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- PDB-8dfh: Crystal structure of non-neutralizing / interfering human monoclo... -

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Basic information

Entry
Database: PDB / ID: 8dfh
TitleCrystal structure of non-neutralizing / interfering human monoclonal antibody 42C3 Fab in complex with MSP1-19
Components
  • 42C3 Fab Heavy Chain
  • 42C3 Fab Light Chain
  • Merozoite surface protein 1
KeywordsSTRUCTURAL PROTEIN/IMMUNE SYSTEM / Merozoite Surface Protein 1 (MSP1) / Antigenic Diversion / Plasmodium falciparum / Antigen-Antibody complex / 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: 2.3 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 30, 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: 42C3 Fab Heavy Chain
L: 42C3 Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)60,2153
Polymers60,2153
Non-polymers00
Water91951
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-24 kcal/mol
Surface area23670 Å2
Unit cell
Length a, b, c (Å)72.390, 75.720, 117.530
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: 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 42C3 Fab Heavy Chain


Mass: 25443.453 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 42C3 Fab Light Chain


Mass: 23011.594 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.: 51 / 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: 2.73 Å3/Da / Density % sol: 54.91 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Sodium Cacodylate, pH 6.5, 5 % (v/v) PEG 8000, 40% (v/v) 2-Methyl-2,4-Pentanediol

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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 EIGER2 X 16M / Detector: PIXEL / Date: Jul 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→19.83 Å / Num. obs: 28468 / % possible obs: 96.5 % / Redundancy: 3.68 % / Biso Wilson estimate: 47.38 Å2 / CC1/2: 0.996 / Net I/σ(I): 10.99
Reflection shellResolution: 2.3→2.36 Å / Num. unique obs: 1994 / CC1/2: 0.996 / % possible all: 93.4

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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 & 6UMX

1ob1

6umx


Resolution: 2.3→19.83 Å / SU ML: 0.2778 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.4966
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2329 1424 5 %
Rwork0.2093 27037 -
obs0.2105 28461 96.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.32 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3928 0 0 51 3979
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00224037
X-RAY DIFFRACTIONf_angle_d0.56745491
X-RAY DIFFRACTIONf_chiral_restr0.0445605
X-RAY DIFFRACTIONf_plane_restr0.0029717
X-RAY DIFFRACTIONf_dihedral_angle_d7.85922438
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.380.25781370.26362598X-RAY DIFFRACTION94.8
2.38-2.470.31831380.2732617X-RAY DIFFRACTION95.3
2.47-2.590.31371400.27522656X-RAY DIFFRACTION95.82
2.59-2.720.29841420.26632715X-RAY DIFFRACTION98.86
2.72-2.890.29541440.24972733X-RAY DIFFRACTION98.63
2.89-3.120.28621440.24822721X-RAY DIFFRACTION98.22
3.12-3.430.24381440.22272747X-RAY DIFFRACTION97.83
3.43-3.920.21711380.19522610X-RAY DIFFRACTION93.28
3.92-4.930.18031470.16312802X-RAY DIFFRACTION98.63
4.93-19.830.20671500.19022838X-RAY DIFFRACTION95.89
Refinement TLS params.Method: refined / Origin x: 13.5350799199 Å / Origin y: 17.1666314068 Å / Origin z: 30.4965539433 Å
111213212223313233
T0.305468579853 Å2-0.0159197017926 Å20.00425234486151 Å2-0.323057135805 Å2-0.00809366899986 Å2--0.44353503156 Å2
L0.319761420392 °2-0.0459360150425 °20.403175255771 °2-0.0772824015251 °20.014292435435 °2--2.41227108534 °2
S-0.00854123552716 Å °-0.023995379807 Å °-0.0249150567694 Å °-0.0118957434348 Å °0.00260731324474 Å °-0.0136734319622 Å °-0.0794161517605 Å °-0.0474051323402 Å °0.00373442001589 Å °
Refinement TLS groupSelection details: All

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