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- PDB-6b08: Crystal structure of Pfs25 in complex with the transmission block... -

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Basic information

Entry
Database: PDB / ID: 6b08
TitleCrystal structure of Pfs25 in complex with the transmission blocking antibody 1276
Components
  • 1276 antibody, heavy chain
  • 1276 antibody, light chain
  • Pfs25
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: 2.2 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
C: 1276 antibody, heavy chain
B: 1276 antibody, light chain
A: Pfs25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4417
Polymers67,0723
Non-polymers3684
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6790 Å2
ΔGint-29 kcal/mol
Surface area28250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.351, 70.264, 83.742
Angle α, β, γ (deg.)90.00, 90.45, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody 1276 antibody, heavy chain


Mass: 23956.748 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 1276 antibody, light chain


Mass: 23011.514 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 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*PLUS
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O

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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: 3.06 Å3/Da / Density % sol: 59.75 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.2 M di-ammonium hydrogen phosphate, 18 % (w/v) PEG 3350

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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: 2.2→40 Å / Num. obs: 40434 / % possible obs: 98 % / Redundancy: 3.1 % / Rpim(I) all: 0.033 / Net I/σ(I): 16.3
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2 / Num. unique obs: 5096 / Rpim(I) all: 0.3 / % possible all: 99.4

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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: 1276 Fab, 1Z27

1z27


Resolution: 2.2→38.748 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2328 1994 4.94 %
Rwork0.1906 --
obs0.1927 40405 97.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→38.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4476 0 24 169 4669
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054608
X-RAY DIFFRACTIONf_angle_d0.6896282
X-RAY DIFFRACTIONf_dihedral_angle_d12.6982789
X-RAY DIFFRACTIONf_chiral_restr0.049716
X-RAY DIFFRACTIONf_plane_restr0.005800
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2550.3941420.30192766X-RAY DIFFRACTION99
2.255-2.3160.35631430.28732726X-RAY DIFFRACTION99
2.316-2.38410.30561460.26082777X-RAY DIFFRACTION99
2.3841-2.46110.28281420.24572728X-RAY DIFFRACTION98
2.4611-2.5490.27891470.24352740X-RAY DIFFRACTION99
2.549-2.6510.2741360.23492745X-RAY DIFFRACTION99
2.651-2.77170.29411420.23142766X-RAY DIFFRACTION98
2.7717-2.91770.26381430.21762736X-RAY DIFFRACTION98
2.9177-3.10050.25231400.21952758X-RAY DIFFRACTION98
3.1005-3.33970.26191420.21392751X-RAY DIFFRACTION98
3.3397-3.67560.23071440.18012742X-RAY DIFFRACTION98
3.6756-4.20690.1921430.1642749X-RAY DIFFRACTION97
4.2069-5.29810.1771410.13682708X-RAY DIFFRACTION97
5.2981-38.75370.21081430.17122719X-RAY DIFFRACTION94
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)
13.3531-0.89981.33212.6922-2.15922.8086-0.2221-0.45310.28160.33480.10040.1057-0.65410.20210.20690.5301-0.046-0.03150.4948-0.08470.364-0.487324.841218.2665
24.7390.2739-0.07760.3255-0.22591.8906-0.19110.17230.0172-0.11620.05380.03420.1245-0.0560.10190.5171-0.0142-0.09170.22120.04530.5056-30.85317.84523.4813
36.99431.1075-1.30593.9687-1.25853.0509-0.12240.06470.54680.0565-0.13320.5281-0.1094-0.43410.10410.4220.0233-0.14080.2921-0.01520.4321-41.024518.7335.7788
44.34140.22151.3445.0938-0.08387.07620.2763-0.0991-0.8257-0.08230.24150.14990.82890.1942-0.50310.45810.075-0.10410.56030.0050.55970.3773.086120.5821
53.60490.3090.6234.70550.90233.3991-0.02890.2875-0.1092-0.0761-0.0095-0.3142-0.340.0420.07720.3657-0.032-0.05730.2410.03160.4223-29.08656.141-4.692
63.97140.28062.73782.16260.42848.0139-0.1045-0.5194-0.58340.5938-0.0078-0.0009-0.0292-1.02450.23220.70920.0304-0.05741.2618-0.0010.546220.368510.563849.2481
76.19690.89072.61232.25081.54858.83880.5472-0.1288-1.20310.27040.01-0.4861.28820.6365-0.73410.79230.1457-0.1951.13830.10930.835824.2372-5.34944.9341
80.25330.27090.10170.715-0.53360.94620.13450.0007-0.9253-0.1739-0.1854-0.10260.62920.6349-0.22420.74110.1809-0.11911.16090.04040.897718.5717-2.779734.8012
94.50410.26344.19941.48850.09425.5439-0.4040.27950.55170.01050.1054-0.1058-0.85081.09320.38650.5413-0.1515-0.02141.15610.03020.442616.827518.006833.1662
105.6365-0.24064.99571.8343-0.8938.3-0.3520.23570.31010.0328-0.0513-0.1638-0.82390.51880.54360.767-0.0161-0.13021.3330.00360.59627.833819.255752.4594
112.78610.07962.54759.5232-2.06932.90930.41250.2737-0.40490.2239-0.6355-0.2947-0.29250.83950.20840.9024-0.0144-0.13050.9525-0.00890.729738.743714.300160.5794
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 1 through 106 )
2X-RAY DIFFRACTION2chain 'C' and (resid 107 through 177 )
3X-RAY DIFFRACTION3chain 'C' and (resid 178 through 214 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 106 )
5X-RAY DIFFRACTION5chain 'B' and (resid 107 through 210 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1 through 25 )
7X-RAY DIFFRACTION7chain 'A' and (resid 26 through 54 )
8X-RAY DIFFRACTION8chain 'A' and (resid 55 through 89 )
9X-RAY DIFFRACTION9chain 'A' and (resid 90 through 131 )
10X-RAY DIFFRACTION10chain 'A' and (resid 132 through 158 )
11X-RAY DIFFRACTION11chain 'A' and (resid 159 through 174 )

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