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- PDB-7usv: Plasmodium falciparum protein Pfs230 D1 in complex with nanobody F10 -

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Basic information

Entry
Database: PDB / ID: 7usv
TitlePlasmodium falciparum protein Pfs230 D1 in complex with nanobody F10
Components
  • Gametocyte surface protein P230
  • Nanobody F10
KeywordsPROTEIN BINDING/IMMUNE SYSTEM / 6-cysteine protein / s48/45 domain / Plasmodium / nanobody / PROTEIN BINDING / PROTEIN BINDING-IMMUNE SYSTEM complex
Function / homology6-Cysteine (6-Cys) domain / 6-Cysteine (6-Cys) domain superfamily / Sexual stage antigen s48/45 domain / 6-Cysteine (6-Cys) domain profile. / Sexual stage antigen s48/45 domain / cell surface / plasma membrane / Gametocyte surface protein P230
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDietrich, M.H. / Tham, W.H.
Funding support Australia, United Kingdom, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP2001385 Australia
Wellcome Trust208693/Z/17/Z United Kingdom
CitationJournal: Biochem.J. / Year: 2022
Title: Nanobodies against Pfs230 block Plasmodium falciparum transmission.
Authors: Dietrich, M.H. / Gabriela, M. / Reaksudsan, K. / Dixon, M.W.A. / Chan, L.J. / Adair, A. / Trickey, S. / O'Neill, M.T. / Tan, L.L. / Lopaticki, S. / Healer, J. / Keremane, S. / Cowman, A.F. / Tham, W.H.
History
DepositionApr 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gametocyte surface protein P230
B: Gametocyte surface protein P230
D: Nanobody F10
C: Nanobody F10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,95112
Polymers62,1824
Non-polymers7698
Water6,287349
1
A: Gametocyte surface protein P230
C: Nanobody F10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4756
Polymers31,0912
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-58 kcal/mol
Surface area12910 Å2
MethodPISA
2
B: Gametocyte surface protein P230
D: Nanobody F10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4756
Polymers31,0912
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-61 kcal/mol
Surface area12850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.083, 101.221, 148.185
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Gametocyte surface protein P230


Mass: 16800.465 Da / Num. of mol.: 2 / Fragment: Domain 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: isolate 3D7 / Gene: PFS230, PF230, S230, PF3D7_0209000 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P68874
#2: Antibody Nanobody F10


Mass: 14290.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O
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: 2.9 Å3/Da / Density % sol: 57.58 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium sulphate, 0.1 M sodium acetate pH 4.6, and 25% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953732 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953732 Å / Relative weight: 1
ReflectionResolution: 2.1→47.894 Å / Num. obs: 43202 / % possible obs: 99.5 % / Redundancy: 9.782 % / Biso Wilson estimate: 40.777 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.227 / Rrim(I) all: 0.242 / Χ2: 0.77 / Net I/σ(I): 11.83 / Num. measured all: 422617
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
2.1-2.229.7341.3581.7665033689766810.6831.43496.9
2.22-2.389.480.9092.761497649064870.8350.961100
2.38-2.569.9080.6024.2860210607860770.920.636100
2.56-2.8110.1760.397.0457180562056190.9630.413100
2.81-3.149.9650.25911.1650560507550740.9810.275100
3.14-3.629.30.18818.9242223454345400.9770.20199.9
3.62-4.4310.1860.1829.3239430387138710.9620.192100
4.43-6.249.6780.15732.5129490304830470.9730.169100
6.24-47.8949.410.09933.9216994181318060.9960.10699.6

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Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7USR

7usr


Resolution: 2.1→47.894 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2354 2154 5 %
Rwork0.198 40912 -
obs0.1999 43066 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.41 Å2 / Biso mean: 43.5588 Å2 / Biso min: 19.33 Å2
Refinement stepCycle: final / Resolution: 2.1→47.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4100 0 40 349 4489
Biso mean--81.02 47.54 -
Num. residues----537
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.14890.34521390.2917264499
2.1489-2.20260.2871420.27452691100
2.2026-2.26220.33421410.25432689100
2.2622-2.32870.29021420.25322687100
2.3287-2.40390.2951420.23942702100
2.4039-2.48980.29371410.22242681100
2.4898-2.58950.29711430.22112713100
2.5895-2.70730.24991430.21872702100
2.7073-2.850.2441440.21772735100
2.85-3.02860.24031420.21422713100
3.0286-3.26240.26591440.19922725100
3.2624-3.59060.23431440.19512734100
3.5906-4.10990.20571460.17192777100
4.1099-5.1770.17351470.14082792100
5.177-47.890.2011540.19362927100
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)
15.2143-0.1814-0.36253.724-2.11973.49170.02680.26830.14220.2260.04030.4016-0.1805-0.19840.05250.310.00820.04940.3407-0.02970.3108-15.869813.2033-11.0183
24.7579-3.73710.69673.34740.28572.0317-0.17250.24570.5353-0.25330.4783-0.8117-0.48950.4789-0.17620.3082-0.0550.04850.3069-0.03870.4031-6.491511.0323-9.2755
32.7149-1.6662-0.04696.6428-0.20130.9910.16-0.0191-0.2555-0.7277-0.01480.7824-0.0603-0.001-0.18950.37180.02670.00540.3216-0.030.2889-15.851313.5613-17.9534
42.6246-0.5316-0.23665.47361.11654.99220.25520.04840.2864-0.1239-0.2106-0.5012-0.45050.1614-0.05170.6043-0.06150.12090.33690.06290.3638-3.936418.2169-22.6657
55.7851-1.9318-0.31787.65-1.37770.31840.05930.19730.30390.3089-0.3937-1.05090.15250.44010.44930.6209-0.04050.16440.412-0.01830.37012.766215.6346-24.2223
65.9148-1.2868-0.75492.88740.50762.06370.16520.6259-0.8324-0.6254-0.18940.3860.0973-0.32240.05260.60220.0078-0.04310.3366-0.04260.299-10.87538.2811-28.6869
71.8712-0.5472-0.18863.56270.6343.1228-0.04230.11120.0187-0.22450.0555-0.1641-0.07230.5512-0.01660.3358-0.00510.05920.3687-0.0160.3048-2.94788.347-19.7845
84.1673-1.10290.51447.3080.74325.72740.093-0.70480.65520.45920.47850.60250.074-0.5719-0.48880.49620.07690.13440.5306-0.03510.5143-19.997728.9185-9.9301
93.45640.2157-3.1193.73573.44016.3392-0.1897-0.81910.80260.52210.6563-1.27530.0490.9232-0.24740.2499-0.01160.00630.4034-0.06080.3335-0.8918.6818-13.7438
104.39832.2766-1.3565.8481-1.29173.97550.3302-0.2150.3154-0.5252-0.4056-0.7562-0.34280.43390.14750.40480.02240.12080.29630.04110.387515.221615.0419-54.8545
112.24841.57651.21532.648-1.08652.80310.0366-0.1790.6348-0.1077-0.04070.702-0.4145-0.181-0.15890.26220.0347-0.00180.22990.02450.30015.778111.4099-55.2366
124.46381.9428-0.17.3219-0.07982.71320.31910.31860.26151.07570.1542-0.6623-0.51170.1966-0.43880.4625-0.03910.08190.29820.01970.323614.81114.6509-46.9929
137.88830.2106-0.9271.8506-0.18387.573-0.053-0.3410.63580.54170.5521-0.2644-0.33180.2727-0.44780.61470.04390.11610.4257-0.0710.38257.591918.6281-39.5299
141.86572.6690.39715.3265-3.20692.0132-0.10410.4891.4267-0.2251-0.50881.2024-1.077-0.69850.28630.80820.18810.11610.57720.02030.5506-3.692618.6501-45.4488
155.11242.3812-1.82563.24440.80071.8662-0.01350.54740.3823-0.2918-0.1756-0.2224-0.8602-1.04620.31420.81060.15010.17270.37280.09190.4257-3.257915.384-40.1834
167.13951.2359-0.8782.5949-0.01442.53590.19390.807-0.61720.7052-0.0937-0.2852-0.03250.32330.02940.65960.0327-0.01620.42590.06090.35485.04725.2522-35.884
174.68621.1053-1.17044.3098-0.63043.27450.026-0.3457-0.04760.58660.0728-0.1135-0.1145-0.0242-0.13780.41780.04940.05810.31260.02010.24877.104310.2138-42.1537
182.70671.3892-0.86446.2989-1.0273.17890.13930.80971.0906-0.19330.43920.3861-0.7523-0.382-0.23910.49740.0850.15850.29830.10620.54828.639319.5203-53.4111
193.5491-0.2678-1.02433.99960.22331.94670.13061.0472-0.7512-0.205-0.11840.23820.17160.36480.14820.2456-0.04080.03330.3504-0.08330.29513.2855-8.8847-73.3728
209.6048-2.96774.59267.555-6.92867.7764-0.17560.484-0.10970.71350.06860.7680.4278-1.21820.08080.3808-0.0840.01190.2687-0.0660.35339.6851-10.3043-69.9975
212.58260.773-0.57120.44120.74233.64770.1896-0.0313-0.52860.0109-0.2769-0.04960.51560.38580.14710.19450.0520.02430.32970.02220.307213.7289-6.8319-60.3468
226.36580.7586-5.45470.737-1.07898.52730.21670.25650.1286-0.2504-0.2478-0.026-0.2049-0.41230.03860.20920.0422-0.00530.35020.05630.278216.10084.2079-70.1749
232.1939-0.8611-0.15260.69671.0621.5949-0.05130.27480.13230.1364-0.02990.1745-0.26210.08220.05250.1928-0.06590.00140.32920.01810.23364.70420.009-64.1388
242.3041-0.4430.15910.4690.4084.3936-0.10940.5533-0.0726-0.2784-0.14720.01180.5354-0.28460.21540.23-0.04350.05110.433-0.01060.34437.2809-4.8315-71.9906
250.9543-0.7619-0.27410.99121.23332.0894-0.07640.2554-0.08360.12530.1278-0.1465-0.15760.0134-0.07830.2468-0.02690.00650.33520.06780.272715.74431.8967-61.728
263.10240.24671.40491.71750.95335.4580.05220.2751-0.2771-0.05260.0224-0.18090.3632-0.0385-0.04850.2201-0.07090.05090.3610.02530.36617.564-4.0661-70.4539
273.33431.1968-0.57043.00141.64784.59330.0104-0.1018-0.5190.04920.0029-0.12870.3783-0.43370.00290.2150.00940.00080.19240.0130.3214-12.381-10.97142.7829
282.69580.1544-0.82140.4018-0.58081.5343-0.0149-0.07050.07210.01770.0294-0.11370.1038-0.0037-0.04620.20790.0005-0.01180.2716-0.03810.287-8.9495-1.51543.34
291.05330.1118-1.10851.9602-0.91223.9891-0.04250.0357-0.0426-0.06320.14070.17980.1987-0.0933-0.06650.13530.0050.01410.2672-0.07810.2663-16.6636-1.65831.0947
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 587 through 607 )A587 - 607
2X-RAY DIFFRACTION2chain 'A' and (resid 608 through 615 )A608 - 615
3X-RAY DIFFRACTION3chain 'A' and (resid 616 through 639 )A616 - 639
4X-RAY DIFFRACTION4chain 'A' and (resid 640 through 656 )A640 - 656
5X-RAY DIFFRACTION5chain 'A' and (resid 657 through 666 )A657 - 666
6X-RAY DIFFRACTION6chain 'A' and (resid 667 through 686 )A667 - 686
7X-RAY DIFFRACTION7chain 'A' and (resid 687 through 707 )A687 - 707
8X-RAY DIFFRACTION8chain 'A' and (resid 708 through 719 )A708 - 719
9X-RAY DIFFRACTION9chain 'A' and (resid 720 through 731 )A720 - 731
10X-RAY DIFFRACTION10chain 'B' and (resid 588 through 607 )B588 - 607
11X-RAY DIFFRACTION11chain 'B' and (resid 608 through 615 )B608 - 615
12X-RAY DIFFRACTION12chain 'B' and (resid 616 through 639 )B616 - 639
13X-RAY DIFFRACTION13chain 'B' and (resid 640 through 648 )B640 - 648
14X-RAY DIFFRACTION14chain 'B' and (resid 649 through 656 )B649 - 656
15X-RAY DIFFRACTION15chain 'B' and (resid 657 through 666 )B657 - 666
16X-RAY DIFFRACTION16chain 'B' and (resid 667 through 676 )B667 - 676
17X-RAY DIFFRACTION17chain 'B' and (resid 677 through 707 )B677 - 707
18X-RAY DIFFRACTION18chain 'B' and (resid 708 through 731 )B708 - 731
19X-RAY DIFFRACTION19chain 'D' and (resid 1 through 17 )D1 - 17
20X-RAY DIFFRACTION20chain 'D' and (resid 18 through 24 )D18 - 24
21X-RAY DIFFRACTION21chain 'D' and (resid 25 through 39 )D25 - 39
22X-RAY DIFFRACTION22chain 'D' and (resid 40 through 51 )D40 - 51
23X-RAY DIFFRACTION23chain 'D' and (resid 52 through 73 )D52 - 73
24X-RAY DIFFRACTION24chain 'D' and (resid 74 through 91 )D74 - 91
25X-RAY DIFFRACTION25chain 'D' and (resid 92 through 109 )D92 - 109
26X-RAY DIFFRACTION26chain 'D' and (resid 110 through 124 )D110 - 124
27X-RAY DIFFRACTION27chain 'C' and (resid 1 through 32 )C1 - 32
28X-RAY DIFFRACTION28chain 'C' and (resid 33 through 91 )C33 - 91
29X-RAY DIFFRACTION29chain 'C' and (resid 92 through 124 )C92 - 124

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