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- PDB-6ohg: Structure of Plasmodium falciparum vaccine candidate Pfs230D1M in... -

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Basic information

Entry
Database: PDB / ID: 6ohg
TitleStructure of Plasmodium falciparum vaccine candidate Pfs230D1M in complex with the Fab of a transmission blocking antibody
Components
  • 4F12 Heavy chain
  • 4F12 Light Chain
  • Gametocyte surface protein P230
KeywordsIMMUNE SYSTEM / malaria / transmission blocking / sexual stage / 6 cysteine-rich Pfs230
Function / homology
Function and homology information


cell surface / plasma membrane
Similarity search - Function
: / 6-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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETIC ACID / METHANOL / 1,3-PROPANDIOL / Gametocyte surface protein P230
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.385 Å
AuthorsGarboczi, D.N. / Singh, K. / Gittis, A.G.
CitationJournal: Commun Biol / Year: 2020
Title: Structure and function of a malaria transmission blocking vaccine targeting Pfs230 and Pfs230-Pfs48/45 proteins.
Authors: Singh, K. / Burkhardt, M. / Nakuchima, S. / Herrera, R. / Muratova, O. / Gittis, A.G. / Kelnhofer, E. / Reiter, K. / Smelkinson, M. / Veltri, D. / Swihart, B.J. / Shimp Jr., R. / Nguyen, V. ...Authors: Singh, K. / Burkhardt, M. / Nakuchima, S. / Herrera, R. / Muratova, O. / Gittis, A.G. / Kelnhofer, E. / Reiter, K. / Smelkinson, M. / Veltri, D. / Swihart, B.J. / Shimp Jr., R. / Nguyen, V. / Zhang, B. / MacDonald, N.J. / Duffy, P.E. / Garboczi, D.N. / Narum, D.L.
History
DepositionApr 5, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Category: citation / citation_author
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 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Gametocyte surface protein P230
B: 4F12 Light Chain
C: 4F12 Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,55423
Polymers70,2713
Non-polymers1,28320
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.954, 191.334, 41.198
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Gametocyte surface protein P230 / Pfs230D1M


Mass: 21881.838 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PFS230, PF230, S230 / Production host: Komagataella pastoris (fungus) / References: UniProt: P68874

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Antibody , 2 types, 2 molecules BC

#2: Antibody 4F12 Light Chain


Mass: 23701.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293 Freestyle cells / Production host: Homo sapiens (human)
#3: Antibody 4F12 Heavy chain


Mass: 24687.826 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293 Freestyle cells / Production host: Homo sapiens (human)

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Non-polymers , 6 types, 80 molecules

#4: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-PDO / 1,3-PROPANDIOL


Mass: 76.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O2
#7: Chemical ChemComp-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH4O
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.38 Å3/Da / Density % sol: 48.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 15-22% PEG 4000, sodium acetate pH=4.6, 0.05-0.1 molar magnesium chloride, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.385→24.049 Å / Num. obs: 25684 / % possible obs: 98.3 % / Redundancy: 4.663 % / Biso Wilson estimate: 57.938 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.057 / Χ2: 1.031 / Net I/σ(I): 17.16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.39-2.534.410.3213.8637560.9570.36391.9
2.53-2.74.8810.2176.2838610.9850.24399.9
2.7-2.914.8420.1439.636230.990.16199.8
2.91-3.194.7750.09314.8733490.9940.10599.9
3.19-3.564.6890.06121.7230170.9970.06999.6
3.56-4.094.6340.04727.8927320.9970.05399.4
4.09-4.984.620.03732.5823120.9990.04299.7
4.98-6.894.5250.03633.0918690.9990.0499.8
6.89-24.0494.1840.03133.111650.9990.03596.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.385→24.049 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 32.11
RfactorNum. reflection% reflection
Rfree0.2771 1999 7.79 %
Rwork0.2292 --
obs0.233 25665 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 287.26 Å2 / Biso mean: 76.5193 Å2 / Biso min: 34.08 Å2
Refinement stepCycle: final / Resolution: 2.385→24.049 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4199 0 96 60 4355
Biso mean--61.15 57.45 -
Num. residues----601
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3855-2.44510.37191170.30591382149982
2.4451-2.51110.37191410.292416651806100
2.5111-2.58490.3761430.286617011844100
2.5849-2.66830.33181410.277216671808100
2.6683-2.76350.33751440.267317081852100
2.7635-2.8740.36321410.277616711812100
2.874-3.00450.33941430.270317011844100
3.0045-3.16260.30081440.264517021846100
3.1626-3.36030.32841440.258816971841100
3.3603-3.61890.31161440.236116951839100
3.6189-3.98160.28421450.21541720186599
3.9816-4.55440.23141470.184217431890100
4.5544-5.72530.23231490.189217581907100
5.7253-24.05060.22691560.23171856201299
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)
11.8960.96990.07556.35415.14455.890.2306-1.3698-0.18680.7503-0.22650.44-0.6069-0.2965-0.09971.2657-0.2154-0.01411.115-0.08850.382297.509356.982982.5549
28.09424.8748-1.85249.0622-4.02169.00950.29450.1442-0.1536-0.0311-0.16180.06980.22590.0832-0.14060.5318-0.0129-0.10090.3116-0.07670.310893.876154.601968.5427
31.997-3.4427-0.55556.48820.6417.84430.2231-0.76180.27731.011-0.67990.4081.12210.09970.47580.7596-0.19960.07420.6764-0.16650.593383.546354.263978.6994
45.1267-0.1699-0.7864.7241-2.11144.95990.19730.30360.45340.6124-0.35530.9082-0.3637-0.03470.12290.87440.05930.03240.4209-0.19160.683189.968467.134975.9863
57.97713.5955-1.47945.67710.31713.01170.2846-0.53110.4480.3176-0.46440.13160.37880.01860.15880.5734-0.0531-0.02270.3703-0.08580.302295.286160.410973.469
65.7784-0.7009-0.14218.14861.19954.1247-0.0587-0.0695-0.74170.41350.288-1.27350.17090.2838-0.18350.5216-0.0414-0.02020.3378-0.08850.636299.720233.091262.9497
77.28260.23391.44945.69423.98027.90780.74290.81370.4122-1.0994-0.8988-0.9127-0.26990.17140.03560.79940.37190.0230.65560.04050.9916105.73475.938844.0445
81.7759-0.89530.22011.1616-0.17460.19641.05130.8075-0.2323-0.3230.1768-0.39580.70250.622-0.19671.22911.5254-0.12261.3128-0.62640.844498.9821-1.589232.7516
93.535-3.9254-2.83216.91353.77243.7750.95422.1609-0.0394-1.9376-0.1036-0.7109-0.36770.705-0.80951.23820.49090.07290.9697-0.13211.3181111.9971-0.508237.8959
103.14481.021.66754.67893.65775.7663-0.0403-0.02580.09580.06510.0096-0.048-0.37470.03010.00480.63120.00170.08620.37310.03560.28479.146728.421758.7532
118.6904-2.70072.63057.2553-2.08794.23760.86630.7843-0.999-0.4853-0.5956-0.43431.26830.9537-0.29180.93260.1263-0.04020.5296-0.04080.400390.53833.791245.6409
126.5395-2.80430.73496.3563-0.73720.30060.5450.2534-0.38890.88420.0008-1.10680.33660.2144-0.45151.01170.1962-0.29220.4726-0.150.660993.40852.109251.1342
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 42 )A20 - 42
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 84 )A43 - 84
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 107 )A85 - 107
4X-RAY DIFFRACTION4chain 'A' and (resid 108 through 145 )A108 - 145
5X-RAY DIFFRACTION5chain 'A' and (resid 146 through 189 )A146 - 189
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 107 )B1 - 107
7X-RAY DIFFRACTION7chain 'B' and (resid 108 through 176 )B108 - 176
8X-RAY DIFFRACTION8chain 'B' and (resid 177 through 190 )B177 - 190
9X-RAY DIFFRACTION9chain 'B' and (resid 191 through 213 )B191 - 213
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 112 )C1 - 112
11X-RAY DIFFRACTION11chain 'C' and (resid 113 through 140 )C113 - 140
12X-RAY DIFFRACTION12chain 'C' and (resid 141 through 218 )C141 - 218

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