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- PDB-7rqr: Structure of chimeric antibody L9heavy_F10light with PfCSP peptid... -

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Basic information

Entry
Database: PDB / ID: 7rqr
TitleStructure of chimeric antibody L9heavy_F10light with PfCSP peptide NANPNVDP
Components
  • F10 Kappa Chain
  • L9 Heavy Chain
  • PfCSP peptide NANPNVDP
KeywordsIMMUNE SYSTEM / Malaria / Antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
Plasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsHurlburt, N.K. / Pancera, M.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates Foundation United States
CitationJournal: Cell Rep / Year: 2022
Title: The light chain of the L9 antibody is critical for binding circumsporozoite protein minor repeats and preventing malaria.
Authors: Wang, L.T. / Hurlburt, N.K. / Schon, A. / Flynn, B.J. / Flores-Garcia, Y. / Pereira, L.S. / Kiyuka, P.K. / Dillon, M. / Bonilla, B. / Zavala, F. / Idris, A.H. / Francica, J.R. / Pancera, M. / Seder, R.A.
History
DepositionAug 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L9 Heavy Chain
B: F10 Kappa Chain
C: PfCSP peptide NANPNVDP
H: L9 Heavy Chain
L: F10 Kappa Chain
P: PfCSP peptide NANPNVDP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,6057
Polymers97,5436
Non-polymers621
Water7,819434
1
A: L9 Heavy Chain
B: F10 Kappa Chain
C: PfCSP peptide NANPNVDP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8334
Polymers48,7713
Non-polymers621
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-22 kcal/mol
Surface area19160 Å2
MethodPISA
2
H: L9 Heavy Chain
L: F10 Kappa Chain
P: PfCSP peptide NANPNVDP


Theoretical massNumber of molelcules
Total (without water)48,7713
Polymers48,7713
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-27 kcal/mol
Surface area19310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.503, 85.817, 145.456
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: Antibody L9 Heavy Chain


Mass: 24458.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293E / Production host: Homo sapiens (human)
#2: Antibody F10 Kappa Chain


Mass: 23473.049 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293E / Production host: Homo sapiens (human)
#3: Protein/peptide PfCSP peptide NANPNVDP


Mass: 839.850 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Plasmodium falciparum 3D7 (eukaryote)
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.29 Å3/Da / Density % sol: 46.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M MES, pH 6.5, 18% PEG 4K, 0.6M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.23→48.49 Å / Num. obs: 44243 / % possible obs: 99.6 % / Redundancy: 6.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.191 / Rpim(I) all: 0.081 / Rrim(I) all: 0.208 / Net I/σ(I): 9 / Num. measured all: 288257 / Scaling rejects: 535
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.23-2.36.61.2282560738980.6480.5091.3322.297.1
8.92-48.495.40.05341097670.9980.0250.05920.196.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7RQP

7rqp


Resolution: 2.23→43.83 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2384 2131 4.83 %
Rwork0.189 42034 -
obs0.1914 44165 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.25 Å2 / Biso mean: 40.7838 Å2 / Biso min: 4.31 Å2
Refinement stepCycle: final / Resolution: 2.23→43.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6658 0 4 434 7096
Biso mean--55.58 42.54 -
Num. residues----873
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.23-2.280.30611350.25482680281597
2.28-2.340.32111320.244727782910100
2.34-2.40.27311450.226827532898100
2.4-2.470.32371460.229627872933100
2.47-2.550.26471330.221527882921100
2.55-2.640.27781470.216527772924100
2.64-2.750.30841130.21528042917100
2.75-2.870.28481580.204327902948100
2.88-3.030.25651530.204627732926100
3.03-3.220.27081320.200528162948100
3.22-3.460.2491310.185928182949100
3.46-3.810.22911590.169128042963100
3.81-4.360.17551580.15682814297299
4.36-5.50.19081310.149328963027100
5.5-43.830.21311580.1952956311498
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.53280.02710.09881.6456-0.3420.9198-0.07970.025-0.10020.0240.0553-0.05010.0511-0.0286-0.02610.2091-0.00260.00190.2324-0.00560.2626-16.95311.449-4.332
21.4348-0.0453-0.12322.8591-0.30031.18340.0125-0.0780.07320.1986-0.01310.0096-0.02290.05660.00440.23780.0043-0.02490.231-0.01190.2242-17.02131.9294.33
36.95111.79741.40282.27131.71592.0249-0.6025-0.5782-0.21981.31730.7784-1.0740.0458-0.3806-0.34220.58870.0968-0.02510.4095-0.01910.4208-15.90515.78416.209
40.99020.45510.15472.42970.07520.8181-0.0094-0.02990.15520.12870.07110.0241-0.03-0.05270.01380.17980.0113-0.0020.19880.00310.2319-27.823-11.462-4.053
51.5668-0.1011-0.22352.88540.72851.226-0.0766-0.1173-0.0520.3180.0599-0.05880.08410.03660.01380.25260.0131-0.02610.23030.01050.2227-26.515-32.0594.521
66.50891.81883.77859.5725-1.74163.0568-0.6892-0.3620.09431.27690.79810.6611-0.77240.883-0.18450.54430.0523-0.01590.4068-0.06320.2552-26.698-15.90516.46
72.79930.0648-0.28832.24880.35213.8813-0.01130.2967-0.11150.02230.0387-0.43610.02530.242-0.0010.281-0.04170.00410.40430.02420.3554-2.80525.886-26.947
81.2567-0.0484-0.43133.24840.20052.9080.06350.53190.1886-0.6539-0.0999-0.0929-0.3335-0.43380.01290.40950.030.00780.57010.09990.3341-10.44139.306-32.294
91.1679-0.7439-0.33581.7158-0.09963.89550.13750.0145-0.1356-0.0094-0.1310.2617-0.0366-0.56960.03670.24720.0148-0.02120.3527-0.0150.3325-43.943-28.351-25.423
100.7087-0.20250.87742.0769-2.10935.47110.0330.2568-0.0773-0.3345-0.10520.11840.44880.39390.0740.30230.0469-0.02420.3623-0.0340.2757-35.377-39.852-31.533
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:119 )A1 - 119
2X-RAY DIFFRACTION2( CHAIN B AND RESID 1:107 )B1 - 107
3X-RAY DIFFRACTION3( CHAIN C AND RESID 106:111 )C106 - 111
4X-RAY DIFFRACTION4( CHAIN H AND RESID 1:119 )H1 - 119
5X-RAY DIFFRACTION5( CHAIN L AND RESID 1:107 )L1 - 107
6X-RAY DIFFRACTION6( CHAIN P AND RESID 106:111 )P106 - 111
7X-RAY DIFFRACTION7( CHAIN A AND RESID 120:213 )A120 - 213
8X-RAY DIFFRACTION8( CHAIN B AND RESID 108:213 )B108 - 213
9X-RAY DIFFRACTION9( CHAIN H AND RESID 120:213 )H120 - 213
10X-RAY DIFFRACTION10( CHAIN L AND RESID 108:213 )L108 - 213

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