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- PDB-8qus: Crystal structure of the Plasmodium vivax Apical membrane antigen... -

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Basic information

Entry
Database: PDB / ID: 8qus
TitleCrystal structure of the Plasmodium vivax Apical membrane antigen (AMA1) in complex with single domain i-body WD34
Components
  • Apical merozoite antigen 1
  • single domain i-body WD34
KeywordsPROTEIN BINDING / Plasmodium / AMA1 / i-body
Function / homologyApical membrane antigen 1 domain superfamily / Apical membrane antigen 1 / Apical membrane antigen 1 / Apical membrane antigen 1 / membrane / Apical merozoite antigen 1
Function and homology information
Biological speciesPlasmodium vivax Sal-1 (eukaryote)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMaddumage, J.C. / Kvansakul, M.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1103871 Australia
Citation
Journal: Nat Commun / Year: 2024
Title: A broadly cross-reactive i-body to AMA1 potently inhibits blood and liver stages of Plasmodium parasites.
Authors: Angage, D. / Chmielewski, J. / Maddumage, J.C. / Hesping, E. / Caiazzo, S. / Lai, K.H. / Yeoh, L.M. / Menassa, J. / Opi, D.H. / Cairns, C. / Puthalakath, H. / Beeson, J.G. / Kvansakul, M. / ...Authors: Angage, D. / Chmielewski, J. / Maddumage, J.C. / Hesping, E. / Caiazzo, S. / Lai, K.H. / Yeoh, L.M. / Menassa, J. / Opi, D.H. / Cairns, C. / Puthalakath, H. / Beeson, J.G. / Kvansakul, M. / Boddey, J.A. / Wilson, D.W. / Anders, R.F. / Foley, M.
#1: Journal: Res Sq / Year: 2024
Title: A broadly cross-reactive i-body to AMA1 potently inhibits blood and liver stages of Plasmodium parasites
Authors: Foley, M. / Angage, D. / Anders, R. / Chmielewski, J. / Maddumage, J.C. / Hesping, E. / Caiazzo, S. / Lai, K.H. / Yeoh, L. / Opi, H. / Cairns, C. / Beeson, J. / Kvansakul, M. / Wilson, D. / Boddey, J.
History
DepositionOct 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Database references / Category: citation / citation_author
Revision 1.2Oct 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
D: Apical merozoite antigen 1
H: single domain i-body WD34


Theoretical massNumber of molelcules
Total (without water)67,3512
Polymers67,3512
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-13 kcal/mol
Surface area22380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.386, 55.265, 229.549
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 Apical merozoite antigen 1


Mass: 53547.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax Sal-1 (eukaryote) / Gene: PVX_092275 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A5K4Z2
#2: Protein single domain i-body WD34


Mass: 13803.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21 (bacteria)
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: 2.09 Å3/Da / Density % sol: 41.15 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES pH 6.5, 12% w/v PEG 20000, 20% Ethylene Glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 3→45.9 Å / Num. obs: 11653 / % possible obs: 97.8 % / Redundancy: 4.4 % / Biso Wilson estimate: 79.08 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.13 / Net I/σ(I): 4.6
Reflection shellResolution: 3→3.18 Å / Num. unique obs: 8213 / CC1/2: 0.829

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→44.8 Å / SU ML: 0.452 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.5065
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2863 521 4.5 %
Rwork0.2541 11062 -
obs0.2555 11583 96.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 93.06 Å2
Refinement stepCycle: LAST / Resolution: 3→44.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3698 0 0 0 3698
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00243775
X-RAY DIFFRACTIONf_angle_d0.45755108
X-RAY DIFFRACTIONf_chiral_restr0.0441557
X-RAY DIFFRACTIONf_plane_restr0.0032671
X-RAY DIFFRACTIONf_dihedral_angle_d11.06831405
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.30.4051430.36292694X-RAY DIFFRACTION97.46
3.3-3.780.33391220.3032732X-RAY DIFFRACTION97.14
3.78-4.760.25721220.23952783X-RAY DIFFRACTION96.9
4.76-44.80.25721340.2192853X-RAY DIFFRACTION95.01
Refinement TLS params.Method: refined / Origin x: -12.2454962399 Å / Origin y: -7.85988740451 Å / Origin z: 27.3632065877 Å
111213212223313233
T0.564712115755 Å20.152757039185 Å20.151015684849 Å2-0.5662391778 Å20.0436753599887 Å2--0.697339848737 Å2
L0.629159404822 °20.292993778249 °20.189130858785 °2-1.27515956781 °2-0.904188427174 °2--3.1703697678 °2
S-0.0579924411967 Å °-0.195225385493 Å °0.010603968937 Å °-0.113108085654 Å °-0.131734942039 Å °-0.000704816757661 Å °0.169726688141 Å °0.112983397087 Å °0.168023899247 Å °
Refinement TLS groupSelection details: all

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