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- PDB-9zm9: Crystal structure of Fab 7160 in complex with short major repeat ... -

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Basic information

Entry
Database: PDB / ID: 9zm9
TitleCrystal structure of Fab 7160 in complex with short major repeat region (NPNA3) from circumsporozoite protein
Components
  • Circumsporozoite protein
  • Heavy Chain of Fab 7160
  • Light Chain of Fab 7160
KeywordsIMMUNE SYSTEM / Antibody
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: 1.88 Å
AuthorsJain, M. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-056202 United States
CitationJournal: PLoS Pathog / Year: 2026
Title: Structural basis for conserved and distinct antigen recognition by a lineage of malaria-protective antibodies.
Authors: Monika Jain / Fabien Cannac / Sashank Agrawal / Wen-Hsin Lee / Johannes R Loeffler / Monica L Fernández-Quintero / Gonzalo E González-Páez / Re'em Moskovitz / Andrew B Ward / Ian A Wilson /
Abstract: Monoclonal antibodies (mAbs) targeting the Plasmodium falciparum circumsporozoite protein (PfCSP) have demonstrated substantial promise in preventing malaria infection and disease. PfCSP is ...Monoclonal antibodies (mAbs) targeting the Plasmodium falciparum circumsporozoite protein (PfCSP) have demonstrated substantial promise in preventing malaria infection and disease. PfCSP is characterized by a central region composed of repetitive NANP motifs, which serve as major targets for protective antibodies. Several potent mAbs targeting this region exhibit homotypic Fab-Fab interactions, which enhance antigen binding and contribute to their neutralization potency. Among these, mAb 399, encoded by the IGHV3-49/IGKV2D-29 (VH3-49/VK2D-29) germline lineages, forms head-to-head inter-Fab contacts mediated primarily by germline-encoded residues. Here, we determined X-ray and cryo-EM structures of two additional Fabs, derived from the same germline lineages, 7160 and 7118, in their unliganded forms and with PfCSP-derived peptides or recombinant shortened CSP. Both Fabs bound NANP6 repeats with high affinity (KD 6-10 nM). Fab 7160 formed germline-encoded inter-Fab homotypic interactions resembling Fab 399, indicating a conserved and preconfigured mode of antigen recognition. In contrast, Fab 7118 does not form homotypic contacts and adopts a distinct binding mode, which precludes inter-Fab interactions. These findings highlight the structural versatility of VH3-49/VK2D-29-derived antibodies and demonstrate that their CDR loop variations can modulate antibody conformation, homotypic Fab-Fab interactions, and epitope engagement. Our study further defines this class of germline-encoded anti-CSP antibodies and provides mechanistic insights into how they achieve high-avidity binding and protective immunity either through or independent of pre-configured Fab-Fab interactions with important implications for germline-targeting malaria vaccine design.
History
DepositionDec 9, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2026Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heavy Chain of Fab 7160
B: Light Chain of Fab 7160
C: Heavy Chain of Fab 7160
D: Light Chain of Fab 7160
E: Circumsporozoite protein
F: Circumsporozoite protein


Theoretical massNumber of molelcules
Total (without water)99,7506
Polymers99,7506
Non-polymers00
Water6,648369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)188.010, 52.348, 102.986
Angle α, β, γ (deg.)90.00, 110.07, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Heavy Chain of Fab 7160


Mass: 24421.510 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Light Chain of Fab 7160


Mass: 24246.094 Da / Num. of mol.: 2
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: 1207.210 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: CSP, PF3D7_0304600 / Production host: synthetic construct (others) / References: UniProt: Q7K740
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H2O
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: 2.39 Å3/Da / Density % sol: 48.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium acetate (pH 7.0) and 20% (w/v) PEG 3350.
PH range: 7

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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: 0.92 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 75043 / % possible obs: 99.7 % / Redundancy: 6.2 % / CC1/2: 0.98 / Net I/σ(I): 11.4
Reflection shellResolution: 1.9→1.93 Å / Num. unique obs: 3573 / CC1/2: 0.69

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→26.79 Å / SU ML: 0.22 / Cross valid method: NONE / σ(F): 1.38 / Phase error: 23.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2452 2000 2.67 %
Rwork0.1997 --
obs0.2009 75043 97.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.88→26.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6831 0 0 369 7200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076987
X-RAY DIFFRACTIONf_angle_d0.9039502
X-RAY DIFFRACTIONf_dihedral_angle_d16.9962524
X-RAY DIFFRACTIONf_chiral_restr0.0561069
X-RAY DIFFRACTIONf_plane_restr0.0071222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.930.29751030.2573766X-RAY DIFFRACTION71
1.93-1.980.28211420.23475170X-RAY DIFFRACTION97
1.98-2.040.32321430.22385261X-RAY DIFFRACTION98
2.04-2.10.2511460.21615290X-RAY DIFFRACTION99
2.1-2.180.27551440.20175285X-RAY DIFFRACTION99
2.18-2.260.24551460.20035315X-RAY DIFFRACTION99
2.26-2.370.27021440.21245288X-RAY DIFFRACTION99
2.37-2.490.27341460.21195326X-RAY DIFFRACTION100
2.49-2.650.30821470.2145333X-RAY DIFFRACTION100
2.65-2.850.23891460.21415339X-RAY DIFFRACTION100
2.85-3.140.27061470.21155382X-RAY DIFFRACTION100
3.14-3.590.23531470.20015361X-RAY DIFFRACTION100
3.59-4.520.20791470.17385374X-RAY DIFFRACTION99
4.52-26.790.20491520.17975553X-RAY DIFFRACTION100

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