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- PDB-9hzk: sdAb9 in complex with PfCSP aTSR domain -

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Basic information

Entry
Database: PDB / ID: 9hzk
TitlesdAb9 in complex with PfCSP aTSR domain
Components
  • Circumsporozoite protein
  • sdAb9
KeywordsIMMUNE SYSTEM / malaria / circumsporozoite protein / camelid single-domain 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
DI(HYDROXYETHYL)ETHER / Circumsporozoite protein
Similarity search - Component
Biological speciesPlasmodium falciparum NF54 (eukaryote)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsSterckx, Y.G.-J. / Geens, R.
Funding support Belgium, 3items
OrganizationGrant numberCountry
Other governmentUAntwerp BOF DOCPRO4-NIEUWZAP 40043 Belgium
Other governmentUAntwerp BOF infrastructure 41391 Belgium
Research Foundation - Flanders (FWO)11P4B24N Belgium
CitationJournal: Infect.Immun. / Year: 2025
Title: Evidence for a model of conformational change by the Plasmodium falciparum circumsporozoite protein during sporozoite development in the mosquito host through the use of camelid single-domain antibodies.
Authors: Geens, R. / De Vocht, L. / Aguirre-Botero, M.C. / Vincke, C. / Romao, E. / Magez, S. / Muyldermans, S. / Amino, R. / Sterckx, Y.G.-.J.
History
DepositionJan 13, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 18, 2025Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jun 25, 2025Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Circumsporozoite protein
A: sdAb9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,45815
Polymers26,2192
Non-polymers1,23913
Water1,54986
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint7 kcal/mol
Surface area9940 Å2
Unit cell
Length a, b, c (Å)53.740, 53.740, 60.840
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Circumsporozoite protein / CS / PfCSP


Mass: 10343.603 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum NF54 (eukaryote) / Gene: CSP / Production host: Escherichia coli (E. coli) / References: UniProt: P19597
#2: Antibody sdAb9


Mass: 15875.271 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.93 Å3/Da / Density % sol: 36.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 35% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.967697 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967697 Å / Relative weight: 1
ReflectionResolution: 2.07→25.46 Å / Num. obs: 23186 / % possible obs: 99.57 % / Redundancy: 1.9 % / CC1/2: 0.993 / Net I/σ(I): 5.36
Reflection shellResolution: 2.07→2.28 Å / Mean I/σ(I) obs: 0.68 / Num. unique obs: 5814 / CC1/2: 0.374

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→25.46 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 28.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2261 592 4.99 %
Rwork0.1841 --
obs0.1863 11856 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.07→25.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1475 0 81 86 1642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071570
X-RAY DIFFRACTIONf_angle_d0.8552091
X-RAY DIFFRACTIONf_dihedral_angle_d15.034585
X-RAY DIFFRACTIONf_chiral_restr0.05214
X-RAY DIFFRACTIONf_plane_restr0.009265
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.280.39451480.3762812X-RAY DIFFRACTION100
2.28-2.610.31621490.24182832X-RAY DIFFRACTION100
2.61-3.290.25241480.18372810X-RAY DIFFRACTION100
3.29-25.460.17191470.14232810X-RAY DIFFRACTION99

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