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- PDB-7rd9: Crystal structure of PfCSP peptide 21 with vaccine-elicited human... -

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Basic information

Entry
Database: PDB / ID: 7rd9
TitleCrystal structure of PfCSP peptide 21 with vaccine-elicited human anti-malaria antibody m43.159
Components
  • Circumsporozoite protein
  • antibody m43.159 heavy chain
  • antibody m43.159 light chain
KeywordsIMMUNE SYSTEM / Malaria / CSP / Junction region / antibody / m43.159
Function / homology
Function and homology information


entry into host cell by a symbiont-containing vacuole / 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: 1.91 Å
AuthorsXu, K. / Kwong, P.D.
CitationJournal: Immunity / Year: 2021
Title: Vaccination in a humanized mouse model elicits highly protective PfCSP-targeting anti-malarial antibodies.
Authors: Kratochvil, S. / Shen, C.H. / Lin, Y.C. / Xu, K. / Nair, U. / Da Silva Pereira, L. / Tripathi, P. / Arnold, J. / Chuang, G.Y. / Melzi, E. / Schon, A. / Zhang, B. / Dillon, M. / Bonilla, B. / ...Authors: Kratochvil, S. / Shen, C.H. / Lin, Y.C. / Xu, K. / Nair, U. / Da Silva Pereira, L. / Tripathi, P. / Arnold, J. / Chuang, G.Y. / Melzi, E. / Schon, A. / Zhang, B. / Dillon, M. / Bonilla, B. / Flynn, B.J. / Kirsch, K.H. / Kisalu, N.K. / Kiyuka, P.K. / Liu, T. / Ou, L. / Pancera, M. / Rawi, R. / Reveiz, M. / Seignon, K. / Wang, L.T. / Waring, M.T. / Warner, J. / Yang, Y. / Francica, J.R. / Idris, A.H. / Seder, R.A. / Kwong, P.D. / Batista, F.D.
History
DepositionJul 9, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 29, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Circumsporozoite protein
H: antibody m43.159 heavy chain
L: antibody m43.159 light chain


Theoretical massNumber of molelcules
Total (without water)53,1183
Polymers53,1183
Non-polymers00
Water8,395466
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-31 kcal/mol
Surface area19310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.920, 62.004, 75.137
Angle α, β, γ (deg.)90.000, 105.870, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11L-519-

HOH

21L-529-

HOH

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Components

#1: Protein/peptide Circumsporozoite protein / / CS


Mass: 1562.553 Da / Num. of mol.: 1 / Fragment: peptide 21 (UNP residues 120-134) / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: P02893
#2: Antibody antibody m43.159 heavy chain


Mass: 27360.695 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 antibody m43.159 light chain


Mass: 24194.770 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 466 / Source method: isolated from a natural source / Formula: H2O

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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: 1.98 Å3/Da / Density % sol: 37.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium acetate trihydrate, pH 4.0, 10% w/v PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. obs: 30463 / % possible obs: 94.1 % / Redundancy: 4.7 % / Biso Wilson estimate: 16.72 Å2 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.092 / Rrim(I) all: 0.201 / Χ2: 1.666 / Net I/σ(I): 6.9 / Num. measured all: 142340
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.91-1.944.40.55515010.7830.2940.6310.76992.1
1.94-1.9850.50415890.870.2530.5660.86599.7
1.98-2.025.10.4915960.8770.2430.5480.93499.8
2.02-2.065.20.42915900.8790.2120.481.04199.8
2.06-2.15.30.38416040.8910.1880.4291.11199.8
2.1-2.155.20.34516120.9060.1690.3851.19299.3
2.15-2.25.20.30615880.9270.1490.3421.25299.3
2.2-2.265.20.28316110.9290.1390.3171.32798.4
2.26-2.335.10.25515640.9530.1260.2861.34298.4
2.33-2.414.70.22715340.9440.1150.2561.45695.5
2.41-2.4950.20415710.9580.1010.2281.52597.8
2.49-2.595.20.18816120.9660.0930.211.65999.3
2.59-2.715.10.16516090.9730.0830.1851.79699.2
2.71-2.854.90.14615660.9730.0750.1652.11598
2.85-3.034.70.12715680.9790.0670.1442.34196.8
3.03-3.274.40.11115450.9840.060.1272.80394.4
3.27-3.593.70.09114170.9850.0530.1063.41887.1
3.59-4.113.50.07814620.990.0470.0913.43490
4.11-5.182.70.06212040.9910.0410.0753.54173.1
5.18-502.80.06911200.990.0460.0843.83966.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6b5l

6b5l


Resolution: 1.91→34.32 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2333 1518 4.98 %
Rwork0.1864 28935 -
obs0.1887 30453 93.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.22 Å2 / Biso mean: 21.2774 Å2 / Biso min: 7.12 Å2
Refinement stepCycle: final / Resolution: 1.91→34.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3436 0 0 466 3902
Biso mean---30.31 -
Num. residues----452
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.91-1.970.28161580.21332581273994
1.97-2.040.23861400.197427802920100
2.04-2.120.28721400.189927782918100
2.12-2.220.23771460.18682764291099
2.22-2.340.23861200.19352764288498
2.34-2.480.22261420.18832679282196
2.48-2.670.23611540.19482783293799
2.67-2.940.25291460.19592749289598
2.94-3.370.25341400.1852603274394
3.37-4.240.19411240.16662468259288
4.24-34.320.20121080.17911986209469

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