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- PDB-8f9e: Crystal structure of Ky15.2 Fab in complex with circumsporozoite ... -

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Basic information

Entry
Database: PDB / ID: 8f9e
TitleCrystal structure of Ky15.2 Fab in complex with circumsporozoite protein KQPA peptide
Components
  • Circumsporozoite protein KQPA peptide
  • Ky15.2 Antibody, heavy chain
  • Ky15.2 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: 2.95 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 23, 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 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Ky15.2 Antibody, heavy chain
L: Ky15.2 Antibody, light chain
A: Ky15.2 Antibody, heavy chain
B: Ky15.2 Antibody, light chain
P: Circumsporozoite protein KQPA peptide
C: Circumsporozoite protein KQPA peptide


Theoretical massNumber of molelcules
Total (without water)98,1076
Polymers98,1076
Non-polymers00
Water00
1
H: Ky15.2 Antibody, heavy chain
L: Ky15.2 Antibody, light chain
P: Circumsporozoite protein KQPA peptide


Theoretical massNumber of molelcules
Total (without water)49,0543
Polymers49,0543
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-30 kcal/mol
Surface area19750 Å2
MethodPISA
2
A: Ky15.2 Antibody, heavy chain
B: Ky15.2 Antibody, light chain
C: Circumsporozoite protein KQPA peptide


Theoretical massNumber of molelcules
Total (without water)49,0543
Polymers49,0543
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-31 kcal/mol
Surface area19460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.167, 85.209, 133.475
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 Ky15.2 Antibody, heavy chain


Mass: 24137.158 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody Ky15.2 Antibody, light chain


Mass: 23366.986 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (isolate NF54) (eukaryote)
References: UniProt: P19597
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: 2.27 Å3/Da / Density % sol: 45.71 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES pH 7.5, 25% (w/v) PEG3350, 0.2 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033192 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033192 Å / Relative weight: 1
ReflectionResolution: 2.95→40 Å / Num. obs: 19407 / % possible obs: 99.8 % / Redundancy: 13.3 % / Biso Wilson estimate: 55.54 Å2 / CC1/2: 0.992 / Net I/σ(I): 7.1
Reflection shellResolution: 2.95→3 Å / Num. unique obs: 934 / CC1/2: 0.795

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Processing

Software
NameVersionClassification
PHENIX1.19_4080refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→39.44 Å / SU ML: 0.4492 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.8046
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2413 970 5.02 %
Rwork0.2164 18336 -
obs0.2177 19306 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.44 Å2
Refinement stepCycle: LAST / Resolution: 2.95→39.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6786 0 0 0 6786
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00276948
X-RAY DIFFRACTIONf_angle_d0.57119457
X-RAY DIFFRACTIONf_chiral_restr0.04431067
X-RAY DIFFRACTIONf_plane_restr0.00431206
X-RAY DIFFRACTIONf_dihedral_angle_d12.64662453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.110.40161350.32442580X-RAY DIFFRACTION99.71
3.11-3.30.31131400.27732582X-RAY DIFFRACTION99.93
3.3-3.550.29211350.262582X-RAY DIFFRACTION99.56
3.55-3.910.26791380.22212586X-RAY DIFFRACTION99.67
3.91-4.480.20791390.18542607X-RAY DIFFRACTION99.56
4.48-5.640.16661380.17272648X-RAY DIFFRACTION99.82
5.64-39.440.22011450.19782751X-RAY DIFFRACTION99.01
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)
11.281972904770.505697435587-1.305426942710.484105537241-0.2123470144361.893082334340.03885179203880.118176823613-0.110173915111-0.00411688984734-0.0277450994238-0.044224806570.0361515340473-0.146840307617-0.03009528244350.3389052318810.0230909184218-0.02965395055780.3439668012960.008923823742440.4102184831655.139-15.175-15.122
23.17644583170.412722097444-0.1960634722520.864102434959-0.3468019109192.42002731640.06350087483930.0648132149746-0.437927733052-0.130869883372-0.20999134123-0.1801828845820.0629035008054-0.2860505639940.06616391606390.4842144583610.0281461371338-0.03856129496430.36745372968-0.0869691138340.46661125027124.362-4.312-43.461
31.367290671251.43437209364-0.3632575803821.86414396979-0.5456921479361.579239992890.0703414455507-0.003577360664230.05727878567750.0583801623731-0.0233962252215-0.0291283670989-0.1456160088760.07944205988170.08421293856880.3985460683640.0515455945768-0.04605722584750.353337720999-0.0366096085920.39720476425612.1344.778-8.23
41.851877761670.9295791618790.2768581263151.74631332-0.06994956334284.725612841260.1779593252860.2756394062450.251786908930.0159202749739-0.08437211210170.234119999029-0.787845233579-0.6836524219420.1061754186380.5385791616770.1417234909330.06914992849040.5299635158870.02702243694110.47580253763416.8269.605-43.668
52.19107255951-0.349543463447-1.381339753750.912614653722-0.07105617635181.75404925689-0.0638435385253-0.180876931309-0.359406152809-0.0105814219930.1623192374210.08964001171040.0220731053285-0.0106014340411-0.07118238741660.388855535476-0.00836605458056-0.01152657298480.2766321873070.03803153544180.402558654635-5.367-15.541-68.886
63.35794195482-0.524035689964-1.858089616811.280948134850.6508924637312.34275991314-0.0895688490418-0.42004395774-0.485162733136-0.0208515381826-0.1697806409930.1507190234930.188475517520.7038633891980.1960863143870.4948226224390.0164876728293-0.01695958550350.5659160209520.07913393333790.390156877819-24.121-4.058-40.263
72.4575394865-0.929192647099-0.9563378578141.977965458761.301102526791.94900972156-0.02907308919590.1093132316880.171771226143-0.0652681228406-0.0367572563610.0680827406916-0.0551679122525-0.2211021358320.03839420252590.322884245257-0.00582968707157-0.01771023865760.3180049916570.007573013330970.333910053847-12.1454.312-76.02
82.73761570307-0.2509705439820.008112456032852.19227332584-0.1320845546083.488797220030.177535691216-0.618274602431-0.1268706150710.255121800807-0.0576036924781-0.134650842441-0.1681127761770.995818387594-0.07905023220720.367427256461-0.1035476249810.03538891370530.6538061251820.02257759677380.396642631892-16.95210.065-40.531
91.548696183922.20859427348-2.429871447364.00545561633-4.263342163094.560548477570.2708249750510.261048404240.15943305489-0.5372987849520.1594939256020.164632529639-0.683639222351-0.00184433435246-0.4297567380950.894108911248-0.08636701749080.09728223762510.377773588603-0.1387155676940.42586456311-1.867-12.092.651
103.47006157554-1.47293158462-2.803929932912.777619555983.400532130645.927300597830.08011519653080.07002406249320.0859181870568-0.863171108376-0.122345701344-0.3267166099380.4241233915320.3639859780570.05217937472810.570656785475-0.03250720054810.0425471264790.555319576988-0.06581964101760.4197691945571.319-12.375-85.857
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 1:123 )H1 - 123
2X-RAY DIFFRACTION2( CHAIN H AND RESID 124:216 )H124 - 216
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 A AND RESID 1:123 )A1 - 123
6X-RAY DIFFRACTION6( CHAIN A AND RESID 124:216 )A124 - 216
7X-RAY DIFFRACTION7( CHAIN B AND RESID 1:106 )B1 - 106
8X-RAY DIFFRACTION8( CHAIN B AND RESID 107:213 )B107 - 213
9X-RAY DIFFRACTION9( CHAIN P AND RESID 5:15 )P5 - 15
10X-RAY DIFFRACTION10( CHAIN C AND RESID 7:15 )C7 - 15

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