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- PDB-8dfi: Crystal structure of moderately neutralizing / interfering human ... -

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Basic information

Entry
Database: PDB / ID: 8dfi
TitleCrystal structure of moderately neutralizing / interfering human monoclonal antibody 42C11 Fab in complex with MSP1-19
Components
  • 42C11 Fab Heavy Chain
  • 42C11 Fab Light Chain
  • Merozoite surface protein 1
KeywordsSTRUCTURAL PROTEIN/IMMUNE SYSTEM / Merozoite Surface Protein 1 (MSP1) / Antigen-Antibody Complex / Antigenic Diversion / Plasmodium falciparum / STRUCTURAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


entry into host cell by a symbiont-containing vacuole / vacuolar membrane / side of membrane / extracellular region / plasma membrane
Similarity search - Function
Merozoite surface 1, C-terminal / Merozoite surface protein, EGF domain 1 / Merozoite surface protein 1 (MSP1) C-terminus / MSP1 EGF domain 1 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Merozoite surface protein 1
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPatel, P.N. / Tang, W.K. / Tolia, N.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nat Commun / Year: 2022
Title: Neutralizing and interfering human antibodies define the structural and mechanistic basis for antigenic diversion.
Authors: Patel, P.N. / Dickey, T.H. / Hopp, C.S. / Diouf, A. / Tang, W.K. / Long, C.A. / Miura, K. / Crompton, P.D. / Tolia, N.H.
History
DepositionJun 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Merozoite surface protein 1
H: 42C11 Fab Heavy Chain
L: 42C11 Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)60,6683
Polymers60,6683
Non-polymers00
Water4,846269
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-21 kcal/mol
Surface area24310 Å2
Unit cell
Length a, b, c (Å)62.560, 68.770, 63.730
Angle α, β, γ (deg.)90.000, 110.678, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Merozoite surface protein 1 / Merozoite surface antigens / PMMSA


Mass: 11759.932 Da / Num. of mol.: 1 / Fragment: UNP residues 1607-1699 / Mutation: S3A, T48A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Strain: isolate 3D7 / Gene: PF3D7_0930300 / Plasmid: pHL-sec / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: Q8I0U8
#2: Antibody 42C11 Fab Heavy Chain


Mass: 25667.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHL-sec / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#3: Antibody 42C11 Fab Light Chain


Mass: 23239.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHL-sec / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 2.16 Å3/Da / Density % sol: 42.95 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES, pH 7.5, 10 % (w/v) PEG 4000, 20% (w/v) Isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→19.85 Å / Num. obs: 37968 / % possible obs: 94.5 % / Redundancy: 3.45 % / Biso Wilson estimate: 27.26 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.85
Reflection shellResolution: 1.9→1.95 Å / Mean I/σ(I) obs: 4.86 / Num. unique obs: 2198 / CC1/2: 0.903 / % possible all: 74.5

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Coot1.16_3549model building
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1OB1 & 1AQK

1ob1

1aqk


Resolution: 1.9→19.85 Å / SU ML: 0.1786 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 20.4991
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2001 1898 5 %
Rwork0.1752 36052 -
obs0.1764 37950 94.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.61 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3903 0 0 269 4172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00393994
X-RAY DIFFRACTIONf_angle_d0.69835433
X-RAY DIFFRACTIONf_chiral_restr0.0471603
X-RAY DIFFRACTIONf_plane_restr0.004706
X-RAY DIFFRACTIONf_dihedral_angle_d11.54522408
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.27571050.23551996X-RAY DIFFRACTION73.93
1.95-20.24951320.19282503X-RAY DIFFRACTION93.21
2-2.060.21541380.18852625X-RAY DIFFRACTION97.49
2.06-2.120.22341410.17972674X-RAY DIFFRACTION98.46
2.12-2.20.22391400.18142654X-RAY DIFFRACTION98.14
2.2-2.290.22381390.17692645X-RAY DIFFRACTION97.62
2.29-2.390.22051380.18122620X-RAY DIFFRACTION96.64
2.39-2.520.24251310.19282495X-RAY DIFFRACTION92.3
2.52-2.670.24081400.18822657X-RAY DIFFRACTION97.69
2.67-2.880.20631390.19122635X-RAY DIFFRACTION97.13
2.88-3.170.20861390.19012643X-RAY DIFFRACTION97.2
3.17-3.620.22711340.17442541X-RAY DIFFRACTION93.01
3.62-4.560.14681410.14982681X-RAY DIFFRACTION97.41
4.56-19.850.16911410.16322683X-RAY DIFFRACTION96.45
Refinement TLS params.Method: refined / Origin x: -6.0717600054 Å / Origin y: 36.7785707262 Å / Origin z: 14.8388203853 Å
111213212223313233
T0.216582085729 Å2-0.0108701891367 Å20.0215876643733 Å2-0.175008238078 Å20.0151781908536 Å2--0.154449472283 Å2
L2.02413988653 °2-0.0200663869936 °20.697703118724 °2-0.261551003235 °20.0627605655907 °2--0.476126320868 °2
S-0.0877925128048 Å °0.0839854442357 Å °0.119682284283 Å °-0.0395929105878 Å °0.0262435722506 Å °-0.0118287873159 Å °-0.0473592739636 Å °-0.0113155165695 Å °0.0681225449262 Å °
Refinement TLS groupSelection details: all

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