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

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Basic information

Entry
Database: PDB / ID: 7lkg
TitleCrystal structure of PfCSP peptide 21 with vaccine-elicited human anti-malaria antibody m43.151
Components
  • Circumsporozoite protein
  • m43.151 Fab Heavy Chain
  • m43.151 Fab Light chain
KeywordsIMMUNE SYSTEM/ANTIGEN / Malaria / CSP / Junction region / antibody / m43.151 / 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: 2.02 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
A: m43.151 Fab Heavy Chain
B: m43.151 Fab Light chain
C: Circumsporozoite protein
D: m43.151 Fab Heavy Chain
E: m43.151 Fab Light chain
F: Circumsporozoite protein


Theoretical massNumber of molelcules
Total (without water)102,1966
Polymers102,1966
Non-polymers00
Water7,242402
1
A: m43.151 Fab Heavy Chain
B: m43.151 Fab Light chain
C: Circumsporozoite protein


Theoretical massNumber of molelcules
Total (without water)51,0983
Polymers51,0983
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: m43.151 Fab Heavy Chain
E: m43.151 Fab Light chain
F: Circumsporozoite protein


Theoretical massNumber of molelcules
Total (without water)51,0983
Polymers51,0983
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.421, 54.169, 75.701
Angle α, β, γ (deg.)77.620, 77.090, 67.590
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody m43.151 Fab Heavy Chain


Mass: 24962.115 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 m43.151 Fab Light chain


Mass: 24573.197 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: Junctional peptide 21 / Source method: obtained synthetically / Source: (synth.) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: P02893
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / 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: 1.95 Å3/Da / Density % sol: 36.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Citric acid pH 3.5 and 25% w/v polyethylene glycol 3350

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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: 2.02→50 Å / Num. obs: 43488 / % possible obs: 87.8 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.103 / Rrim(I) all: 0.17 / Χ2: 1.356 / Net I/σ(I): 6.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.05-2.092.40.4822950.6470.3850.6180.53390.6
2.09-2.122.40.46222130.6340.3630.590.58491.7
2.12-2.162.40.40523420.7090.3140.5150.63293.4
2.16-2.212.50.41422890.670.3170.5240.69392.8
2.21-2.262.50.38822940.740.290.4870.67691.5
2.26-2.312.60.37322040.7450.2780.4670.73490.9
2.31-2.372.60.34822770.7880.2520.4320.82490.6
2.37-2.432.70.34221890.8270.2450.4230.7889.6
2.43-2.52.70.31121800.8390.2220.3840.86287.7
2.5-2.582.70.26919910.8860.1910.3321.01380.2
2.58-2.682.70.25322530.9020.1790.3121.09892.1
2.68-2.782.70.22923200.9240.160.2811.3393.1
2.78-2.912.70.18922570.9410.1350.2341.5690.8
2.91-3.062.60.15222330.960.1120.191.84890.1
3.06-3.252.50.1221730.9740.0910.1522.17888
3.25-3.512.30.09121200.9820.0740.1182.63685.6
3.51-3.862.20.06919620.9860.0580.0912.76179.2
3.86-4.422.10.05520660.9890.0480.0732.82784
4.42-5.562.10.05119310.990.0440.0683.04478
5.56-502.30.04818990.9920.0380.0622.82276.5

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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: 2.02→38.38 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 27.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2535 2034 4.68 %
Rwork0.2128 41426 -
obs0.2148 43460 86.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.84 Å2 / Biso mean: 32.9596 Å2 / Biso min: 11.19 Å2
Refinement stepCycle: final / Resolution: 2.02→38.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6938 0 0 402 7340
Biso mean---36.08 -
Num. residues----910
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037102
X-RAY DIFFRACTIONf_angle_d0.7059676
X-RAY DIFFRACTIONf_dihedral_angle_d10.211972
X-RAY DIFFRACTIONf_chiral_restr0.0481092
X-RAY DIFFRACTIONf_plane_restr0.0041244
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.02-2.070.31511130.2652234072
2.07-2.120.35721320.2592288592
2.12-2.180.29171430.25300493
2.18-2.250.3041550.2446292292
2.25-2.320.28451280.2498289791
2.32-2.40.29061340.2336284190
2.4-2.50.30921190.2435283988
2.5-2.610.30481490.2497266284
2.61-2.750.33971260.2505298793
2.75-2.920.31171100.2407293391
2.92-3.150.26751600.2196283990
3.15-3.460.25141430.2019272386
3.46-3.960.22281600.1833257882
3.96-4.990.19831140.1612252779
4.99-100.17451480.17244978

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