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- PDB-8dfg: Crystal structure of potently neutralizing human monoclonal antib... -

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Basic information

Entry
Database: PDB / ID: 8dfg
TitleCrystal structure of potently neutralizing human monoclonal antibody 42D6 Fab in complex with MSP1-19
Components
  • 42D6 Fab Heavy Chain
  • 42D6 Fab Light Chain
  • Merozoite surface protein 1
KeywordsSTRUCTURAL PROTEIN/IMMUNE SYSTEM / Merozoite Surface Protein 1 (MSP1) / Antigen-Antibody Complex / Plasmodium falciparum / Antigenic Diversion / 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 speciesHomo sapiens (human)
Plasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 16, 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
H: 42D6 Fab Heavy Chain
L: 42D6 Fab Light Chain
I: 42D6 Fab Heavy Chain
M: 42D6 Fab Light Chain
B: Merozoite surface protein 1
A: Merozoite surface protein 1


Theoretical massNumber of molelcules
Total (without water)123,3236
Polymers123,3236
Non-polymers00
Water6,143341
1
H: 42D6 Fab Heavy Chain
L: 42D6 Fab Light Chain
A: Merozoite surface protein 1


Theoretical massNumber of molelcules
Total (without water)61,6623
Polymers61,6623
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: 42D6 Fab Heavy Chain
M: 42D6 Fab Light Chain
B: Merozoite surface protein 1


Theoretical massNumber of molelcules
Total (without water)61,6623
Polymers61,6623
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.680, 71.370, 196.500
Angle α, β, γ (deg.)90.000, 94.635, 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: Antibody 42D6 Fab Heavy Chain


Mass: 26224.277 Da / Num. of mol.: 2
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)
#2: Antibody 42D6 Fab Light Chain


Mass: 23677.430 Da / Num. of mol.: 2
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: Protein Merozoite surface protein 1 / Merozoite surface antigens / PMMSA


Mass: 11759.932 Da / Num. of mol.: 2 / 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 2.4 Å3/Da / Density % sol: 48.74 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Potassium chloride, 20 % PEG 3350

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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: Sep 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→19.92 Å / Num. obs: 75221 / % possible obs: 96.3 % / Redundancy: 3.247 % / Biso Wilson estimate: 29.6 Å2 / CC1/2: 0.994 / Rrim(I) all: 0.127 / Net I/σ(I): 6.03
Reflection shellResolution: 2→2.05 Å / Redundancy: 2.985 % / Mean I/σ(I) obs: 1.61 / Num. unique obs: 5165 / CC1/2: 0.766 / Rrim(I) all: 0.809 / % possible all: 91.1

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Cootmodel building
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1OB1 & 3B2U

1ob1

3b2u


Resolution: 2→19.92 Å / SU ML: 0.2342 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 32.7978
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.266 3759 5.01 %
Rwork0.2249 71345 -
obs0.2269 75104 96.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.19 Å2
Refinement stepCycle: LAST / Resolution: 2→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7985 0 0 341 8326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00998171
X-RAY DIFFRACTIONf_angle_d0.928811103
X-RAY DIFFRACTIONf_chiral_restr0.05961229
X-RAY DIFFRACTIONf_plane_restr0.00641437
X-RAY DIFFRACTIONf_dihedral_angle_d12.85694943
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.30451210.31112302X-RAY DIFFRACTION85.95
2.02-2.050.29521370.28072598X-RAY DIFFRACTION96.03
2.05-2.080.2921410.26952682X-RAY DIFFRACTION95.99
2.08-2.110.26471390.26372643X-RAY DIFFRACTION97.58
2.11-2.140.30041380.26672614X-RAY DIFFRACTION97
2.14-2.170.32381400.26472670X-RAY DIFFRACTION96.9
2.17-2.210.2861390.25882658X-RAY DIFFRACTION97.02
2.21-2.250.28461390.24652631X-RAY DIFFRACTION97.26
2.25-2.290.28711430.23952711X-RAY DIFFRACTION97.61
2.29-2.330.26421390.24082649X-RAY DIFFRACTION96.97
2.33-2.380.28711400.24542647X-RAY DIFFRACTION97.69
2.38-2.430.27771410.23962678X-RAY DIFFRACTION96.71
2.43-2.490.281320.24282494X-RAY DIFFRACTION91.63
2.49-2.550.31681380.24332626X-RAY DIFFRACTION96.71
2.55-2.620.31761430.24182716X-RAY DIFFRACTION97.81
2.62-2.690.26371390.23062634X-RAY DIFFRACTION98.33
2.69-2.780.32591440.2392724X-RAY DIFFRACTION97.72
2.78-2.880.28911410.24342687X-RAY DIFFRACTION98.57
2.88-2.990.3061420.24252690X-RAY DIFFRACTION97.55
2.99-3.130.31551410.23642674X-RAY DIFFRACTION97.78
3.13-3.290.27241410.23032675X-RAY DIFFRACTION97.17
3.29-3.50.25611380.21752640X-RAY DIFFRACTION95.6
3.5-3.770.2441340.20762530X-RAY DIFFRACTION90.95
3.77-4.140.23831410.18662687X-RAY DIFFRACTION97.48
4.14-4.740.21351420.16872691X-RAY DIFFRACTION97.62
4.74-5.940.21891440.1952732X-RAY DIFFRACTION96.97
5.94-19.920.24281420.2482662X-RAY DIFFRACTION94.41
Refinement TLS params.Method: refined / Origin x: -4.00835750711 Å / Origin y: 42.3141480552 Å / Origin z: 48.6956832401 Å
111213212223313233
T0.201443373845 Å20.024699718105 Å20.00832246070793 Å2-0.22388545825 Å2-0.00229000790977 Å2--0.213715952993 Å2
L0.00398476437225 °20.0155113543444 °20.125916829231 °2--0.0258099937336 °2-0.0189453068718 °2--0.526664587592 °2
S-0.00672528592024 Å °-0.00814677195084 Å °0.00357656594624 Å °-0.00609678447747 Å °0.0061726679478 Å °0.0184008900638 Å °0.0100851835438 Å °0.00632702614203 Å °-0.0205842448064 Å °
Refinement TLS groupSelection details: all

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