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- PDB-8f9u: Crystal structure of Ky15.7 Fab in complex with circumsporozoite ... -

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Basic information

Entry
Database: PDB / ID: 8f9u
TitleCrystal structure of Ky15.7 Fab in complex with circumsporozoite protein NPDP peptide
Components
  • Circumsporozoite protein NPDP peptide
  • Ky15.7 Antibody, heavy chain
  • Ky15.7 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: 1.7 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 24, 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 NPDP peptide
A: Ky15.7 Antibody, heavy chain
B: Ky15.7 Antibody, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,82313
Polymers49,2033
Non-polymers62110
Water8,377465
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-17 kcal/mol
Surface area20120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.990, 60.696, 147.834
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: Protein/peptide Circumsporozoite protein NPDP peptide / CS


Mass: 1659.668 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (isolate NF54) (eukaryote)
References: UniProt: P08307
#2: Antibody Ky15.7 Antibody, heavy chain


Mass: 24140.084 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 Ky15.7 Antibody, light chain


Mass: 23402.889 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.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / 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: 2.32 Å3/Da / Density % sol: 47.09 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M di-ammonium hydrogen phosphate, 20% 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: 1.033167 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033167 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. obs: 50113 / % possible obs: 97.4 % / Redundancy: 5.5 % / Biso Wilson estimate: 22.34 Å2 / CC1/2: 0.833 / Net I/σ(I): 10.3
Reflection shellResolution: 1.7→1.73 Å / Num. unique obs: 2481 / CC1/2: 0.794

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Processing

Software
NameVersionClassification
PHENIX1.19_4080refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→38.26 Å / SU ML: 0.2507 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.5647
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2295 1999 4 %
Rwork0.2081 48023 -
obs0.2089 50022 97.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.11 Å2
Refinement stepCycle: LAST / Resolution: 1.7→38.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3414 0 40 465 3919
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00293575
X-RAY DIFFRACTIONf_angle_d0.61694862
X-RAY DIFFRACTIONf_chiral_restr0.0463544
X-RAY DIFFRACTIONf_plane_restr0.0041623
X-RAY DIFFRACTIONf_dihedral_angle_d12.48571291
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.40671390.33783347X-RAY DIFFRACTION97.32
1.74-1.790.33631410.29723381X-RAY DIFFRACTION97.35
1.79-1.840.28051430.27763421X-RAY DIFFRACTION97.94
1.84-1.90.32351350.24613286X-RAY DIFFRACTION94.98
1.9-1.970.2851440.22573435X-RAY DIFFRACTION98.41
1.97-2.050.24711420.22443435X-RAY DIFFRACTION98.57
2.05-2.140.28151440.23733441X-RAY DIFFRACTION98.87
2.14-2.250.24681430.2073444X-RAY DIFFRACTION98.25
2.25-2.40.2531450.21493483X-RAY DIFFRACTION99.07
2.4-2.580.2661440.21733452X-RAY DIFFRACTION98.33
2.58-2.840.2411420.21583415X-RAY DIFFRACTION96.42
2.84-3.250.2311450.20023476X-RAY DIFFRACTION98.24
3.25-4.10.17421450.18613495X-RAY DIFFRACTION96.83
4.1-38.260.17731470.17293512X-RAY DIFFRACTION93.32
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)
13.478223260125.49994115448-2.58609787768.70108347034-4.091157903651.924099333880.238509423303-0.84208689343-0.3639800440891.23773506694-0.206823670262-0.27036749504-0.3118195129110.44402562975-0.0671832559090.5061804314940.02009365790840.01976215438890.3672955131060.07278904063410.2336726209790.236-7.347.29
20.997940451296-0.0884076292890.3251521167980.954851665988-0.05558948655252.151594069260.027674657273-0.0918320981568-0.00209375745440.2083121924470.01898377574890.0712777821571-0.0377686241652-0.0230289300603-0.0495413695150.2022300030140.01427724389110.04083174355390.1473995384070.009942109710090.16110155784-7.927-1.039-9.465
31.15479825246-1.00067924461-0.6373904466073.076351492121.440963549341.879114256110.01987136253740.0808587886278-0.0374305922732-0.0967797390925-0.02001876353310.08965410521730.0121645884459-0.154839894590.004029447873430.165136452554-0.00892787720721-0.002275118821950.153866635760.01885049185860.161495161444-6.657-10.747-37.825
41.64159227682-0.844548011665-1.559050012841.384126729710.9394566997513.294305952290.0235296360634-0.2570567404410.1970764568830.107084092440.169891611721-0.207415820721-0.09569800680880.455876677305-0.2046675856970.186031078473-0.0255173527376-0.02321289160340.233533107351-0.03372145239870.17356426207714.143-2.048-11.894
53.11275794546-0.7301460004971.884914164481.3509029088-0.3259543077452.9152880645-0.05598548661680.3362467940560.00237236449599-0.1220757477090.04333572068450.00779673317045-0.1386603386370.1582286626430.0002572909247480.148935196307-0.01737479916070.01559699017180.15064496928-0.003280878535430.1324885469822.12-2.594-47.439
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN P AND RESID 3:13 )P3 - 13
2X-RAY DIFFRACTION2( CHAIN A AND RESID 1:122 )A1 - 122
3X-RAY DIFFRACTION3( CHAIN A AND RESID 123:216 )A123 - 216
4X-RAY DIFFRACTION4( CHAIN B AND RESID 1:106 )B1 - 106
5X-RAY DIFFRACTION5( CHAIN B AND RESID 107:213 )B107 - 213

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