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- PDB-8fb8: Crystal structure of Ky15.10-Y100EK Fab in complex with circumspo... -

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Basic information

Entry
Database: PDB / ID: 8fb8
TitleCrystal structure of Ky15.10-Y100EK Fab in complex with circumsporozoite protein KQPA peptide
Components
  • Circumsporozoite protein KQPA peptide
  • Ky15.10-YK Antibody, heavy chain
  • Ky15.10-YK 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: 1.69 Å
AuthorsKang, R.W. / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Ky15.10-YK Antibody, heavy chain
L: Ky15.10-YK Antibody, light chain
P: Circumsporozoite protein KQPA peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1509
Polymers49,5973
Non-polymers5536
Water8,215456
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6350 Å2
ΔGint-33 kcal/mol
Surface area19420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.385, 47.721, 85.012
Angle α, β, γ (deg.)90.000, 101.200, 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-YK Antibody, heavy chain


Mass: 24513.373 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-YK 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 456 / 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: 2.34 Å3/Da / Density % sol: 47.49 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.5, 20% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033167 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033167 Å / Relative weight: 1
ReflectionResolution: 1.69→40 Å / Num. obs: 51242 / % possible obs: 98.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 21.24 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.5
Reflection shellResolution: 1.69→1.71 Å / Num. unique obs: 1783 / CC1/2: 0.658

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→37.34 Å / SU ML: 0.1775 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.1816
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1843 2000 3.9 %
Rwork0.16 49217 -
obs0.161 51217 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.85 Å2
Refinement stepCycle: LAST / Resolution: 1.69→37.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3375 0 36 456 3867
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00573555
X-RAY DIFFRACTIONf_angle_d0.87754854
X-RAY DIFFRACTIONf_chiral_restr0.057543
X-RAY DIFFRACTIONf_plane_restr0.0057619
X-RAY DIFFRACTIONf_dihedral_angle_d12.42541284
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.730.26211420.22863483X-RAY DIFFRACTION98.83
1.73-1.780.26681420.22063512X-RAY DIFFRACTION99.19
1.78-1.830.23151410.20933473X-RAY DIFFRACTION98.39
1.83-1.890.251400.22033436X-RAY DIFFRACTION98.03
1.89-1.960.27421430.18553504X-RAY DIFFRACTION99.7
1.96-2.040.18471440.16063542X-RAY DIFFRACTION99.84
2.04-2.130.19671420.16163502X-RAY DIFFRACTION99.37
2.13-2.240.20751450.16593553X-RAY DIFFRACTION99.65
2.24-2.380.21831410.16673493X-RAY DIFFRACTION98.35
2.38-2.570.1941410.1663465X-RAY DIFFRACTION98.39
2.57-2.820.20821420.16873495X-RAY DIFFRACTION98.3
2.82-3.230.18821450.15763564X-RAY DIFFRACTION99.97
3.23-4.070.15171450.13453590X-RAY DIFFRACTION99.84
4.07-37.340.13261470.143605X-RAY DIFFRACTION97.91
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)
10.8413842947480.614035532318-0.7479676989280.842661383025-0.7842383891441.14394272805-0.0234540058989-0.0478894837823-0.0069583346590.00326155097283-0.0344331662305-0.0718997184050.05042319153990.07456147692860.05460295089550.1498201232040.00888677279816-0.01238820205430.145464857564-0.005844120903940.15895862118311.81-9.4934.611
22.66669831461-1.847293007370.7091995341264.86898092195-1.053811532181.411339522450.00165733509160.05038344417930.129923956777-0.0907741439425-0.0910479379324-0.044111244459-0.1156541462410.06546895789630.09485561018170.153009563508-0.01982204440290.007284672572390.1771675302690.004319948280540.12657789942217.54316.86413.727
31.34522525979-0.7703291689170.2415210180722.82281669709-0.8625507806141.243027866330.0520647388160.184777302613-0.0305382057991-0.139194334934-0.06622555230640.1040854878290.0488584373347-0.01547216077330.01531248652450.129921123684-0.0099164852928-0.01448592262210.135598631072-0.01806798481430.128786732239-8.424-6.91626.201
45.46696858158-0.502561276373-2.288873326610.84323451355-0.01415616507063.11312946606-0.06826040539980.237089089947-0.0724174025104-0.1457523537050.00131846796145-0.01482261525810.1968316851820.1630299006710.06163403388280.2199208560880.0015523648084-0.011238121790.157042039311-0.003438852437060.14476224768510.7619.0971.304
57.3412421273-0.70486048097-1.494947690674.479716520024.294252508764.29576732889-0.304851459555-0.05749374538-0.5524885550120.3407630488920.02999614740510.08251739159240.6716359474480.4528811320210.1815029253120.2134689938960.013741226130.007486029446960.143637510040.02682951703550.1861610988280.457-21.77740.7
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 126:213 )H126 - 213
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 8:15 )P8 - 15

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