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- PDB-6b0e: Crystal structure of Pfs25 in complex with the transmission block... -

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Basic information

Entry
Database: PDB / ID: 6b0e
TitleCrystal structure of Pfs25 in complex with the transmission blocking antibody 1260
Components
  • 1260 antibody, heavy chain
  • 1260 antibody, light chain
  • 25 kDa ookinete surface antigen
KeywordsIMMUNE SYSTEM / Transmission blocking vaccine / malaria / antibody / EGF-like domain
Function / homology
Function and homology information


side of membrane / cell surface / plasma membrane
Similarity search - Function
Plasmodium vivax P25 fold / Plasmodium vivax P25 domain / Ookinete surface antigen, EGF domain / Pvs28 EGF domain / Orthogonal Prism / Epidermal growth factor-like domain. / EGF-like domain signature 2. / EGF-like domain / Immunoglobulins / Immunoglobulin-like ...Plasmodium vivax P25 fold / Plasmodium vivax P25 domain / Ookinete surface antigen, EGF domain / Pvs28 EGF domain / Orthogonal Prism / Epidermal growth factor-like domain. / EGF-like domain signature 2. / EGF-like domain / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
25 kDa ookinete surface antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsScally, S.W. / McLeod, B. / Bosch, A. / King, C.R. / Julien, J.P.
CitationJournal: Nat Commun / Year: 2017
Title: Molecular definition of multiple sites of antibody inhibition of malaria transmission-blocking vaccine antigen Pfs25.
Authors: Scally, S.W. / McLeod, B. / Bosch, A. / Miura, K. / Liang, Q. / Carroll, S. / Reponen, S. / Nguyen, N. / Giladi, E. / Ramisch, S. / Yusibov, V. / Bradley, A. / Lemiale, F. / Schief, W.R. / ...Authors: Scally, S.W. / McLeod, B. / Bosch, A. / Miura, K. / Liang, Q. / Carroll, S. / Reponen, S. / Nguyen, N. / Giladi, E. / Ramisch, S. / Yusibov, V. / Bradley, A. / Lemiale, F. / Schief, W.R. / Emerling, D. / Kellam, P. / King, C.R. / Julien, J.P.
History
DepositionSep 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation
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 1.2Oct 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 1260 antibody, light chain
B: 1260 antibody, heavy chain
E: 25 kDa ookinete surface antigen


Theoretical massNumber of molelcules
Total (without water)68,6523
Polymers68,6523
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-22 kcal/mol
Surface area28200 Å2
Unit cell
Length a, b, c (Å)53.223, 79.635, 78.065
Angle α, β, γ (deg.)90.00, 90.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody 1260 antibody, light chain


Mass: 23980.666 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody 1260 antibody, heavy chain


Mass: 24567.396 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein 25 kDa ookinete surface antigen / Pfs25


Mass: 20104.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Production host: Homo sapiens (human) / References: UniProt: P13829

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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: 2.4 Å3/Da / Density % sol: 48.76 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 2.0 M ammonium sulfate, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Sep 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3.3→40 Å / Num. obs: 9915 / % possible obs: 99.8 % / Redundancy: 3.8 % / Rpim(I) all: 0.044 / Net I/σ(I): 14.6
Reflection shellResolution: 3.3→3.4 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 835 / Rpim(I) all: 0.362 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XPREPdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z27, 5D1X

1z27

5d1x


Resolution: 3.3→39.818 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.53
RfactorNum. reflection% reflection
Rfree0.2802 497 5.02 %
Rwork0.2304 --
obs0.233 9909 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.3→39.818 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4204 0 0 0 4204
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024300
X-RAY DIFFRACTIONf_angle_d0.4765890
X-RAY DIFFRACTIONf_dihedral_angle_d8.8472556
X-RAY DIFFRACTIONf_chiral_restr0.04690
X-RAY DIFFRACTIONf_plane_restr0.003761
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3001-3.6320.37111160.31862337X-RAY DIFFRACTION100
3.632-4.1570.34431270.27492347X-RAY DIFFRACTION100
4.157-5.23560.23491300.2142338X-RAY DIFFRACTION100
5.2356-39.82040.26931240.20582390X-RAY DIFFRACTION100
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)
15.79452.75714.26898.16122.57799.22010.79161.0606-1.3135-1.63320.8046-0.13021.49151.2635-0.87451.435-0.1045-0.29230.7441-0.07111.3535-16.3983-13.3676-39.7872
27.4556-5.63115.22888.1728-2.60228.23520.34480.6716-0.1232-0.6923-0.0979-0.35890.32690.752-0.22650.7907-0.08360.07680.805-0.15960.9863-12.5274-6.901-36.3572
36.8145-4.1409-5.7836.498-1.54922.07862.7595-0.9741-1.4234-0.1036-0.6217-0.4974-3.81130.2402-0.40972.44150.3136-0.92852.2913-0.45551.3543-6.1996-15.12834.6192
47.3543-3.6319-0.44656.10540.062810.00890.3732-0.51380.11890.66620.8187-0.57742.04481.3573-0.88131.38310.439-0.50931.0024-0.40391.035-5.4045-19.4276-9.2085
56.91933.3811-2.45325.55892.21036.74041.0633-0.6803-0.44241.74110.1144-0.3102-0.8532-0.166-0.86141.3520.2523-0.67721.2758-0.21351.755-6.7916-16.4382-11.808
64.1815-1.70541.09938.594-1.67194.14050.2959-1.2953-0.89281.73951.1194-0.36341.4530.3356-0.78651.82590.4803-0.62961.43790.01181.385-6.3686-24.2539-0.9881
77.7457-2.6234-1.81019.5938-6.60216.4481-0.1687-2.79850.34011.8854-0.134-0.7998-2.42740.58140.14051.20530.0712-0.10671.4716-0.06981.249-26.97475.6301-19.8408
82.4728-2.34071.43184.4127-0.88833.3931-1.1677-1.1689-0.49592.10911.94921.4481-2.6783-0.7312-0.73540.94610.24130.22070.97530.11480.8691-28.88046.0938-30.2194
93.2209-2.0757-2.35194.5914-0.1687.4155-0.52820.8206-1.1394-0.18270.78871.18180.7317-1.125-1.35850.8146-0.1072-0.00311.10180.45241.7547-33.2129-3.7175-30.4778
106.9794-1.57381.1777.5857-5.00634.3682-0.484-1.33070.71351.1826-0.1847-1.4401-1.9235-2.19040.21191.16540.54310.40211.42470.20441.0413-36.11695.8002-26.0064
114.19480.34441.95112.76171.56934.4167-0.2926-1.1431-1.37592.30881.8381.0670.5199-0.223-0.32711.08690.23210.70420.97490.3091.3065-28.2704-2.9356-22.0457
123.8785-2.47051.80045.7331-4.80656.7455-0.6751-1.14720.02751.06831.3345-0.0076-1.3888-0.5605-0.49511.11440.1642-0.03370.8226-0.21271.036-18.5999-2.8413-18.0239
131.9385-2.9086-1.33617.6514.3392.6526-0.5089-0.7631.12081.81092.4465-1.7714-1.2544-1.28870.11572.50730.4031-0.74621.8398-0.11811.2625-3.2693-0.2171-6.058
146.67620.2125-3.79342.0243-2.98723.05351.288-3.75721.89492.8936-0.6674-2.1598-0.7372-1.81560.14541.3170.6158-0.09242.0697-0.24220.9773-10.0694-8.7252-5.3944
153.0393-0.1524-3.42378.0995-6.31769.4672-1.1778-1.42513.23820.6903-1.0369-2.6309-2.35661.53561.42121.3609-0.3516-0.69342.5649-0.50151.85067.2845-4.34442.9259
162.0163-5.33025.1367.4261-8.29059.223-0.759-1.12762.92012.60541.9616-2.5811-2.63740.90290.29232.58520.53630.01321.6529-0.7691.4166-6.69380.99063.1653
177.50520.9581-2.09728.18820.66830.74531.10490.85481.46-2.8169-1.04992.40271.849-1.26590.8511.8659-0.4659-0.54210.8537-0.01251.3187-35.02268.0553-59.3379
186.1928-6.7232-6.44048.25817.49447.32490.53610.5479-2.0148-0.1091-1.10622.01811.3215-0.52320.98092.5346-0.1139-0.59241.2641-0.17061.9343-32.8403-10.2595-64.8994
192.29020.0971.13912.4382-1.77952.7321.9959-0.8580.8395-1.8793-0.01992.92233.05591.3777-1.55692.57420.072-0.03651.4296-0.18411.2381-20.2175-3.9638-62.0742
204.18130.85093.84552.0072-6.27288.45521.54230.4423-0.5752-3.53930.348-1.26561.02333.51131.15131.7654-0.09150.75141.25020.43031.2656-18.5177.6595-60.1756
213.2556-4.4751.63387.8728-0.99186.9718-1.0690.2830.6826-0.22861.01760.34340.0601-0.4814-0.11311.0389-0.2652-0.19990.81920.26660.9197-33.283612.6679-50.02
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 32 )
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 113 )
3X-RAY DIFFRACTION3chain 'A' and (resid 114 through 128 )
4X-RAY DIFFRACTION4chain 'A' and (resid 129 through 150 )
5X-RAY DIFFRACTION5chain 'A' and (resid 151 through 174 )
6X-RAY DIFFRACTION6chain 'A' and (resid 175 through 212 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 17 )
8X-RAY DIFFRACTION8chain 'B' and (resid 18 through 40 )
9X-RAY DIFFRACTION9chain 'B' and (resid 41 through 63 )
10X-RAY DIFFRACTION10chain 'B' and (resid 64 through 82 )
11X-RAY DIFFRACTION11chain 'B' and (resid 82A through 95 )
12X-RAY DIFFRACTION12chain 'B' and (resid 96 through 145 )
13X-RAY DIFFRACTION13chain 'B' and (resid 146 through 165 )
14X-RAY DIFFRACTION14chain 'B' and (resid 166 through 185 )
15X-RAY DIFFRACTION15chain 'B' and (resid 186 through 197 )
16X-RAY DIFFRACTION16chain 'B' and (resid 198 through 211 )
17X-RAY DIFFRACTION17chain 'E' and (resid 2 through 25 )
18X-RAY DIFFRACTION18chain 'E' and (resid 26 through 76 )
19X-RAY DIFFRACTION19chain 'E' and (resid 77 through 89 )
20X-RAY DIFFRACTION20chain 'E' and (resid 90 through 109 )
21X-RAY DIFFRACTION21chain 'E' and (resid 110 through 172 )

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