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

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Basic information

Entry
Database: PDB / ID: 7rda
TitleCrystal structure of PfCSP peptide 21 with vaccine-elicited human anti-malaria antibody m43.138
Components
  • Circumsporozoite protein
  • antibody m43.138 heavy chain
  • antibody m43.138 light chain
KeywordsIMMUNE SYSTEM / Malaria / CSP / Junction region / antibody / m43.138
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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
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: 1.92 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
Revision 1.3Oct 23, 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
C: Circumsporozoite protein
H: antibody m43.138 heavy chain
L: antibody m43.138 light chain


Theoretical massNumber of molelcules
Total (without water)53,0383
Polymers53,0383
Non-polymers00
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-32 kcal/mol
Surface area18990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.492, 79.263, 90.922
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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 m43.138 heavy chain


Mass: 27315.693 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 m43.138 light chain


Mass: 24159.809 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


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.05 Å3/Da / Density % sol: 40.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium citrate tribasic dihydrate, pH 5.0, 10% w/v PEG6000

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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: 1.92→50 Å / Num. obs: 33841 / % possible obs: 99.4 % / Redundancy: 7 % / Biso Wilson estimate: 25.87 Å2 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.044 / Rrim(I) all: 0.115 / Χ2: 1.483 / Net I/σ(I): 7 / Num. measured all: 235291
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.92-1.956.50.56416690.8930.2350.6130.53299.5
1.95-1.996.80.46516630.9340.1890.5030.63599.8
1.99-2.0370.42216710.9410.170.4560.682100
2.03-2.077.10.39516880.9370.1570.4260.74499.9
2.07-2.117.30.35316600.9530.140.380.839100
2.11-2.167.30.31116780.9670.1230.3350.907100
2.16-2.227.30.28616960.9660.1130.3090.96299.9
2.22-2.287.20.26516770.9650.1060.2861.04799.9
2.28-2.347.10.24216620.9720.0980.2611.13699.9
2.34-2.426.40.21216900.9750.0890.231.2199.8
2.42-2.517.30.19416980.9780.0770.2091.28199.9
2.51-2.617.60.17616830.9830.0680.1891.40499.9
2.61-2.727.50.15616870.9820.0610.1681.64499.9
2.72-2.877.30.13517090.9870.0540.1451.80299.8
2.87-3.057.10.11416880.9910.0470.1242.09299.4
3.05-3.286.60.09516920.9920.040.1032.37298.9
3.28-3.615.90.0816840.9920.0370.0892.83998.2
3.61-4.146.90.06816970.9960.0280.0732.82497.5
4.14-5.216.60.05616950.9960.0240.0612.78596.4
5.21-506.40.04918540.9980.020.0542.24999.3

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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: 1.92→42.51 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2319 1666 4.93 %
Rwork0.198 32110 -
obs0.1998 33776 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.1 Å2 / Biso mean: 31.4723 Å2 / Biso min: 14.11 Å2
Refinement stepCycle: final / Resolution: 1.92→42.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3430 0 0 241 3671
Biso mean---36.24 -
Num. residues----452
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.92-1.970.34511310.26282468259993
1.97-2.040.26861560.229526472803100
2.04-2.110.30761270.224226772804100
2.11-2.20.27921490.215526572806100
2.2-2.30.24891430.227726572800100
2.3-2.420.26321280.223827012829100
2.42-2.570.25541250.219827012826100
2.57-2.770.25781220.214727172839100
2.77-3.040.261360.212527042840100
3.04-3.480.20611430.19042670281399
3.49-4.390.19841640.16652673283797
4.39-42.510.19541420.17492838298098

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