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Basic information

Entry
Database: PDB / ID: 8gif
TitleCrystal structure of a designed single-component Plasmodium falciparum AMA1-RON2L insertion fusion immunogen 3
ComponentsApical membrane antigen 1, rhoptry neck protein 2 chimera
KeywordsCELL INVASION / Single component immunogens / Malaria vaccines
Function / homology
Function and homology information


rhoptry neck / apical complex / microneme / host cell surface binding / symbiont entry into host / membrane
Similarity search - Function
Apical membrane antigen 1 domain superfamily / Apical membrane antigen 1 / Apical membrane antigen 1 / Apical membrane antigen 1
Similarity search - Domain/homology
Apical membrane antigen 1 / Rhoptry neck protein 2
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPatel, P.N. / Tolia, N.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1ZIAAI001253 United States
CitationJournal: Nat Commun / Year: 2023
Title: Structure-based design of a strain transcending AMA1-RON2L malaria vaccine.
Authors: Patel, P.N. / Dickey, T.H. / Diouf, A. / Salinas, N.D. / McAleese, H. / Ouahes, T. / Long, C.A. / Miura, K. / Lambert, L.E. / Tolia, N.H.
History
DepositionMar 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: 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
Revision 1.2Oct 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
A: Apical membrane antigen 1, rhoptry neck protein 2 chimera


Theoretical massNumber of molelcules
Total (without water)39,3931
Polymers39,3931
Non-polymers00
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.360, 62.920, 60.010
Angle α, β, γ (deg.)90.000, 96.250, 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 Apical membrane antigen 1, rhoptry neck protein 2 chimera / Merozoite surface antigen


Mass: 39392.902 Da / Num. of mol.: 1 / Mutation: T64A,T233A,S333A,S334A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PF3D7_1133400, PF3D7_1452000 / Plasmid: pHL-sec / Cell (production host): 293-derived Cells / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: Q7KQK5, UniProt: Q8IKV6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 1.89 Å3/Da / Density % sol: 36.03 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Magnesium chloride, 0.1 M Tris (pH 8.5), 20 % (w/v) PEG 8000

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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: Apr 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→19.71 Å / Num. obs: 17236 / % possible obs: 98.4 % / Redundancy: 3.2 % / Biso Wilson estimate: 27.93 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.0686 / Rpim(I) all: 0.0445 / Rrim(I) all: 0.082 / Net I/σ(I): 12.07
Reflection shellResolution: 2.101→2.176 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.1663 / Mean I/σ(I) obs: 5.41 / Num. unique obs: 1600 / CC1/2: 0.953 / CC star: 0.988 / Rpim(I) all: 0.113 / Rrim(I) all: 0.2019 / % possible all: 92.38

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Processing

Software
NameVersionClassification
SERGUIdata collection
XDSv Feb 5, 2021data reduction
XDSv Feb 5, 2021data scaling
PHENIX1.20.1_4487phasing
Coot0.9model building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→19.71 Å / SU ML: 0.2234 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 21.3225
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2157 862 5 %
Rwork0.1696 16374 -
obs0.1719 17236 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.6 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2466 0 0 100 2566
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212527
X-RAY DIFFRACTIONf_angle_d0.48163428
X-RAY DIFFRACTIONf_chiral_restr0.0422362
X-RAY DIFFRACTIONf_plane_restr0.0035454
X-RAY DIFFRACTIONf_dihedral_angle_d10.4404928
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.230.24091380.19632627X-RAY DIFFRACTION95.05
2.23-2.40.22471440.17522732X-RAY DIFFRACTION99.17
2.4-2.650.23131430.1852729X-RAY DIFFRACTION99.14
2.65-3.030.24041440.18242734X-RAY DIFFRACTION99
3.03-3.810.19921450.16112756X-RAY DIFFRACTION99.18
3.81-19.710.20511480.15832796X-RAY DIFFRACTION98.89
Refinement TLS params.Method: refined / Origin x: 11.3207581173 Å / Origin y: 10.413349248 Å / Origin z: 5.03661866507 Å
111213212223313233
T0.140627593881 Å2-0.00407712618675 Å2-0.0132428573942 Å2-0.11154592096 Å20.0129144730306 Å2--0.213880139347 Å2
L0.656878877088 °2-0.258461676563 °2-0.600216036714 °2-0.906826164509 °20.901609730355 °2--4.38844294246 °2
S-0.0488959392627 Å °-0.0553280483099 Å °-0.0518710085309 Å °0.0520569759917 Å °-0.00215196433866 Å °0.0888719079271 Å °0.105511594302 Å °0.0193862570211 Å °0.0614279366605 Å °
Refinement TLS groupSelection details: all

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