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- PDB-9dsr: Crystal structure of Fab MS-1805 in complex with NPNA3 peptide fr... -

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Basic information

Entry
Database: PDB / ID: 9dsr
TitleCrystal structure of Fab MS-1805 in complex with NPNA3 peptide from circumsporozoite protein
Components
  • Circumsporozoite protein
  • Heavy chain of Fab MS-1805
  • Light chain of Fab MS-1805
KeywordsIMMUNE SYSTEM / Engineered Fab / 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: 2.25 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 NPNA3 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
A: Heavy chain of Fab MS-1805
B: Light chain of Fab MS-1805
C: Circumsporozoite protein


Theoretical massNumber of molelcules
Total (without water)49,1303
Polymers49,1303
Non-polymers00
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-32 kcal/mol
Surface area19250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.544, 73.847, 60.747
Angle α, β, γ (deg.)90.00, 99.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: 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)
#2: 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)
#3: Protein/peptide Circumsporozoite protein / CS / PfCSP


Mass: 1207.210 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.27 Å3/Da / Density % sol: 45.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Zinc acetate, 20% (w/v) polyethylene glycol

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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 EIGER2 XE 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: 2.25→28 Å / Num. obs: 20906 / % possible obs: 98.87 % / Redundancy: 6.7 % / CC1/2: 0.982 / Net I/σ(I): 11.5
Reflection shellResolution: 2.25→2.29 Å / Num. unique obs: 1027 / CC1/2: 0.807

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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: 2.25→27.84 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 22.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2394 1999 9.63 %
Rwork0.1883 --
obs0.1932 20753 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→27.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3363 0 0 78 3441
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d6.33469
X-RAY DIFFRACTIONf_chiral_restr0.05522
X-RAY DIFFRACTIONf_plane_restr0.007601
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.310.32661310.23771228X-RAY DIFFRACTION92
2.31-2.370.24431410.20811323X-RAY DIFFRACTION99
2.37-2.440.28891420.19761334X-RAY DIFFRACTION99
2.44-2.520.2441430.20241342X-RAY DIFFRACTION99
2.52-2.610.28441390.20631299X-RAY DIFFRACTION99
2.61-2.710.27871450.21961361X-RAY DIFFRACTION99
2.71-2.830.2791420.21411333X-RAY DIFFRACTION99
2.83-2.980.2731460.20961370X-RAY DIFFRACTION100
2.98-3.170.27341430.21171338X-RAY DIFFRACTION100
3.17-3.410.23571450.19871358X-RAY DIFFRACTION100
3.41-3.760.24421440.17851350X-RAY DIFFRACTION100
3.76-4.30.21161430.1621356X-RAY DIFFRACTION100
4.3-5.410.17281460.14161360X-RAY DIFFRACTION100
5.41-27.840.20311490.18161402X-RAY DIFFRACTION100

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