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- PDB-7rxj: Fab236 in complex with the C-terminal alpha-TSR domain of P. falc... -

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Basic information

Entry
Database: PDB / ID: 7rxj
TitleFab236 in complex with the C-terminal alpha-TSR domain of P. falciparum
Components
  • Circumsporozoite protein
  • Fab236 heavy chain
  • Fab236 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: 2.345 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 1.3Oct 16, 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
B: Fab236 light chain
A: Fab236 heavy chain
L: Fab236 light chain
H: Fab236 heavy chain
I: Circumsporozoite protein
G: Circumsporozoite protein


Theoretical massNumber of molelcules
Total (without water)108,5116
Polymers108,5116
Non-polymers00
Water2,504139
1
B: Fab236 light chain
A: Fab236 heavy chain
G: Circumsporozoite protein


Theoretical massNumber of molelcules
Total (without water)54,2563
Polymers54,2563
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
L: Fab236 light chain
H: Fab236 heavy chain
I: Circumsporozoite protein


Theoretical massNumber of molelcules
Total (without water)54,2563
Polymers54,2563
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.137, 45.564, 201.087
Angle α, β, γ (deg.)90.00, 94.04, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Fab236 light chain


Mass: 22792.162 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 Fab236 heavy chain


Mass: 24009.908 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.: 139 / 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: 2.82 Å3/Da / Density % sol: 56.35 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 30% PEG2000 MME, 0.2 M ammonium sulfate, 0.1 M 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-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: 2.345→50 Å / Num. obs: 46380 / % possible obs: 96.7 % / Redundancy: 5.2 % / CC1/2: 0.946 / Rpim(I) all: 0.055 / Rsym value: 0.12 / Net I/σ(I): 13.7
Reflection shellResolution: 2.345→2.44 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1678 / CC1/2: 0.828 / Rpim(I) all: 0.254 / Rsym value: 0.463 / % possible all: 71.1

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Homology model

Resolution: 2.345→42.24 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2486 2436 5.26 %
Rwork0.2175 --
obs0.2193 46326 92.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.345→42.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7260 0 0 139 7399
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067437
X-RAY DIFFRACTIONf_angle_d0.75210168
X-RAY DIFFRACTIONf_dihedral_angle_d11.2764408
X-RAY DIFFRACTIONf_chiral_restr0.0491166
X-RAY DIFFRACTIONf_plane_restr0.0051304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.345-2.39270.261310.2762681X-RAY DIFFRACTION24
2.3927-2.44470.3223980.28991907X-RAY DIFFRACTION70
2.4447-2.50160.34091070.29632409X-RAY DIFFRACTION87
2.5016-2.56410.34671280.31082669X-RAY DIFFRACTION94
2.5641-2.63340.42881470.31092676X-RAY DIFFRACTION98
2.6334-2.71090.37251400.29022759X-RAY DIFFRACTION99
2.7109-2.79840.33151360.27932764X-RAY DIFFRACTION99
2.7984-2.89840.28871670.27352768X-RAY DIFFRACTION100
2.8984-3.01440.33011510.27122787X-RAY DIFFRACTION100
3.0144-3.15160.30681480.2852787X-RAY DIFFRACTION100
3.1516-3.31770.31331480.24672767X-RAY DIFFRACTION100
3.3177-3.52540.26471610.222810X-RAY DIFFRACTION100
3.5254-3.79750.23451750.20362787X-RAY DIFFRACTION100
3.7975-4.17930.22511870.18392757X-RAY DIFFRACTION100
4.1793-4.78340.1641720.14362792X-RAY DIFFRACTION100
4.7834-6.02380.1771750.16772829X-RAY DIFFRACTION100
6.0238-42.240.21921650.18672941X-RAY DIFFRACTION99

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