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- PDB-7rd3: Crystal structure of PfCSP peptide 21 with vaccine-elicited human... -

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Basic information

Entry
Database: PDB / ID: 7rd3
TitleCrystal structure of PfCSP peptide 21 with vaccine-elicited human anti-malaria antibody m42.126
Components
  • Circumsporozoite protein
  • antibody m42.126 heavy chain
  • antibody m42.126 light chain
KeywordsIMMUNE SYSTEM / Malaria / CSP / Junction region / antibody / m42.126
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: 1.81 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 16, 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
A: antibody m42.126 heavy chain
B: antibody m42.126 light chain
H: antibody m42.126 heavy chain
L: antibody m42.126 light chain
C: Circumsporozoite protein
D: Circumsporozoite protein


Theoretical massNumber of molelcules
Total (without water)106,4936
Polymers106,4936
Non-polymers00
Water9,962553
1
A: antibody m42.126 heavy chain
B: antibody m42.126 light chain
C: Circumsporozoite protein


Theoretical massNumber of molelcules
Total (without water)53,2463
Polymers53,2463
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-30 kcal/mol
Surface area19330 Å2
MethodPISA
2
H: antibody m42.126 heavy chain
L: antibody m42.126 light chain
D: Circumsporozoite protein


Theoretical massNumber of molelcules
Total (without water)53,2463
Polymers53,2463
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-29 kcal/mol
Surface area19130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.854, 57.176, 74.493
Angle α, β, γ (deg.)86.500, 76.860, 72.440
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody antibody m42.126 heavy chain


Mass: 27542.980 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 m42.126 light chain


Mass: 24140.742 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.: 553 / 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: 2.04 Å3/Da / Density % sol: 39.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium citrate tribasic dihydrate, pH 5.5, 18% 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: Apr 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.81→50 Å / Num. obs: 66229 / % possible obs: 86.3 % / Redundancy: 3 % / Biso Wilson estimate: 23.86 Å2 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.046 / Rrim(I) all: 0.082 / Χ2: 0.885 / Net I/σ(I): 7.5 / Num. measured all: 198861
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.81-1.842.90.4332620.8760.2850.5180.36484.8
1.84-1.872.90.35833680.9160.2360.430.3889.2
1.87-1.9130.32535140.930.2130.3890.40790.5
1.91-1.953.10.28935030.9390.190.3470.44390.8
1.95-1.993.10.23634440.9590.1550.2830.45590.9
1.99-2.043.10.19235100.9710.1270.2310.49690.3
2.04-2.093.10.18333670.9710.1210.220.5488.4
2.09-2.153.20.15133140.9770.10.1820.57285.8
2.15-2.213.10.13130830.9820.0870.1580.62879.3
2.21-2.283.10.12335020.9830.0820.1490.68792.2
2.28-2.363.10.10635900.9870.070.1280.72193.8
2.36-2.463.10.09435430.990.0610.1120.76892.8
2.46-2.573.10.08335410.990.0550.10.83592.4
2.57-2.730.07534530.9920.050.0910.95190
2.7-2.8730.06833190.9920.0460.0821.14685.7
2.87-3.092.90.05929790.9950.040.0711.39378
3.09-3.412.80.05129520.9950.0350.0621.92476.6
3.41-3.92.80.04331390.9960.030.0522.04381.7
3.9-4.912.60.03827850.9960.0270.0472.07573
4.91-502.80.03830610.9970.0250.0462.12379.6

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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: 1.81→44.38 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 2.02 / Phase error: 29.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.26 3244 4.9 %
Rwork0.2161 62932 -
obs0.2183 66176 86.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.52 Å2 / Biso mean: 34.4068 Å2 / Biso min: 10.82 Å2
Refinement stepCycle: final / Resolution: 1.81→44.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6850 0 0 553 7403
Biso mean---38.83 -
Num. residues----898
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.81-1.830.36391310.30642542267380
1.83-1.860.34661360.28532807294388
1.86-1.890.35931350.26592941307690
1.89-1.930.2951540.24592815296990
1.93-1.960.32271580.24992911306991
1.96-20.33081530.25292848300191
2-2.040.26661340.24742925305990
2.04-2.080.28291530.23962747290088
2.08-2.130.28041750.22452737291286
2.13-2.190.26941420.22482542268481
2.19-2.250.3161320.23692709284186
2.25-2.310.28511800.22673001318194
2.31-2.390.27811460.22552987313393
2.39-2.470.27191510.22722952310393
2.47-2.570.30521340.23132928306292
2.57-2.690.3031370.21952879301690
2.69-2.830.30921480.22842734288286
2.83-3.010.24851190.22972639275882
3.01-3.240.28381040.22272243234770
3.24-3.560.30971220.20222681280384
3.56-4.080.1871320.19232566269881
4.08-5.140.19241200.17342248236871
5.14-44.380.20311480.18842550269881

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