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- PDB-8fb6: Crystal structure of Ky15.10 Fab in complex with circumsporozoite... -

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Basic information

Entry
Database: PDB / ID: 8fb6
TitleCrystal structure of Ky15.10 Fab in complex with circumsporozoite protein KQPA peptide
Components
  • Circumsporozoite protein KQPA peptide
  • Ky15.10 Antibody, Heavy Chain
  • Ky15.10 Antibody, Light Chain
KeywordsIMMUNE SYSTEM / Malaria / Antibody
Function / homology
Function and homology information


entry into host cell by a symbiont-containing vacuole / external side of 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: 2.15 Å
AuthorsPrieto, K. / Thai, 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 29, 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 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ky15.10 Antibody, Heavy Chain
B: Ky15.10 Antibody, Light Chain
P: Circumsporozoite protein KQPA peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,56218
Polymers49,6313
Non-polymers93115
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint-6 kcal/mol
Surface area20090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.606, 45.668, 83.111
Angle α, β, γ (deg.)90.000, 97.640, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Antibody Ky15.10 Antibody, Heavy Chain


Mass: 24547.369 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 Ky15.10 Antibody, Light Chain


Mass: 23534.154 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 KQPA peptide / CS / PfCSP


Mass: 1549.577 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (isolate NF54) (eukaryote)
References: UniProt: P19597
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.99 Å3/Da / Density % sol: 38.3 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium acetate pH 4.5, 40% 1,2-propanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.15→40 Å / Num. obs: 21555 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 37.78 Å2 / CC1/2: 0.994 / Net I/σ(I): 9.7
Reflection shellResolution: 2.15→2.18 Å / Num. unique obs: 880 / CC1/2: 0.734

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→34.64 Å / SU ML: 0.2904 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.1262
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2363 1077 5 %
Rwork0.1891 20462 -
obs0.1914 21539 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.31 Å2
Refinement stepCycle: LAST / Resolution: 2.15→34.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3412 0 60 121 3593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00253551
X-RAY DIFFRACTIONf_angle_d0.56414809
X-RAY DIFFRACTIONf_chiral_restr0.0434532
X-RAY DIFFRACTIONf_plane_restr0.0046615
X-RAY DIFFRACTIONf_dihedral_angle_d12.14941254
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.250.34141340.26232547X-RAY DIFFRACTION99.74
2.25-2.370.29331330.24082529X-RAY DIFFRACTION99.92
2.37-2.510.2961340.24652539X-RAY DIFFRACTION99.81
2.51-2.710.311330.21892532X-RAY DIFFRACTION99.78
2.71-2.980.26521340.19912549X-RAY DIFFRACTION99.85
2.98-3.410.22411340.17862550X-RAY DIFFRACTION99.85
3.41-4.30.19731350.15682581X-RAY DIFFRACTION99.78
4.3-34.640.20921400.17852635X-RAY DIFFRACTION99.43
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)
15.54780334341-1.4934647932-2.368502580043.804340022861.572913215682.761921289-0.209596957468-0.1615410059110.007757257096970.05604342132630.1263400126050.2321467203290.124289026293-0.05102301447960.07297486798090.2430471837360.009049420250.004155172255490.2373230811910.02630078945180.258981765082-12.4785112443-15.5878054938-35.0638585845
23.29699770591.648339501531.58284733.701756016183.040999312125.1719610811-0.07908206721480.05353622461730.257802995991-0.3434268184020.0887063399537-0.0565572712306-0.6267997592440.03732644619180.0356351674780.3259666953480.02170747976410.0773677165910.2717433885920.02505578240460.320593317433-16.5342309913.2172583467-13.096174877
34.078381711662.95363294010.9585111886814.002453292121.934233922152.932864874350.151123403694-0.1557637710310.08137837589480.262297157815-0.0825247884733-0.1834386542220.1322963069780.0514340411917-0.04005542746760.2744588696630.0565034099070.01650334363080.2480481269710.01797270555690.3200076180866.7106133043-12.7526095233-25.5526016527
47.030378608230.317654801391-2.541108461751.485845453230.3299032245192.741197983340.0515146383421-0.308231378409-0.1396601592440.174873101154-0.02393299313940.04411375460620.0329969509297-0.00779588568239-0.01541111525770.2937715790020.04217318686550.02412507562280.2581231158490.03789803849480.320046681352-10.46237689657.9621949742-0.185446537696
53.968142202113.328937240941.931494350872.835741432021.608928016010.960425550796-0.04660086601180.0702417713044-1.058941910810.05778354661030.19156156521-0.09803040714230.211401933275-0.131087897224-0.5266899293470.342280069086-0.04657278003080.07169827309420.308657110278-0.03717428724880.410981222069-4.68460713898-27.8883858197-40.7277173128
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 113)AA1 - 1131 - 125
22chain 'A' and (resid 114 through 216 )AA114 - 216126 - 228
33chain 'B' and (resid 1 through 107)BJ1 - 1071 - 106
44chain 'B' and (resid 108 through 213 )BJ108 - 213107 - 212
55chain 'P' and (resid 6 through 15 )PR6 - 151 - 10

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