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- PDB-8fa8: Crystal structure of Ky15.11 Fab in complex with circumsporozoite... -

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Basic information

Entry
Database: PDB / ID: 8fa8
TitleCrystal structure of Ky15.11 Fab in complex with circumsporozoite protein NDN peptide
Components
  • Circumsporozoite protein NDN peptide
  • Ky15.11 Antibody, heavy chain
  • Ky15.11 Antibody, light chain
KeywordsIMMUNE SYSTEM / Malaria / Antibody
Function / homology
Function and homology information


side of membrane / cell surface / plasma membrane / cytoplasm
Similarity search - Function
Plasmodium circumsporozoite protein / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat
Similarity search - Domain/homology
Circumsporozoite protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsThai, E. / Julien, J.P.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1179906 United States
CitationJournal: Cell Rep / Year: 2023
Title: Molecular determinants of cross-reactivity and potency by VH3-33 antibodies against the Plasmodium falciparum circumsporozoite protein.
Authors: Thai, E. / Murugan, R. / Binter, S. / Burn Aschner, C. / Prieto, K. / Kassardjian, A. / Obraztsova, A.S. / Kang, R.W. / Flores-Garcia, Y. / Mathis-Torres, S. / Li, K. / Horn, G.Q. / ...Authors: Thai, E. / Murugan, R. / Binter, S. / Burn Aschner, C. / Prieto, K. / Kassardjian, A. / Obraztsova, A.S. / Kang, R.W. / Flores-Garcia, Y. / Mathis-Torres, S. / Li, K. / Horn, G.Q. / Huntwork, R.H.C. / Bolscher, J.M. / de Bruijni, M.H.C. / Sauerwein, R. / Dennison, S.M. / Tomaras, G.D. / Zavala, F. / Kellam, P. / Wardemann, H. / Julien, J.P.
History
DepositionNov 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 20, 2024Group: Source and taxonomy / Category: pdbx_entity_src_syn
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Ky15.11 Antibody, heavy chain
L: Ky15.11 Antibody, light chain
P: Circumsporozoite protein NDN peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,36311
Polymers49,8663
Non-polymers4978
Water7,332407
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-6 kcal/mol
Surface area20780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.735, 83.149, 92.267
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Antibody Ky15.11 Antibody, heavy chain


Mass: 25168.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody Ky15.11 Antibody, light chain


Mass: 23462.064 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Protein/peptide Circumsporozoite protein NDN peptide / CS


Mass: 1236.248 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (isolate NF54) (eukaryote)
References: UniProt: P08307
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 2.45 Å3/Da / Density % sol: 49.82 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M magnesium chloride, 20% PEG8000, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03319 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 46199 / % possible obs: 99.9 % / Redundancy: 12.9 % / Biso Wilson estimate: 25.4 Å2 / CC1/2: 0.998 / Net I/σ(I): 15.7
Reflection shellResolution: 1.8→1.83 Å / Num. unique obs: 2205 / CC1/2: 0.676

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Processing

Software
NameVersionClassification
PHENIX1.19_4080refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→28.85 Å / SU ML: 0.2141 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.1607
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2014 1999 4.33 %
Rwork0.1774 44130 -
obs0.1785 46129 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.03 Å2
Refinement stepCycle: LAST / Resolution: 1.8→28.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3432 0 32 407 3871
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00333757
X-RAY DIFFRACTIONf_angle_d0.68525150
X-RAY DIFFRACTIONf_chiral_restr0.0474577
X-RAY DIFFRACTIONf_plane_restr0.0044664
X-RAY DIFFRACTIONf_dihedral_angle_d12.60641415
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.35811400.34143123X-RAY DIFFRACTION99.88
1.85-1.890.27051410.26013086X-RAY DIFFRACTION99.94
1.89-1.950.21871400.21913106X-RAY DIFFRACTION99.97
1.95-2.010.24231410.19463106X-RAY DIFFRACTION99.97
2.01-2.090.26441420.1983126X-RAY DIFFRACTION99.97
2.09-2.170.23411410.19713112X-RAY DIFFRACTION100
2.17-2.270.21461420.17743126X-RAY DIFFRACTION100
2.27-2.390.19171420.17933154X-RAY DIFFRACTION99.94
2.39-2.540.19981430.18163145X-RAY DIFFRACTION100
2.54-2.730.21141420.18423122X-RAY DIFFRACTION99.94
2.73-3.010.23421430.18333158X-RAY DIFFRACTION99.97
3.01-3.440.1961440.1663184X-RAY DIFFRACTION100
3.44-4.330.14671460.14583237X-RAY DIFFRACTION100
4.33-28.850.19011520.16443345X-RAY DIFFRACTION99.94
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)
12.446469050621.25495131059-1.479907616271.57793317027-1.165687557931.557850835220.0315699867883-0.244859322007-0.1922097837880.102433452554-0.0729802324328-0.0811671371177-0.001984965245520.1041636110540.04998953360780.1801694682750.0202205891793-0.002163545317940.1730225957720.03375294911540.16663393177.6414.18229.147
24.20204616571-0.319383237671-0.4449137925082.437832331860.09486385293132.38528937739-0.105071157847-0.1682906055690.2255766505380.1516588410530.0662477368797-0.3523538193-0.001798176562940.2588926886280.06590701007190.1691148435140.01675771732680.002699831436020.242009369873-0.01696675582680.18714094766830.3621.3089.318
32.870603860852.96973287991-0.9331630593924.61787400863-0.8048196094191.615052908320.256939935715-0.3405283725260.4957089346410.390357377109-0.2041212624920.582678136785-0.2566424079110.0349036057986-0.03815420107310.223589580057-0.008808148216760.05738040937120.191337761932-0.0332417470870.2334541422982.37623.67534.042
41.56983061451-0.3650114258270.08801611544882.111763870190.7326836727162.467200607350.07855547202340.1820173109670.0210513582481-0.07080451141730.0327788032347-0.07860247126010.07624834463650.0406983301302-0.1005293896480.124614345426-0.01876871857020.02459084808860.161331097034-0.004968519181960.15885061025517.78830.6053.241
56.25138053884-5.750042334987.52139432745.29628507294-6.967796871549.40237384496-0.299890248154-0.995406397490.0207721584491.145914404010.4536577603630.415933319595-0.83363386444-0.325826891689-0.1171811148780.415245968378-0.00907827792840.05397883883190.3928185735210.1076371109350.263056342853-3.0832.88344.152
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 1:128 )H1 - 128
2X-RAY DIFFRACTION2( CHAIN H AND RESID 129:215 )H129 - 215
3X-RAY DIFFRACTION3( CHAIN L AND RESID 1:106 )L1 - 106
4X-RAY DIFFRACTION4( CHAIN L AND RESID 107:213 )L107 - 213
5X-RAY DIFFRACTION5( CHAIN P AND RESID 1:8 )P1 - 8

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