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- PDB-8fa9: Crystal structure of Ky15.5 Fab in complex with circumsporozoite ... -

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Basic information

Entry
Database: PDB / ID: 8fa9
TitleCrystal structure of Ky15.5 Fab in complex with circumsporozoite protein NPDP peptide
Components
  • Circumsporozoite protein NPDP peptide
  • Ky15.5 Antibody, heavy chain
  • Ky15.5 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: 2.45 Å
AuthorsThai, E. / Prieto, K. / 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
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Ky15.5 Antibody, heavy chain
L: Ky15.5 Antibody, light chain
P: Circumsporozoite protein NPDP peptide


Theoretical massNumber of molelcules
Total (without water)49,6053
Polymers49,6053
Non-polymers00
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-31 kcal/mol
Surface area19380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.852, 87.786, 71.587
Angle α, β, γ (deg.)90.000, 119.283, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Antibody Ky15.5 Antibody, heavy chain


Mass: 24501.455 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 Ky15.5 Antibody, light chain


Mass: 23444.070 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 NPDP peptide / CS


Mass: 1659.668 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (isolate NF54) (eukaryote)
References: UniProt: P08307
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
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: 2.76 Å3/Da / Density % sol: 55.41 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2 M tri-lithium citrate

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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: 2.45→40 Å / Num. obs: 18410 / % possible obs: 92.1 % / Redundancy: 2.5 % / Biso Wilson estimate: 46.11 Å2 / CC1/2: 0.99 / Net I/σ(I): 8.2
Reflection shellResolution: 2.45→2.49 Å / Num. unique obs: 894 / CC1/2: 0.571

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Processing

Software
NameVersionClassification
PHENIX1.19_4080refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→28.14 Å / SU ML: 0.338 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.607
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2122 920 5 %
Rwork0.1867 17488 -
obs0.188 18408 92.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.96 Å2
Refinement stepCycle: LAST / Resolution: 2.45→28.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3411 0 0 47 3458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00323590
X-RAY DIFFRACTIONf_angle_d0.59724909
X-RAY DIFFRACTIONf_chiral_restr0.0447548
X-RAY DIFFRACTIONf_plane_restr0.0048635
X-RAY DIFFRACTIONf_dihedral_angle_d11.85771311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.580.35761340.32162568X-RAY DIFFRACTION95.41
2.58-2.740.32591350.28022555X-RAY DIFFRACTION95.46
2.74-2.950.29971330.25642520X-RAY DIFFRACTION94.38
2.95-3.250.24941330.22322538X-RAY DIFFRACTION93.46
3.25-3.720.18181300.17142465X-RAY DIFFRACTION91.31
3.72-4.680.16081260.13292396X-RAY DIFFRACTION88.74
4.68-28.140.17571290.15842446X-RAY DIFFRACTION88.95
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)
12.81326419678-0.9159463031641.302869235761.26901035635-0.6065201728221.531474020230.07549914702620.07482546220150.04717690180230.0238012804624-0.0334235608315-0.1123969801630.04948066076290.128597293281-0.03014903699340.343908588796-0.016280629270.01255053762390.247645654803-0.01269665611220.299004882329-10.897-2.96261.065
24.449403935341.50260592421-0.1758558725452.28623418493-0.5349926899132.09488886213-0.1498875379240.2393183297760.1889665486310.0290874146190.03623362851380.126173114258-0.130069887942-0.0698706651140.1027272612850.4300422633920.0459150135412-0.01779332102490.368841629970.0199694230990.327522529294-40.781-2.8643.064
32.184144969561.769513144141.682481445883.046424539250.6937788328282.68275429861-0.0365151121527-0.0331294791515-0.052068286378-0.1484106864280.0305055088330.02768340846020.08787911984740.006692482102210.008548936042090.3113551394820.04537810905810.008260068437850.287652722012-0.001077435366060.313251853672-10.698-23.48953.787
41.784185310040.1212686469380.6471724152484.96559352162-2.005620141242.93372233982-0.01731461291050.3393465606410.0611894078545-0.01195655347960.00357546900098-0.11525802736-0.171528710270.188039081222-0.02258422188060.403306261874-0.0230725555865-0.01795330195090.513427077547-0.009564529760760.305633108464-33.73-9.79630.509
56.885150390040.194601381211-3.596369339726.321450632160.6795038617532.11409084351-0.075280416543-0.36294275627-0.723124811630.390531877443-0.381581640556-0.5795568486950.05987150643581.336494636440.4722981505950.3152578047130.0374593412181-0.04344975400950.4361043984410.001607263864290.3657738891493.493-12.02869.3
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 1:125 )H1 - 125
2X-RAY DIFFRACTION2( CHAIN H AND RESID 126:214 )H126 - 214
3X-RAY DIFFRACTION3( CHAIN L AND RESID 1:106 )L1 - 106
4X-RAY DIFFRACTION4( CHAIN L AND RESID 107:212 )L107 - 212
5X-RAY DIFFRACTION5( CHAIN P AND RESID 2:12 )P2 - 12

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