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- PDB-7ust: Plasmodium falciparum protein Pfs230 D1 in complex with nanobody F5 -

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Basic information

Entry
Database: PDB / ID: 7ust
TitlePlasmodium falciparum protein Pfs230 D1 in complex with nanobody F5
Components
  • Gametocyte surface protein P230
  • Nanobody F5
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 speciesVicugna pacos (alpaca)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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
B: Nanobody F5
A: Gametocyte surface protein P230
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8445
Polymers31,5562
Non-polymers2883
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-46 kcal/mol
Surface area12940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.299, 84.179, 184.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Antibody Nanobody F5


Mass: 14755.307 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#2: Protein Gametocyte surface protein P230


Mass: 16800.465 Da / Num. of mol.: 1 / 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
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.61 Å3/Da / Density % sol: 52.83 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / Details: 2.0 M ammonium sulphate, 0.1 sodium citrate pH 5.5

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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: Jan 31, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953732 Å / Relative weight: 1
ReflectionResolution: 1.7→46.22 Å / Num. obs: 36891 / % possible obs: 99.9 % / Redundancy: 12.089 % / Biso Wilson estimate: 39.337 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.05 / Χ2: 0.853 / Net I/σ(I): 24.85 / Num. measured all: 445981
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
1.7-1.812.4181.0042.1772424587758320.8291.04799.2
1.8-1.9312.3790.5044.4468692554955490.9530.525100
1.93-2.0812.1850.2598.6162670514351430.9860.27100
2.08-2.2811.5770.14614.9155363478247820.9940.153100
2.28-2.5512.0630.09722.5452306433643360.9980.102100
2.55-2.9412.6370.06236.2148944387338730.9990.065100
2.94-3.612.0340.03959.5739434327732770.9990.04100
3.6-5.0711.0530.02877.99284292573257210.03100
5.07-46.2211.6040.02685.1177191530152710.02799.8

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Processing

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

7usr


Resolution: 1.7→42.09 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2201 2027 5.5 %
Rwork0.1894 34842 -
obs0.1911 36869 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.01 Å2 / Biso mean: 50.7908 Å2 / Biso min: 20.89 Å2
Refinement stepCycle: final / Resolution: 1.7→42.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2080 0 15 118 2213
Biso mean--85.77 50.38 -
Num. residues----272
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.7-1.74250.31941410.29672443
1.7425-1.78970.26961430.25062450
1.7897-1.84230.31381420.23792451
1.8423-1.90180.27661430.21232459
1.9018-1.96980.22511440.19932465
1.9698-2.04860.2351440.22473
2.0486-2.14180.26011440.19822478
2.1418-2.25480.24991430.19942455
2.2548-2.3960.2281430.20472463
2.396-2.5810.241450.20562491
2.581-2.84070.22221460.20952507
2.8407-3.25160.23041460.19922511
3.2516-4.09610.2191470.17642529
4.0961-42.090.18351560.16622667
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)
13.1495-2.0509-1.09541.21670.33270.9344-0.43810.0288-0.6301-0.52330.12770.16020.40410.00210.19480.83810.00350.16340.5689-0.03460.393412.5562-19.5162-42.5684
25.4945-1.71932.27922.028-1.25512.3103-0.4269-0.27020.1496-0.81060.18360.00690.2619-0.64540.27940.8260.12410.01420.6112-0.00270.27545.8903-12.8254-35.2967
32.50990.27520.37134.299-1.31623.0605-0.3433-0.6494-0.54390.3055-0.21750.13050.6050.63150.35860.91950.28070.16680.81520.05410.379513.4472-20.3523-28.3179
42.76710.8783-0.07151.412-0.24222.1548-0.6197-0.35330.3414-0.28070.24-0.0988-0.1139-0.09810.27720.69820.1185-0.01530.561-0.01640.332515.0641-9.8008-37.0078
52.3052-0.18580.5831.42970.54020.8271-1.3007-0.8716-0.65760.08520.52130.44080.77480.07750.38660.89670.25620.24430.69310.09860.251615.8101-19.7699-34.6275
61.6311-0.3991-1.05750.90910.93072.8348-0.5168-0.08990.0077-0.4619-0.0134-0.0920.2825-0.12440.45250.78150.15490.09560.58110.00980.35158.8137-16.8396-29.4401
72.73471.023-0.60361.36070.86822.4280.2133-0.1552-0.00320.21940.2078-0.09150.46160.6417-0.34740.28880.04990.00660.2459-0.00150.40680.7635-3.43822.8027
82.6297-1.4149-0.0923.9065-0.45412.93380.19060.49360.2824-0.6503-0.15390.1536-0.3795-0.3423-0.07950.3520.0579-0.01610.33660.06220.3583-2.6716-2.7449-13.2838
93.5850.8097-1.50193.6574-0.62735.59680.31980.3447-0.6157-0.8842-0.27870.11960.42550.3786-0.01430.36140.0703-0.06450.2864-0.05490.36662.5304-17.0644-13.1829
102.7248-0.0180.33692.839-1.47312.11140.15220.1691-0.6647-0.3714-0.03560.180.3953-0.017-0.10850.28830.0143-0.03990.2604-0.00880.4352.3434-19.1842-4.3657
111.8383-1.17040.86053.8182-1.05952.2440.0473-0.0233-0.1884-0.13240.08830.38610.1316-0.2451-0.09530.18160.0135-0.00070.2127-0.00170.3102-0.8687-11.7704-5.3205
123.58652.51530.29172.8775-1.53612.83620.02552.05781.2346-1.5065-0.03141.2075-0.9472-0.5259-0.06180.89220.2362-0.17870.92670.18760.4889-6.7073-1.1988-27.8553
133.6026-2.03213.41513.5496-1.69359.2043-0.15630.44990.4654-0.1539-0.0938-0.8445-0.47890.71350.06350.2093-0.0186-0.0120.262-0.01150.35979.4566-8.5282-6.4175
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 1 through 25 )B1 - 25
2X-RAY DIFFRACTION2chain 'B' and (resid 26 through 39 )B26 - 39
3X-RAY DIFFRACTION3chain 'B' and (resid 40 through 51 )B40 - 51
4X-RAY DIFFRACTION4chain 'B' and (resid 52 through 83 )B52 - 83
5X-RAY DIFFRACTION5chain 'B' and (resid 84 through 99 )B84 - 99
6X-RAY DIFFRACTION6chain 'B' and (resid 100 through 128 )B100 - 128
7X-RAY DIFFRACTION7chain 'A' and (resid 585 through 594 )A585 - 594
8X-RAY DIFFRACTION8chain 'A' and (resid 595 through 639 )A595 - 639
9X-RAY DIFFRACTION9chain 'A' and (resid 640 through 656 )A640 - 656
10X-RAY DIFFRACTION10chain 'A' and (resid 657 through 676 )A657 - 676
11X-RAY DIFFRACTION11chain 'A' and (resid 677 through 707 )A677 - 707
12X-RAY DIFFRACTION12chain 'A' and (resid 708 through 719 )A708 - 719
13X-RAY DIFFRACTION13chain 'A' and (resid 720 through 731 )A720 - 731

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