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- PDB-9c79: Human monoclonal antibody MAD21-101 bound to the N-terminus of cl... -

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Basic information

Entry
Database: PDB / ID: 9c79
TitleHuman monoclonal antibody MAD21-101 bound to the N-terminus of cleaved circumsporozoite protein
Components
  • (Monoclonal antibody MAD21-101 Fab ...) x 2
  • Circumsporozoite protein
KeywordsIMMUNE SYSTEM / Antibody / malaria
Function / homology
Function and homology information


host cell surface binding / symbiont entry into host / entry into host cell by a symbiont-containing vacuole / heparan sulfate proteoglycan binding / 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: 1.46 Å
AuthorsMoskovitz, R. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationDAC-1601-INV-056202 United States
CitationJournal: Science / Year: 2025
Title: Protective antibodies target cryptic epitope unmasked by cleavage of malaria sporozoite protein.
Authors: Dacon, C. / Moskovitz, R. / Swearingen, K. / Da Silva Pereira, L. / Flores-Garcia, Y. / Aleshnick, M. / Kanatani, S. / Flynn, B. / Molina-Cruz, A. / Wollenberg, K. / Traver, M. / Kirtley, P. ...Authors: Dacon, C. / Moskovitz, R. / Swearingen, K. / Da Silva Pereira, L. / Flores-Garcia, Y. / Aleshnick, M. / Kanatani, S. / Flynn, B. / Molina-Cruz, A. / Wollenberg, K. / Traver, M. / Kirtley, P. / Purser, L. / Dillon, M. / Bonilla, B. / Franco, A. / Petros, S. / Kritzberg, J. / Tucker, C. / Paez, G.G. / Gupta, P. / Shears, M.J. / Pazzi, J. / Edgar, J.M. / Teng, A.A. / Belmonte, A. / Oda, K. / Doumbo, S. / Krymskaya, L. / Skinner, J. / Li, S. / Ghosal, S. / Kayentao, K. / Ongoiba, A. / Vaughan, A. / Campo, J.J. / Traore, B. / Barillas-Mury, C. / Wijayalath, W. / Idris, A. / Crompton, P.D. / Sinnis, P. / Wilder, B.K. / Zavala, F. / Seder, R.A. / Wilson, I.A. / Tan, J.
History
DepositionJun 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 22, 2025Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Monoclonal antibody MAD21-101 Fab Heavy Chain
L: Monoclonal antibody MAD21-101 Fab Light Chain
D: Circumsporozoite protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,88212
Polymers50,0193
Non-polymers8649
Water7,584421
1
H: Monoclonal antibody MAD21-101 Fab Heavy Chain
L: Monoclonal antibody MAD21-101 Fab Light Chain
D: Circumsporozoite protein
hetero molecules

hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,88212
Polymers50,0193
Non-polymers8649
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7150 Å2
ΔGint-2 kcal/mol
Surface area20350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.493, 73.892, 86.573
Angle α, β, γ (deg.)90.000, 104.132, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11L-538-

HOH

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Components

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Antibody , 2 types, 2 molecules HL

#1: Antibody Monoclonal antibody MAD21-101 Fab Heavy Chain


Mass: 24225.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Monoclonal antibody MAD21-101 Fab Light Chain


Mass: 23964.623 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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Protein/peptide / Sugars , 2 types, 2 molecules D

#3: Protein/peptide Circumsporozoite protein / CS / PfCSP


Mass: 1828.804 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q7K740
#4: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE

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Non-polymers , 2 types, 429 molecules

#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.4 Å3/Da / Density % sol: 48.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2.0 M ammonium sulfate, 0.2 M sodium chloride, 0.1 M cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.46→42 Å / Num. obs: 81657 / % possible obs: 99.4 % / Redundancy: 3.2 % / Biso Wilson estimate: 17.92 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.041 / Net I/σ(I): 6
Reflection shellResolution: 1.46→1.48 Å / Rmerge(I) obs: 1.223 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4113 / CC1/2: 0.362 / Rpim(I) all: 0.625

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5127refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.46→41.98 Å / SU ML: 0.2044 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.5792
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1996 4058 4.98 %
Rwork0.1733 77465 -
obs0.1746 81523 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.57 Å2
Refinement stepCycle: LAST / Resolution: 1.46→41.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3497 0 56 421 3974
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00833784
X-RAY DIFFRACTIONf_angle_d1.0675181
X-RAY DIFFRACTIONf_chiral_restr0.0877602
X-RAY DIFFRACTIONf_plane_restr0.0086666
X-RAY DIFFRACTIONf_dihedral_angle_d13.25371370
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.480.45841240.41462323X-RAY DIFFRACTION86.74
1.48-1.50.37221350.36552642X-RAY DIFFRACTION99.36
1.5-1.510.34981490.3312658X-RAY DIFFRACTION99.68
1.51-1.530.36441290.29252679X-RAY DIFFRACTION99.4
1.53-1.560.28821390.26452652X-RAY DIFFRACTION99.68
1.56-1.580.30241600.25022666X-RAY DIFFRACTION99.65
1.58-1.60.24691400.23852655X-RAY DIFFRACTION99.79
1.6-1.630.28541480.23752700X-RAY DIFFRACTION99.79
1.63-1.650.27131280.23422653X-RAY DIFFRACTION99.64
1.65-1.680.26331370.22522695X-RAY DIFFRACTION99.72
1.68-1.710.27241520.22912629X-RAY DIFFRACTION99.71
1.71-1.740.26321240.20642687X-RAY DIFFRACTION99.89
1.74-1.780.24211310.1942727X-RAY DIFFRACTION99.93
1.78-1.820.20851370.18482624X-RAY DIFFRACTION100
1.82-1.860.21881470.18082698X-RAY DIFFRACTION99.89
1.86-1.910.19911300.17232710X-RAY DIFFRACTION99.86
1.91-1.960.1761310.16382678X-RAY DIFFRACTION99.89
1.96-2.020.19631240.1662683X-RAY DIFFRACTION99.89
2.02-2.080.23171340.16432689X-RAY DIFFRACTION99.93
2.08-2.160.20411210.16272719X-RAY DIFFRACTION100
2.16-2.240.20141630.15232666X-RAY DIFFRACTION99.96
2.24-2.350.19431440.15312690X-RAY DIFFRACTION100
2.35-2.470.18841490.15452664X-RAY DIFFRACTION100
2.47-2.620.16911500.15372684X-RAY DIFFRACTION100
2.62-2.830.17931460.15912713X-RAY DIFFRACTION100
2.83-3.110.19771380.15662707X-RAY DIFFRACTION100
3.11-3.560.16251430.15562716X-RAY DIFFRACTION100
3.56-4.480.15721520.14142703X-RAY DIFFRACTION100
4.49-41.980.17741530.16922755X-RAY DIFFRACTION99.9

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