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- PDB-8fdc: Crystal structure of Ky311 Fab in complex with circumsporozoite p... -

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Basic information

Entry
Database: PDB / ID: 8fdc
TitleCrystal structure of Ky311 Fab in complex with circumsporozoite protein KQPA peptide
Components
  • Circumsporozoite protein KQPA peptide
  • Ky311 Antibody, heavy chain
  • Ky311 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: 1.8 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
P: Circumsporozoite protein KQPA peptide
A: Ky311 Antibody, heavy chain
B: Ky311 Antibody, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4248
Polymers49,1143
Non-polymers3105
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-21 kcal/mol
Surface area19640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.019, 66.456, 84.037
Angle α, β, γ (deg.)90.000, 132.570, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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Components

#1: 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
#2: Antibody Ky311 Antibody, heavy chain


Mass: 24210.141 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: Antibody Ky311 Antibody, light chain


Mass: 23353.975 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)
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.53 Å3/Da / Density % sol: 51.47 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES pH 7.5, 0.2 M lithium sulfate, 25% PEG3350

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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: Dec 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 44112 / % possible obs: 98.5 % / Redundancy: 6.2 % / Biso Wilson estimate: 22.19 Å2 / CC1/2: 0.935 / Net I/σ(I): 7.1
Reflection shellResolution: 1.8→1.83 Å / Num. unique obs: 2104 / CC1/2: 0.811

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→30.94 Å / SU ML: 0.2725 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.2607
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2344 2035 4.75 %
Rwork0.1985 40817 -
obs0.2002 42852 95.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.92 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3309 0 20 322 3651
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00323481
X-RAY DIFFRACTIONf_angle_d0.68294757
X-RAY DIFFRACTIONf_chiral_restr0.0464531
X-RAY DIFFRACTIONf_plane_restr0.0044620
X-RAY DIFFRACTIONf_dihedral_angle_d11.92341230
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.37161380.34952726X-RAY DIFFRACTION96.27
1.84-1.890.43041220.33112712X-RAY DIFFRACTION96.04
1.89-1.940.35951410.29922707X-RAY DIFFRACTION95.92
1.94-20.27851350.26042714X-RAY DIFFRACTION95.03
2-2.060.27451330.23632681X-RAY DIFFRACTION94.65
2.06-2.130.26571370.2332715X-RAY DIFFRACTION96.25
2.13-2.220.28191410.23462707X-RAY DIFFRACTION95.86
2.22-2.320.27491410.22032732X-RAY DIFFRACTION96.77
2.32-2.440.25611350.20842754X-RAY DIFFRACTION96.4
2.44-2.60.23991290.20122729X-RAY DIFFRACTION95.97
2.6-2.80.26511420.19372725X-RAY DIFFRACTION95.95
2.8-3.080.22141380.19112744X-RAY DIFFRACTION96.32
3.08-3.520.20091320.16862692X-RAY DIFFRACTION93.88
3.52-4.430.16951330.14372697X-RAY DIFFRACTION93.8
4.44-30.940.17881380.17082782X-RAY DIFFRACTION94.99
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)
15.55136397929-0.654183470845.557392556224.04676450882-1.160926478725.62804500130.242518474829-0.9422905318040.3043574781860.0357436367230.01643083162080.05846812141160.166674911199-0.553142375636-0.2038089162030.2258676092740.01636080590990.02460688591970.277619212484-0.01393560288360.1849625639638.7268220339111.549088007743.7135116583
21.02858565201-0.16313178316-0.3067971779591.374163221590.6533370029772.83373191267-0.0338102625496-0.0687859371952-0.02675659785030.04734892308820.0303545882078-0.08008017102560.0881161379555-0.0224518593052-0.003994312118520.132925654606-5.67120571635E-5-0.001224673865570.07475849299630.03409021481590.16805712311117.52178562296.8378619740430.1591387485
31.532107333440.961191825759-0.5673769836761.75916433175-0.9428789229032.036922445820.01767828172570.09503792929880.0983010695829-0.0569687288188-0.00535660994074-0.121455791805-0.03133045925630.04366836379140.007914477120610.1869190713520.0153204948965-0.002661068716610.1112263470050.008013241445060.20444913995326.348969426514.4916757142-3.81910783072
40.3987952454520.161196896929-0.5775907508851.00074343695-0.9195198808992.827609882990.0483072388121-0.008386651807210.0583274459587-0.01053671402620.0537302642458-0.00871235047169-0.0662281941536-0.0426030191566-0.0871269870920.1567149325180.01108045529710.01756850734380.120783440867-0.0008237201430.2079393880566.7162861914226.077128584824.2651487429
50.964167563706-0.2162149805980.5556968031512.729662269560.9651274977262.324820538520.1015949798520.0223632775064-0.0844339531441-0.0612911715964-0.05167470779650.1012443437190.1492763193540.00723190835943-0.01595429174480.1751417087190.00574614732543-0.0003375667344640.117541492720.01170813444890.16876840245910.974645167817.1404392659-8.41584957559
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'P' and (resid 5 through 13 )PA5 - 131 - 9
22chain 'A' and (resid 1 through 113)AB1 - 1131 - 122
33chain 'A' and (resid 114 through 212 )AB114 - 212123 - 218
44chain 'B' and (resid 1 through 113 )BE1 - 1131 - 112
55chain 'B' and (resid 114 through 213 )BE114 - 213113 - 212

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