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

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Basic information

Entry
Database: PDB / ID: 7lkb
TitleCrystal structure of PfCSP peptide 21 with vaccine-elicited human anti-malaria antibody m42.127
Components
  • Circumsporozoite protein
  • m42.127 Fab heavy Chain
  • m42.127 Fab light chain
KeywordsIMMUNE SYSTEM/ANTIGEN / Malaria / CSP / Junction region / antibody / m42.127 / IMMUNE SYSTEM / IMMUNE SYSTEM-ANTIGEN complex
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 speciesHomo sapiens (human)
Plasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
DepositionFeb 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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
H: m42.127 Fab heavy Chain
L: m42.127 Fab light chain
A: Circumsporozoite protein
B: m42.127 Fab heavy Chain
C: m42.127 Fab light chain
D: Circumsporozoite protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,2407
Polymers102,1446
Non-polymers961
Water11,908661
1
H: m42.127 Fab heavy Chain
L: m42.127 Fab light chain
A: Circumsporozoite protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1684
Polymers51,0723
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-37 kcal/mol
Surface area19840 Å2
MethodPISA
2
B: m42.127 Fab heavy Chain
C: m42.127 Fab light chain
D: Circumsporozoite protein


Theoretical massNumber of molelcules
Total (without water)51,0723
Polymers51,0723
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-30 kcal/mol
Surface area19410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.888, 58.182, 75.198
Angle α, β, γ (deg.)87.460, 77.520, 72.040
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody m42.127 Fab heavy Chain


Mass: 24996.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody m42.127 Fab light chain


Mass: 24513.143 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein/peptide Circumsporozoite protein / / CS


Mass: 1562.553 Da / Num. of mol.: 2 / Fragment: Peptide 21 / Source method: obtained synthetically / Source: (synth.) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: P02893
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 661 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.18 Å3/Da / Density % sol: 43.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium acetate trihydrate pH 4.5, and 30% w/v polyethylene glycol 1500

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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 EIGER X 16M / Detector: PIXEL / Date: Aug 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 70885 / % possible obs: 89.3 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.037 / Rrim(I) all: 0.055 / Χ2: 1.079 / Net I/σ(I): 12.2 / Num. measured all: 146677
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.832.10.31136050.8430.2830.4220.44890.3
1.83-1.862.10.27936070.860.2550.3790.47191.3
1.86-1.92.10.23736010.8910.2170.3220.50490.5
1.9-1.942.10.20835740.910.190.2830.58190.3
1.94-1.982.10.16635490.9460.1530.2260.62289.8
1.98-2.032.10.14535350.9590.1320.1960.69488.6
2.03-2.082.10.13534900.9630.1230.1830.77487.6
2.08-2.1320.11533660.9670.1060.1570.85185.3
2.13-2.220.10330840.9720.0950.1410.94378.1
2.2-2.272.10.09635940.9750.0870.131.07689.6
2.27-2.352.10.08436370.9820.0760.1141.1292.9
2.35-2.442.10.07536530.9850.0680.1021.21192
2.44-2.552.10.06636720.9870.060.091.31492.1
2.55-2.6920.05735970.990.0520.0781.41390.9
2.69-2.862.10.05235240.9910.0470.071.70188.6
2.86-3.0820.04133280.9950.0380.0561.77283.8
3.08-3.392.10.03134330.9960.0280.0421.70386.5
3.39-3.882.10.02737580.9970.0230.0361.75394.5
3.88-4.882.10.02136990.9980.0180.0281.37793.5
4.88-502.10.0235790.9980.0170.0261.29790.3

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXdev_3936refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6B5M

6b5m


Resolution: 1.8→36.7 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 22.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2172 3543 5 %
Rwork0.1814 67329 -
obs0.1832 70872 89.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.72 Å2 / Biso mean: 26.7531 Å2 / Biso min: 11.74 Å2
Refinement stepCycle: final / Resolution: 1.8→36.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6943 0 5 661 7609
Biso mean--30 34.29 -
Num. residues----912
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057113
X-RAY DIFFRACTIONf_angle_d0.9069696
X-RAY DIFFRACTIONf_dihedral_angle_d10.42980
X-RAY DIFFRACTIONf_chiral_restr0.0581102
X-RAY DIFFRACTIONf_plane_restr0.0061246
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.830.30451220.25582601272385
1.83-1.850.27991350.24472708284391
1.85-1.880.28331350.23122808294391
1.88-1.910.27811480.22322715286391
1.91-1.940.26561420.20632734287690
1.94-1.980.26911460.19572687283389
1.98-2.010.21391100.20272732284289
2.01-2.050.24681470.20192659280688
2.05-2.090.25141560.20332625278188
2.09-2.140.23811310.20062569270085
2.14-2.190.19081230.19442387251079
2.19-2.240.25011190.18972549266884
2.24-2.30.23651280.19122844297293
2.3-2.370.20421730.19342762293593
2.37-2.450.24481600.20242761292192
2.45-2.540.21811680.20812768293692
2.54-2.640.2441490.19542753290292
2.64-2.760.23791350.2012763289890
2.76-2.90.23431320.19522664279688
2.9-3.080.25181380.18992475261383
3.08-3.320.23731340.18092555268984
3.32-3.660.21571690.16582855302495
3.66-4.180.16071560.15772835299194
4.18-5.270.17471310.13472777290892
5.27-36.70.18461560.16412743289991

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