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- PDB-8f9f: Crystal structure of Ky15.2 Fab in complex with circumsporozoite ... -

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Basic information

Entry
Database: PDB / ID: 8f9f
TitleCrystal structure of Ky15.2 Fab in complex with circumsporozoite protein NANP3 peptide
Components
  • Circumsporozoite protein NANP 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 / 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: 2.2 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

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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
C: Circumsporozoite protein NANP peptide
P: Circumsporozoite protein NANP peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,23019
Polymers97,4236
Non-polymers80713
Water4,414245
1
H: Ky15.2 Antibody, heavy chain
L: Ky15.2 Antibody, light chain
P: Circumsporozoite protein NANP peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0849
Polymers48,7113
Non-polymers3726
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-13 kcal/mol
Surface area19800 Å2
MethodPISA
2
A: Ky15.2 Antibody, heavy chain
B: Ky15.2 Antibody, light chain
C: Circumsporozoite protein NANP peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,14610
Polymers48,7113
Non-polymers4347
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-15 kcal/mol
Surface area19590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.372, 86.574, 134.212
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 NANP peptide / CS


Mass: 1207.210 Da / Num. of mol.: 2 / Fragment: residues 148-159 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (isolate NF54) (eukaryote)
References: UniProt: P02893
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.31 Å3/Da / Density % sol: 46.68 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M magnesium acetate, 20% (w/v) PEG3350

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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: 2.2→40 Å / Num. obs: 46439 / % possible obs: 99.7 % / Redundancy: 13.4 % / Biso Wilson estimate: 42.17 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.2
Reflection shellResolution: 2.2→2.23 Å / Num. unique obs: 1823 / CC1/2: 0.77

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Processing

Software
NameVersionClassification
PHENIX1.19_4080refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→38.73 Å / SU ML: 0.3191 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.3501
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2405 1998 4.31 %
Rwork0.213 44317 -
obs0.2142 46315 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.4 Å2
Refinement stepCycle: LAST / Resolution: 2.2→38.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6821 0 52 245 7118
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00327162
X-RAY DIFFRACTIONf_angle_d0.69049758
X-RAY DIFFRACTIONf_chiral_restr0.04491100
X-RAY DIFFRACTIONf_plane_restr0.00511248
X-RAY DIFFRACTIONf_dihedral_angle_d13.4722586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.36751400.32443109X-RAY DIFFRACTION99.54
2.26-2.320.37351410.32043120X-RAY DIFFRACTION99.63
2.32-2.380.37211390.30773125X-RAY DIFFRACTION99.66
2.38-2.460.30571410.30043133X-RAY DIFFRACTION99.63
2.46-2.550.33521410.29193108X-RAY DIFFRACTION99.72
2.55-2.650.35371420.28843135X-RAY DIFFRACTION99.12
2.65-2.770.28861420.24673166X-RAY DIFFRACTION99.76
2.77-2.920.2851420.2483123X-RAY DIFFRACTION99.63
2.92-3.10.30171420.25043173X-RAY DIFFRACTION99.85
3.1-3.340.27061420.22613143X-RAY DIFFRACTION99.94
3.34-3.680.19481440.19323196X-RAY DIFFRACTION99.76
3.68-4.210.19071440.1773181X-RAY DIFFRACTION99.22
4.21-5.30.16921460.14773237X-RAY DIFFRACTION99.94
5.3-38.730.20011520.18793368X-RAY DIFFRACTION99.29
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)
12.54635797993-0.856497838233-1.678423158531.463173346550.2573059730812.8788593546-0.0672912566004-0.388291466233-0.1710466460260.1799526817880.0863404391015-0.0468288466260.02854772580760.3362402358770.005572774352990.229896150051-0.0157353015951-0.02819334515470.3428317398550.01262587906820.282711062194-5.536-15.68515.077
23.91210923234-1.46655925548-1.914019565031.997911949430.3126714621185.502033890240.1064733520010.220607931298-0.4337033330770.076083149248-0.150360201625-0.03257229698990.4404066038420.4370178443870.1033388922270.3783774915350.0560355026085-0.06717497426520.410935257207-0.05222785506190.338494642844-23.608-4.77844.119
33.25425556131-2.05215971808-0.6994471332713.086528360360.8249907060572.444032194460.0308798913602-0.08091539107540.2687066948980.103703959234-0.0809794059348-0.0132537147374-0.2809952933430.07494454769280.03078885657850.317460123401-0.06562111232960.01769252874260.299146721454-0.01847167086390.327269855189-12.2184.2288.424
42.26087828699-0.203895790366-0.1038066346712.397787681780.4468736387524.911478074390.174673663202-0.2330775745910.3411670916650.1548948861560.0285384339792-0.242517178188-1.428973084751.04269803812-0.2315180445870.692642793524-0.2253163670490.1315814807580.648167948712-0.09341467732780.424761445032-14.9878.53744.097
52.19573255591-0.196312839974-2.226323233580.700807927977-0.3813090737794.14422921705-0.2441639631040.0764124872459-0.468230577343-0.2139742684490.1334867652560.009396767292830.698688152302-0.1345313874110.09483350121850.464323244226-0.0222494278932-0.02320312144260.2763726629470.01206440188870.3956670604915.661-15.22870.049
61.827608613950.7006284498-0.4881228474351.92499134571-1.160044428784.188941502790.0495779073595-0.0200888685185-0.223568454515-0.349971718915-0.154206141417-0.3005860063551.088490614360.8118102551180.1146782196760.6086400615940.231986822403-0.02996263195170.592756302688-0.03572630122010.33473138163524.11-4.75241.027
72.780271179162.09027379738-0.9928586712862.1897560369-1.180683834082.884990655040.01759726837020.1232149665440.1446081864830.04872052901620.05384689726890.116358418151-0.0924339753007-0.0325441276357-0.0476409246970.2802993338050.0637687389381-0.02853751514240.318479662015-0.02321200942640.32114666747712.1074.93176.269
82.381819729541.447166763640.4501337722592.095852082310.8060652336074.848481467560.04348161763680.3363312379230.0352861268278-0.2279428042370.0388562134330.104775130968-0.0802301778015-0.21205214408-0.07840085697530.3464215500990.1306414263930.03294511580710.510950456209-0.003637885964170.35085912323416.8569.05140.979
92.02947800312-2.75509068752.529384740222.026024727-6.378045444377.10040401881-0.538294827711-0.522697755323-0.008500994955310.6881742020240.228617413419-1.127106604880.923732387051-0.8352277856380.4855894005660.5955252219290.000444979257746-0.09874460439180.4236131203170.04754337280440.4965331287861.128-13.35887.962
105.560224765710.159007230136-2.368742670942.039679055384.291794464199.99727895692-0.02625269913360.591750719863-0.499419288668-0.348290613880.569683170777-0.430133961930.3979481391150.856483494201-0.4996063408840.3735144929680.0374293214026-0.06241104208330.317958625345-0.003521964970620.398081164627-1.287-14.276-2.883
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 C AND RESID 2:12 )C2 - 12
10X-RAY DIFFRACTION10( CHAIN P AND RESID 2:12 )P2 - 12

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