.151-79.9145
126.03060.93620.09497.87531.06324.4648-0.11430.7701-0.1392-1.5970.0950.4710.3276-0.7113-0.05290.7483-0.06230.05170.5565-0.00890.3288-149.500720.5507-81.7801
135.83470.1127-0.74655.5548-2.14244.07710.11710.2220.17940.02890.01260.43490.0587-0.3281-0.0550.57480.03650.09940.37060.03470.3434-154.420126.9802-71.1823
145.399-0.7432-2.29645.4045-3.02346.904-0.0945-0.622-0.07060.3544-0.1819-0.1494-0.00940.54550.27010.7607-0.050.05680.49390.06130.2938-150.769317.2486-54.1893
154.4182-0.2717-4.14863.29071.51856.15490.03810.3507-0.02310.0816-0.54210.10220.247-0.87750.69140.7826-0.1835-0.07830.5926-0.07020.3505-171.25039.0589-35.8165
161.2915-1.424-1.96364.37883.26494.3905-0.23420.4534-0.9141-0.2773-1.11211.40640.4859-1.91280.52560.767-0.28030.0790.9111-0.40280.8203-186.02318.5223-27.003
174.63391.5878-0.24425.67891.92557.8713-0.5949-0.0202-0.13120.99430.03370.56060.4785-1.08760.40320.5955-0.17250.12210.7405-0.08280.395-181.889915.6923-13.3459
184.89110.6573-0.38477.96921.34688.84090.0779-0.0047-0.72130.9504-0.30890.24560.4166-0.60150.19520.5136-0.07050.01720.50920.03020.3341-173.887515.0956-12.0823
194.17821.2033-0.84924.8931-5.54046.5070.2599-0.40120.24162.3739-0.4697-0.6006-0.48190.07460.20710.75040.0531-0.00930.58680.03330.4345-169.356127.2349-10.0026
203.5823-1.1577-1.25124.0172.48826.32770.3250.30640.2704-0.7211-0.3345-0.3623-0.7775-0.04520.05850.5762-0.02460.05590.35940.05720.3253-164.135726.1141-26.5931
212.57161.03142.74161.66510.73543.16090.2260.6964-0.1446-0.5101-0.36610.1094-0.7635-0.9161-0.31250.79140.12970.06440.7931-0.14640.2723-167.168317.2768-39.4265
228.3368-1.555-0.42425.14510.94336.7994-0.21031.3798-0.71110.0414-0.31550.60830.7672-1.3110.33460.6316-0.06-0.02020.7892-0.21330.3565-168.269911.1217-38.3722
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 46 )A1 - 46
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 134 )A47 - 134
3X-RAY DIFFRACTION3chain 'A' and (resid 135 through 180 )A135 - 180
4X-RAY DIFFRACTION4chain 'A' and (resid 181 through 332 )A181 - 332
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 46 )B1 - 46
6X-RAY DIFFRACTION6chain 'B' and (resid 47 through 122 )B47 - 122
7X-RAY DIFFRACTION7chain 'B' and (resid 123 through 220 )B123 - 220
8X-RAY DIFFRACTION8chain 'B' and (resid 221 through 332 )B221 - 332
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 46 )C1 - 46
10X-RAY DIFFRACTION10chain 'C' and (resid 47 through 63 )C47 - 63
11X-RAY DIFFRACTION11chain 'C' and (resid 64 through 134 )C64 - 134
12X-RAY DIFFRACTION12chain 'C' and (resid 135 through 180 )C135 - 180
13X-RAY DIFFRACTION13chain 'C' and (resid 181 through 249 )C181 - 249
14X-RAY DIFFRACTION14chain 'C' and (resid 250 through 333 )C250 - 333
15X-RAY DIFFRACTION15chain 'D' and (resid 0 through 29 )D0 - 29
16X-RAY DIFFRACTION16chain 'D' and (resid 30 through 67 )D30 - 67
17X-RAY DIFFRACTION17chain 'D' and (resid 68 through 109 )D68 - 109
18X-RAY DIFFRACTION18chain 'D' and (resid 110 through 153 )D110 - 153
19X-RAY DIFFRACTION19chain 'D' and (resid 154 through 180 )D154 - 180
20X-RAY DIFFRACTION20chain 'D' and (resid 181 through 278 )D181 - 278
21X-RAY DIFFRACTION21chain 'D' and (resid 279 through 307 )D279 - 307
22X-RAY DIFFRACTION22chain 'D' and (resid 308 through 333 )D308 - 333

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