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- PDB-8gid: Crystal structure of a strain-transcending single-component Plasm... -

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Basic information

Entry
Database: PDB / ID: 8gid
TitleCrystal structure of a strain-transcending single-component Plasmodium falciparum AMA1-RON2L structure-based design immunogen 1 (SBD1)
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 / Apical membrane antigen 1 / Rhoptry neck protein 2
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.2Nov 6, 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)41,7291
Polymers41,7291
Non-polymers00
Water2,954164
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)131.620, 38.340, 71.970
Angle α, β, γ (deg.)90.000, 95.140, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-407-

HOH

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Components

#1: Protein Apical membrane antigen 1, rhoptry neck protein 2 chimera / Merozoite surface antigen


Mass: 41729.453 Da / Num. of mol.: 1 / Mutation: T137A,T261A,S41A,S42A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: ama1, 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: D9MXR5, UniProt: Q7KQK5, UniProt: Q8IKV6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.36 Å3/Da / Density % sol: 47.81 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Ammonium sulfate, 20% (w/v) 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: Apr 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→19.81 Å / Num. obs: 32748 / % possible obs: 97.05 % / Redundancy: 3.4 % / Biso Wilson estimate: 27.8 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.0701 / Rpim(I) all: 0.0447 / Rrim(I) all: 0.0834 / Net I/σ(I): 12.22
Reflection shellResolution: 1.8→1.864 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.7521 / Mean I/σ(I) obs: 2.02 / Num. unique obs: 3112 / CC1/2: 0.663 / CC star: 0.893 / Rpim(I) all: 0.4763 / Rrim(I) all: 0.8935 / % possible all: 96.48

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Processing

Software
NameVersionClassification
SERGUIdata collection
XDSv Feb 5, 2021data reduction
XSCALEv Feb 5, 2021data scaling
PHENIXv1.20.1-4487phasing
Cootv0.9model building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→19.81 Å / SU ML: 0.2176 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.1616
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2092 1637 5 %
Rwork0.1785 31111 -
obs0.18 32748 97.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.87 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2692 0 0 164 2856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00582759
X-RAY DIFFRACTIONf_angle_d0.78813742
X-RAY DIFFRACTIONf_chiral_restr0.0505393
X-RAY DIFFRACTIONf_plane_restr0.0064497
X-RAY DIFFRACTIONf_dihedral_angle_d11.87961026
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.35391280.33992436X-RAY DIFFRACTION91.64
1.85-1.910.28111370.23652604X-RAY DIFFRACTION98.53
1.91-1.980.25111370.21752600X-RAY DIFFRACTION98.88
1.98-2.060.25671380.19432615X-RAY DIFFRACTION98.64
2.06-2.150.2351370.17852619X-RAY DIFFRACTION98.11
2.15-2.260.22721330.17872532X-RAY DIFFRACTION95.55
2.26-2.410.21421390.16752637X-RAY DIFFRACTION99
2.41-2.590.22161370.17812616X-RAY DIFFRACTION98.71
2.59-2.850.21171370.19012603X-RAY DIFFRACTION97.79
2.85-3.260.22671350.18642551X-RAY DIFFRACTION94.28
3.26-4.10.16651370.16112619X-RAY DIFFRACTION97.52
4.1-19.810.18891420.16122679X-RAY DIFFRACTION96.12
Refinement TLS params.Method: refined / Origin x: 20.0874617637 Å / Origin y: 1.07071813671 Å / Origin z: 19.411366733 Å
111213212223313233
T0.250948932769 Å20.0131482240338 Å2-0.0108758329581 Å2-0.165614105397 Å20.00481007791871 Å2--0.19126366366 Å2
L1.52079907877 °20.287317326498 °2-0.625200508306 °2-0.819039114691 °2-0.113257887869 °2--1.86628233491 °2
S-0.00876807381729 Å °-0.0224156917938 Å °-0.0130002483084 Å °-0.0160372100475 Å °0.00836531756747 Å °0.0880073792291 Å °0.0217853249241 Å °-0.114409693469 Å °0.00120347235058 Å °
Refinement TLS groupSelection details: all

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