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- PDB-7rxi: Fab234 in complex with the C-terminal alpha-TSR domain of P. falc... -

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Basic information

Entry
Database: PDB / ID: 7rxi
TitleFab234 in complex with the C-terminal alpha-TSR domain of P. falciparum
Components
  • Circumsporozoite protein
  • Fab234 heavy chain
  • Fab234 light chain
KeywordsIMMUNE SYSTEM / Malaria / Antibody / Sporozoite / Circumsporozoite protein / alpha-TSR domain
Function / homology
Function and homology information


host cell surface binding / symbiont entry into host / entry into host cell by a symbiont-containing vacuole / heparan sulfate proteoglycan binding / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Circumsporozoite protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsPholcharee, T. / Oyen, D. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1170236 United States
CitationJournal: Plos Pathog. / Year: 2022
Title: A novel CSP C-terminal epitope targeted by an antibody with protective activity against Plasmodium falciparum.
Authors: Beutler, N. / Pholcharee, T. / Oyen, D. / Flores-Garcia, Y. / MacGill, R.S. / Garcia, E. / Calla, J. / Parren, M. / Yang, L. / Volkmuth, W. / Locke, E. / Regules, J.A. / Dutta, S. / ...Authors: Beutler, N. / Pholcharee, T. / Oyen, D. / Flores-Garcia, Y. / MacGill, R.S. / Garcia, E. / Calla, J. / Parren, M. / Yang, L. / Volkmuth, W. / Locke, E. / Regules, J.A. / Dutta, S. / Emerling, D. / Early, A.M. / Neafsey, D.E. / Winzeler, E. / King, C.R. / Zavala, F. / Burton, D.R. / Wilson, I.A. / Rogers, T.F.
History
DepositionAug 23, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: 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_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Fab234 light chain
H: Fab234 heavy chain
A: Circumsporozoite protein


Theoretical massNumber of molelcules
Total (without water)54,2693
Polymers54,2693
Non-polymers00
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-24 kcal/mol
Surface area22290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.690, 115.690, 119.297
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Antibody Fab234 light chain


Mass: 22780.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Fab234 heavy chain


Mass: 24035.115 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein Circumsporozoite protein


Mass: 7453.486 Da / Num. of mol.: 1
Fragment: C-terminal alpha-TSR domain (UNP residues 310-375)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PF3D7_0304600 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7K740
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
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: 3.79 Å3/Da / Density % sol: 67.58 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% PEG8000, 0.1 M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 43634 / % possible obs: 97.9 % / Redundancy: 5.5 % / Biso Wilson estimate: 36.59 Å2 / CC1/2: 0.928 / Rpim(I) all: 0.042 / Rsym value: 0.092 / Net I/σ(I): 21.2
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2124 / CC1/2: 0.73 / Rpim(I) all: 0.458 / Rsym value: 0.94 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX(1.19_4092: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Homology model

Resolution: 2.15→39.08 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2647 2243 5.15 %
Rwork0.2188 --
obs0.2211 43550 97.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→39.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3662 0 0 193 3855
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123761
X-RAY DIFFRACTIONf_angle_d1.0375129
X-RAY DIFFRACTIONf_dihedral_angle_d6.664525
X-RAY DIFFRACTIONf_chiral_restr0.064577
X-RAY DIFFRACTIONf_plane_restr0.009661
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.20.30181590.27142427X-RAY DIFFRACTION96
2.2-2.250.3591510.27442558X-RAY DIFFRACTION98
2.25-2.30.29611260.27932586X-RAY DIFFRACTION99
2.3-2.370.30491350.27672573X-RAY DIFFRACTION99
2.37-2.440.32041310.27042626X-RAY DIFFRACTION99
2.44-2.510.27511510.27112570X-RAY DIFFRACTION100
2.51-2.60.31481080.25712629X-RAY DIFFRACTION100
2.6-2.710.32811070.26062650X-RAY DIFFRACTION99
2.71-2.830.30711570.26972516X-RAY DIFFRACTION97
2.83-2.980.31851480.26272616X-RAY DIFFRACTION99
2.98-3.170.28591490.2382616X-RAY DIFFRACTION100
3.17-3.410.31461330.22062650X-RAY DIFFRACTION100
3.41-3.760.2741190.20252641X-RAY DIFFRACTION99
3.76-4.30.20731640.16852483X-RAY DIFFRACTION94
4.3-5.410.17871510.15122550X-RAY DIFFRACTION94
5.41-39.080.2631540.21842616X-RAY DIFFRACTION92

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