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- PDB-8fat: Crystal structure of Ky224 Fab in complex with circumsporozoite p... -

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Basic information

Entry
Database: PDB / ID: 8fat
TitleCrystal structure of Ky224 Fab in complex with circumsporozoite protein NPDP peptide
Components
  • Circumsporozoite protein NPDP peptide
  • Ky224 Antibody, heavy chain
  • Ky224 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: 2.95 Å
AuthorsKassardjian, A. / 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 28, 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 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ky224 Antibody, heavy chain
B: Ky224 Antibody, light chain
C: Ky224 Antibody, heavy chain
D: Ky224 Antibody, light chain
E: Circumsporozoite protein NPDP peptide
F: Circumsporozoite protein NPDP peptide


Theoretical massNumber of molelcules
Total (without water)98,1406
Polymers98,1406
Non-polymers00
Water00
1
A: Ky224 Antibody, heavy chain
B: Ky224 Antibody, light chain
E: Circumsporozoite protein NPDP peptide


Theoretical massNumber of molelcules
Total (without water)49,0703
Polymers49,0703
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-31 kcal/mol
Surface area19100 Å2
MethodPISA
2
C: Ky224 Antibody, heavy chain
D: Ky224 Antibody, light chain
F: Circumsporozoite protein NPDP peptide


Theoretical massNumber of molelcules
Total (without water)49,0703
Polymers49,0703
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-36 kcal/mol
Surface area19050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.515, 115.262, 120.385
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 Ky224 Antibody, heavy chain


Mass: 23295.219 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 Ky224 Antibody, light chain


Mass: 24114.947 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 NPDP peptide / CS


Mass: 1659.668 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (isolate NF54) (eukaryote)
References: UniProt: P08307
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: 2.28 Å3/Da / Density % sol: 46.06 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 2 M ammonium sulfate, 0.1 M sodium acetate pH 4.6

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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 PILATUS 6M / Detector: PIXEL / Date: Jul 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.95→40 Å / Num. obs: 19561 / % possible obs: 99.8 % / Redundancy: 10.7 % / Biso Wilson estimate: 56.34 Å2 / CC1/2: 0.981 / Net I/σ(I): 7.3
Reflection shellResolution: 2.95→3 Å / Num. unique obs: 929 / CC1/2: 0.569

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6O25

6o25


Resolution: 2.95→37.9 Å / SU ML: 0.4065 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.2005
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2743 978 5.01 %
Rwork0.224 18529 -
obs0.2265 19507 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.95 Å2
Refinement stepCycle: LAST / Resolution: 2.95→37.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6744 0 0 0 6744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026899
X-RAY DIFFRACTIONf_angle_d0.50869396
X-RAY DIFFRACTIONf_chiral_restr0.04351068
X-RAY DIFFRACTIONf_plane_restr0.00471210
X-RAY DIFFRACTIONf_dihedral_angle_d11.32772465
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.110.37791390.33412593X-RAY DIFFRACTION99.89
3.11-3.30.31831340.28162600X-RAY DIFFRACTION99.85
3.3-3.550.35611380.25392604X-RAY DIFFRACTION99.85
3.55-3.910.29431370.23582620X-RAY DIFFRACTION99.96
3.91-4.480.26721370.19642649X-RAY DIFFRACTION99.93
4.48-5.640.20011440.17712659X-RAY DIFFRACTION99.96
5.64-37.90.25331490.21352804X-RAY DIFFRACTION99.76
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)
10.959056581978-1.19727144956-0.8522058735732.737555742091.05544894481.79220483482-0.02861933388690.343235409921-0.202429629935-0.178629699081-0.1985193209730.3665793333790.0373055631807-0.4448980208750.1941370468060.2555569682750.0003621093012320.005536899153720.582946169468-0.1244873111230.364501999183-27.10215.431-22.298
22.377404322541.56163931648-0.5651498830133.76342016607-0.04448580669832.97704989924-0.0493667787695-0.0672066940622-0.333141046074-0.01677688346750.05392204293970.7065146412530.221538872616-0.3130742996160.04227133266370.61457219611-0.1270564393350.192522353110.432249121173-0.07199168187340.759928074635-30.051-13.331-12.123
32.27102864984-0.2084626255180.000951205566193.97528971069-1.833661441232.73558416876-0.0819327241606-0.169991451803-0.2803821863790.2202682309040.126244987273-0.04250205592530.0962812618165-0.0257317773119-0.06245643411010.3607795077180.006590781805040.06013432664210.448149559612-0.01916856759820.241162627026-24.99819.973-0.639
42.42145255607-1.30297266381-0.6140023620375.099980274843.069042319791.858237462270.08266530864860.108221413429-0.777917402325-0.232761743704-0.159141946932-0.3016336199740.2836577609640.08689718805060.04989191629180.680162056084-0.005197118315290.1375650800830.4677866244260.1198004776370.722825675291-20.078-17.851-0.282
51.4031841477-1.35057881342-0.3783667928051.38165278279-0.1301743589623.11152221094-0.0428628649164-0.1113795697950.182841109408-0.1231910074170.349004154917-0.3850182487010.2372307389440.60288850804-0.3363561657090.308686444296-0.0125840107085-0.006840536820720.58972529661-0.1852881467720.3915278551884.54414.865-24.504
64.48242509594-1.62543159956-0.6840782798194.436068864420.5382806494580.1692679942050.168357414159-0.482077633599-0.3508556155120.00858499112728-0.160767476940.03385790498360.00913512395510.05612818722960.03113965548310.4192490724720.0431718430953-0.1102765817740.4284636218260.0317670789560.200171177669.7583.623.806
72.27710129051.107296272650.6768194719584.30221725888-1.441261039332.52882089622-0.01989299751340.0723723376328-0.2542119664680.3732717816750.214098779491-0.3143176715740.7769276992170.438430008145-0.1489807490940.6020518227260.228086081061-0.1202258899310.606651784115-0.2178244813010.3868035945333.343-7.288-28.488
82.81303314202-1.44436124271-1.309663640234.906048250043.277630342797.861021948120.0561087556841-0.189588023497-0.491988301925-0.0352805363659-0.1517110774440.8053731171680.2424850503280.1655746843730.1340872887260.511050377626-0.0204989253228-0.08752385173090.3120674832940.04934750526350.519705855835-0.824-6.5869.368
94.7774015742.503016454113.967963821385.675686466973.993568519124.13551307576-0.01120971572240.4509512398070.552888262269-0.211493001526-0.2697276731661.14300008003-1.23382092589-0.8237743690430.4018704686790.4146904123130.0122898131110.02837885164190.846040941729-0.0002210278090940.375929407863-31.28233.196-17.802
102.58978929547-1.3071640501-2.196696321372.645339059920.5209305584465.390771326670.01701079612311.26461566705-0.542487411597-0.3846036715280.107409673407-0.543362234536-0.0404522038398-0.1900206108380.4595990270240.2820147489480.01949357951540.1201517546210.802536870026-0.1775662125270.7634476666036.8519.927-41.756
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 114:215 )A114 - 215
3X-RAY DIFFRACTION3( CHAIN B AND RESID 1:107 )B1 - 107
4X-RAY DIFFRACTION4( CHAIN B AND RESID 108:212 )B108 - 212
5X-RAY DIFFRACTION5( CHAIN C AND RESID 1:113 )C1 - 113
6X-RAY DIFFRACTION6( CHAIN C AND RESID 114:213 )C114 - 213
7X-RAY DIFFRACTION7( CHAIN D AND RESID 1:107 )D1 - 107
8X-RAY DIFFRACTION8( CHAIN D AND RESID 108:212 )D108 - 212
9X-RAY DIFFRACTION9( CHAIN E AND RESID 5:16 )E5 - 16
10X-RAY DIFFRACTION10( CHAIN F AND RESID 3:16 )F3 - 16

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