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- PDB-9c7d: Human monoclonal antibody MAD22-38 bound to the N-terminus of cle... -

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Basic information

Entry
Database: PDB / ID: 9c7d
TitleHuman monoclonal antibody MAD22-38 bound to the N-terminus of cleaved circumsporozoite protein
Components
  • Circumsporozoite protein
  • Monoclonal antibody MAD22-38 Fab Heavy Chain
  • Monoclonal antibody MAD22-38 Fab Light Chain
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: 1.99 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 MAD22-38 Fab Heavy Chain
L: Monoclonal antibody MAD22-38 Fab Light Chain
B: Circumsporozoite protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4074
Polymers49,3503
Non-polymers1,0571
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-7 kcal/mol
Surface area19820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.803, 76.355, 88.797
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Antibody Monoclonal antibody MAD22-38 Fab Heavy Chain


Mass: 24166.145 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 MAD22-38 Fab Light Chain


Mass: 23354.844 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)
#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-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.53 Å3/Da / Density % sol: 51.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 20% PEG 3350, 0.2 M ammonium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.99→44.4 Å / Num. obs: 34343 / % possible obs: 97.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 29.4 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.067 / Net I/σ(I): 6.44
Reflection shellResolution: 1.99→2.03 Å / Rmerge(I) obs: 1.625 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1703 / CC1/2: 0.357 / Rpim(I) all: 0.677

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5127refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→44.4 Å / SU ML: 0.2651 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.2171
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2322 1729 5.04 %
Rwork0.1837 32565 -
obs0.1861 34294 97.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.89 Å2
Refinement stepCycle: LAST / Resolution: 1.99→44.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3382 0 71 253 3706
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01413547
X-RAY DIFFRACTIONf_angle_d1.35684839
X-RAY DIFFRACTIONf_chiral_restr0.076564
X-RAY DIFFRACTIONf_plane_restr0.0103603
X-RAY DIFFRACTIONf_dihedral_angle_d16.97651234
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.050.33581530.2772634X-RAY DIFFRACTION96.64
2.05-2.120.30391490.23682678X-RAY DIFFRACTION98.67
2.12-2.190.26771260.22072722X-RAY DIFFRACTION99.03
2.19-2.280.24831430.21052687X-RAY DIFFRACTION98.92
2.28-2.380.25461150.21722750X-RAY DIFFRACTION98.35
2.38-2.510.3021590.22042603X-RAY DIFFRACTION95.9
2.51-2.670.28861530.21512665X-RAY DIFFRACTION97.24
2.67-2.870.26041350.20642737X-RAY DIFFRACTION98.49
2.87-3.160.28371580.19692710X-RAY DIFFRACTION98.79
3.16-3.620.21121450.17072716X-RAY DIFFRACTION97.11
3.62-4.560.181250.1442802X-RAY DIFFRACTION98.72
4.56-44.40.1761680.1532861X-RAY DIFFRACTION97.27

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