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- PDB-7s0x: Fab352 in complex with the C-terminal alphaTSR domain of P. falciparum -

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Basic information

Entry
Database: PDB / ID: 7s0x
TitleFab352 in complex with the C-terminal alphaTSR domain of P. falciparum
Components
  • Circumsporozoite protein
  • Fab352 heavy chain
  • Fab352 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: 2.8 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 31, 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 6, 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: Fab352 light chain
H: Fab352 heavy chain
D: Fab352 light chain
C: Fab352 heavy chain
E: Circumsporozoite protein
F: Circumsporozoite protein


Theoretical massNumber of molelcules
Total (without water)107,4066
Polymers107,4066
Non-polymers00
Water88349
1
L: Fab352 light chain
H: Fab352 heavy chain
E: Circumsporozoite protein


Theoretical massNumber of molelcules
Total (without water)53,7033
Polymers53,7033
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Fab352 light chain
C: Fab352 heavy chain
F: Circumsporozoite protein


Theoretical massNumber of molelcules
Total (without water)53,7033
Polymers53,7033
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.060, 70.502, 105.960
Angle α, β, γ (deg.)90.00, 100.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Fab352 light chain


Mass: 22558.045 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Fab352 heavy chain


Mass: 23691.635 Da / Num. of mol.: 2
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.: 2
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.: 49 / 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: 2.88 Å3/Da / Density % sol: 57.24 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 20% isopropanol, 20% PEG4000, 0.1 M sodium citrate, pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 30400 / % possible obs: 98.5 % / Redundancy: 2.9 % / CC1/2: 0.849 / Rpim(I) all: 0.141 / Rsym value: 0.207 / Net I/σ(I): 5.6
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1420 / CC1/2: 0.553 / Rpim(I) all: 0.619 / Rsym value: 0.86 / % possible all: 91.4

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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: 2.8→41.36 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2757 1495 4.94 %
Rwork0.225 --
obs0.2275 30292 96.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→41.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7275 0 0 49 7324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037445
X-RAY DIFFRACTIONf_angle_d0.65410155
X-RAY DIFFRACTIONf_dihedral_angle_d5.9031049
X-RAY DIFFRACTIONf_chiral_restr0.0461151
X-RAY DIFFRACTIONf_plane_restr0.0051311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.77-2.850.4328950.33181859X-RAY DIFFRACTION69
2.85-2.960.37311130.31792641X-RAY DIFFRACTION96
2.96-3.070.36971500.30852654X-RAY DIFFRACTION98
3.07-3.210.31181230.29212689X-RAY DIFFRACTION99
3.21-3.380.32451290.26782707X-RAY DIFFRACTION100
3.38-3.60.32011510.24072643X-RAY DIFFRACTION99
3.6-3.870.29731490.2242717X-RAY DIFFRACTION99
3.87-4.260.24791320.18752712X-RAY DIFFRACTION100
4.26-4.880.20061450.15762723X-RAY DIFFRACTION100
4.88-6.140.26071610.18222724X-RAY DIFFRACTION100
6.14-41.360.2041470.20732728X-RAY DIFFRACTION97

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