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- PDB-7rd4: Crystal structure of PfCSP peptide 21 with vaccine-elicited human... -

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Basic information

Entry
Database: PDB / ID: 7rd4
TitleCrystal structure of PfCSP peptide 21 with vaccine-elicited human anti-malaria antibody m43.149
Components
  • Circumsporozoite protein
  • antibody m43.149 heavy chain
  • antibody m43.149 light chain
KeywordsIMMUNE SYSTEM / Malaria / CSP / Junction region / antibody / m43.149
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: 1.75 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

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Assembly

Deposited unit
H: antibody m43.149 heavy chain
L: antibody m43.149 light chain
A: antibody m43.149 heavy chain
B: antibody m43.149 light chain
G: Circumsporozoite protein
I: Circumsporozoite protein


Theoretical massNumber of molelcules
Total (without water)106,3846
Polymers106,3846
Non-polymers00
Water15,493860
1
H: antibody m43.149 heavy chain
L: antibody m43.149 light chain
G: Circumsporozoite protein


Theoretical massNumber of molelcules
Total (without water)53,1923
Polymers53,1923
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-30 kcal/mol
Surface area19150 Å2
MethodPISA
2
A: antibody m43.149 heavy chain
B: antibody m43.149 light chain
I: Circumsporozoite protein


Theoretical massNumber of molelcules
Total (without water)53,1923
Polymers53,1923
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-28 kcal/mol
Surface area19240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.826, 55.099, 74.434
Angle α, β, γ (deg.)77.620, 78.960, 69.720
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody antibody m43.149 heavy chain


Mass: 27432.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody antibody m43.149 light chain


Mass: 24196.764 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Protein/peptide Circumsporozoite protein / CS


Mass: 1562.553 Da / Num. of mol.: 2 / Fragment: peptide 21 (UNP residues 120-134) / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: P02893
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 860 / 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: 1.92 Å3/Da / Density % sol: 35.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium formate, 20% w/v PEG3350

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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: Mar 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 67330 / % possible obs: 84.4 % / Redundancy: 1.9 % / Biso Wilson estimate: 12.74 Å2 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.06 / Rrim(I) all: 0.087 / Χ2: 1.074 / Net I/σ(I): 10.9 / Num. measured all: 125698
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.75-1.781.80.2332900.8620.2220.320.52382.2
1.78-1.811.90.20534190.9020.1970.2850.54486.7
1.81-1.851.90.19635290.9040.1890.2730.57887.3
1.85-1.891.90.17634990.9240.170.2450.62188
1.89-1.931.90.15834690.9390.1510.2190.64487.5
1.93-1.971.90.14335270.9450.1370.1980.69887.2
1.97-2.021.90.13634010.9470.130.1880.82886.1
2.02-2.071.90.11534040.9640.110.1590.79585.5
2.07-2.141.90.10533000.9670.10.1450.90882.1
2.14-2.21.90.09429230.9720.0890.130.99473.6
2.2-2.281.90.08834940.9730.0840.1220.98987.3
2.28-2.381.90.07935720.980.0750.1091.07189.6
2.38-2.481.90.07535250.9780.0720.1051.14188.3
2.48-2.611.90.06534690.9830.0630.0911.24586.3
2.61-2.781.80.0633020.9840.0580.0831.31983.5
2.78-2.991.80.05431640.9890.0520.0751.54779
2.99-3.291.80.04529330.9920.0440.0631.72774.1
3.29-3.771.90.03734850.9940.0360.0511.86887.1
3.77-4.751.80.03232860.9950.0310.0451.92282.6
4.75-501.90.03233390.9950.0310.0441.8483.3

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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: 1.75→45.21 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 23.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2327 3369 5 %
Rwork0.1938 63946 -
obs0.1957 67315 84.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.45 Å2 / Biso mean: 18.195 Å2 / Biso min: 2.99 Å2
Refinement stepCycle: final / Resolution: 1.75→45.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6879 0 0 860 7739
Biso mean---26.99 -
Num. residues----902
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.770.32541360.24532521265779
1.77-1.80.27261380.21712682282086
1.8-1.830.25761560.21242823297988
1.83-1.860.23991360.20332757289388
1.86-1.890.25641490.20512779292887
1.89-1.930.26261310.19762727285887
1.93-1.960.25231420.20662828297088
1.96-20.2461490.21132685283486
2-2.050.25791370.20392751288886
2.05-2.090.22521420.19612651279384
2.09-2.150.2191370.19672536267381
2.15-2.20.25361080.20082316242473
2.2-2.270.28121560.19852763291987
2.27-2.340.2071520.1972774292689
2.34-2.430.2661300.20452864299489
2.43-2.520.23711700.2062754292488
2.52-2.640.26251450.20472691283686
2.64-2.780.2591480.20952634278283
2.78-2.950.28461150.20722521263680
2.95-3.180.24621330.20472251238472
3.18-3.50.20381570.18212685284285
3.5-4.010.19281120.1682761287387
4.01-5.040.17381360.15342545268180
5.05-45.210.2071540.18662647280184

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