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- PDB-8fdd: Crystal structure of Ky15.3 Fab in complex with circumsporozoite ... -

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Basic information

Entry
Database: PDB / ID: 8fdd
TitleCrystal structure of Ky15.3 Fab in complex with circumsporozoite protein NPDP peptide
Components
  • Circumsporozoite protein NPDP peptide
  • Ky15.3 Antibody, heavy chain
  • Ky15.3 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: 1.54 Å
AuthorsBurn Aschner, C. / 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
DepositionDec 2, 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
A: Ky15.3 Antibody, heavy chain
B: Ky15.3 Antibody, light chain
P: Circumsporozoite protein NPDP peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,86014
Polymers49,1773
Non-polymers68311
Water7,512417
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6640 Å2
ΔGint-11 kcal/mol
Surface area20120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.452, 83.301, 66.364
Angle α, β, γ (deg.)90.000, 99.700, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Antibody Ky15.3 Antibody, heavy chain


Mass: 24163.240 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 Ky15.3 Antibody, light chain


Mass: 23353.904 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: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 2.15 Å3/Da / Density % sol: 42.77 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M CHES pH 9.5, 30% PEG3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920088 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920088 Å / Relative weight: 1
ReflectionResolution: 1.54→40 Å / Num. obs: 60897 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 19.74 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.2
Reflection shellResolution: 1.54→1.56 Å / Num. unique obs: 2259 / CC1/2: 0.656

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→37.9 Å / SU ML: 0.214 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.0724
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2035 1999 3.28 %
Rwork0.1753 58857 -
obs0.1762 60856 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.28 Å2
Refinement stepCycle: LAST / Resolution: 1.54→37.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3382 0 44 417 3843
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00773693
X-RAY DIFFRACTIONf_angle_d0.95285058
X-RAY DIFFRACTIONf_chiral_restr0.0644574
X-RAY DIFFRACTIONf_plane_restr0.007653
X-RAY DIFFRACTIONf_dihedral_angle_d13.01161347
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.580.35881420.31324159X-RAY DIFFRACTION99.86
1.58-1.620.29141420.28534198X-RAY DIFFRACTION99.93
1.62-1.670.28521430.2434192X-RAY DIFFRACTION99.95
1.67-1.720.26571400.22044163X-RAY DIFFRACTION99.93
1.72-1.780.25261430.21144204X-RAY DIFFRACTION100
1.78-1.860.23071440.20394212X-RAY DIFFRACTION99.98
1.86-1.940.25061410.20044183X-RAY DIFFRACTION99.95
1.94-2.040.21911430.17474187X-RAY DIFFRACTION100
2.04-2.170.22971420.17274197X-RAY DIFFRACTION100
2.17-2.340.21011430.17454206X-RAY DIFFRACTION99.95
2.34-2.570.20881440.17384230X-RAY DIFFRACTION99.98
2.57-2.950.2191430.17354219X-RAY DIFFRACTION100
2.95-3.710.1821430.15594216X-RAY DIFFRACTION99.86
3.71-37.90.14851460.14744291X-RAY DIFFRACTION100
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)
11.20280101964-0.04587284590110.4071229163931.556763963660.7987058693931.82940347627-0.112345074107-0.01730309759280.129539713081-0.01641562188220.009335416824150.0744300809843-0.170079907361-0.0687113551170.08403219698960.1151856703370.01595229046390.004044128384220.1225688557430.0159281918110.1432490929556.504-4.239-2.669
22.99017658219-0.2489895965240.8492087317991.188008482680.8253150135882.74516780472-0.132868935778-0.1780666372370.1423865496860.370215618480.127682604389-0.1997262004430.250368012580.3389447034860.04291137195020.2853555808640.0409947062638-0.03049892750280.21939789901-0.003685266775920.15199167660625.8386.28326.945
32.29405933776-0.3796835655631.384774799181.35389532036-0.2545074535781.448996816950.0249721999309-0.0680791518789-0.1833849268890.100096170830.0489839107868-0.1031000018340.0300891418253-0.0318398675206-0.06585576860830.0967556471677-0.0004365768890810.01099638355550.1248908970650.01962038276480.18156953455214.658-23.3376.139
41.47742647213-1.277401918340.0008143460557593.396930527271.682074376532.374143176890.000518321862338-0.173135987046-0.070358483127-0.064572291696-0.05800485044750.135805160262-0.115480059947-0.1519603832060.04971569882280.2432843707410.03685137900440.009823457334910.2078423255510.0149647594220.14098810149919.788-4.93636.499
55.62185738031.172005616111.725659057367.31389530437-0.6911887550456.022655673920.15266525890.488172872609-0.406758356581-0.579975527281-0.008810554061550.1582475024250.163312280275-0.2327439515840.02442592353340.1586306773560.0256258412895-0.04191727051790.172598804119-0.03439298456970.1643581071863.402-16.508-15.539
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:113 )A1 - 113
2X-RAY DIFFRACTION2( CHAIN A AND RESID 114:214 )A114 - 214
3X-RAY DIFFRACTION3( CHAIN B AND RESID 1:107 )B1 - 107
4X-RAY DIFFRACTION4( CHAIN B AND RESID 108:213 )B108 - 213
5X-RAY DIFFRACTION5( CHAIN P AND RESID 2:14 )P2 - 14

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