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- PDB-9dst: Crystal structure of Fab MS-1805 in complex with N-terminal junct... -

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Entry
Database: PDB / ID: 9dst
TitleCrystal structure of Fab MS-1805 in complex with N-terminal junction peptide from circumsporozoite protein
Components
  • Circumsporozoite protein
  • Heavy chain of Fab MS-1805
  • Light Chain of Fab MS-1805
KeywordsIMMUNE SYSTEM / Engineered antibody for 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
CITRIC ACID / Circumsporozoite protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Plasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsJain, M. / Wilson, I.A.
Funding support United States, 2items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-004923 United States
Bill & Melinda Gates FoundationINV-056202 United States
CitationJournal: To Be Published
Title: Crystal structure of Fab MS-1805 in complex with N-terminal junction peptide from circumsporozoite protein
Authors: Jain, M. / Wilson, I.A.
History
DepositionSep 28, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Light Chain of Fab MS-1805
A: Circumsporozoite protein
C: Heavy chain of Fab MS-1805
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7634
Polymers49,5713
Non-polymers1921
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-31 kcal/mol
Surface area19770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.325, 76.744, 74.453
Angle α, β, γ (deg.)90.00, 88.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Light Chain of Fab MS-1805


Mass: 23566.066 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: Protein/peptide Circumsporozoite protein / CS / PfCSP


Mass: 1648.708 Da / Num. of mol.: 1
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
#3: Antibody Heavy chain of Fab MS-1805


Mass: 24356.387 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)
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.44 Å3/Da / Density % sol: 49.56 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium citrate, 20% (v/v) 2-propanol and 20% (w/v) polyethylene glycol 4000

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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: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 21, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 1.74→28 Å / Num. obs: 45572 / % possible obs: 93.1 % / Redundancy: 3.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.045 / Net I/σ(I): 21.4
Reflection shellResolution: 1.75→1.8 Å / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 1.89 / Num. unique obs: 2226 / CC1/2: 0.838 / Rpim(I) all: 0.045

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→26.72 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2278 1972 4.33 %
Rwork0.197 --
obs0.1983 45531 92.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.74→26.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3366 0 13 163 3542
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d1.041
X-RAY DIFFRACTIONf_dihedral_angle_d9.245476
X-RAY DIFFRACTIONf_chiral_restr0.068524
X-RAY DIFFRACTIONf_plane_restr0.009607
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.780.32441240.29652764X-RAY DIFFRACTION82
1.78-1.830.31691410.2523156X-RAY DIFFRACTION95
1.83-1.880.25311530.22483149X-RAY DIFFRACTION96
1.88-1.950.24821390.21713199X-RAY DIFFRACTION95
1.95-2.010.27421480.20823180X-RAY DIFFRACTION95
2.01-2.10.30251420.21673113X-RAY DIFFRACTION94
2.1-2.190.23931410.20522945X-RAY DIFFRACTION88
2.19-2.310.25361370.20363177X-RAY DIFFRACTION96
2.31-2.450.24441550.20913168X-RAY DIFFRACTION95
2.45-2.640.26741510.21683193X-RAY DIFFRACTION95
2.64-2.90.25821420.21453115X-RAY DIFFRACTION94
2.9-3.320.22891270.19873010X-RAY DIFFRACTION89
3.32-4.190.18371510.17613228X-RAY DIFFRACTION96
4.19-26.720.15941210.16083162X-RAY DIFFRACTION92

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