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- PDB-8qu7: Crystal structure of the Plasmodium falciparum Apical membrane an... -

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Basic information

Entry
Database: PDB / ID: 8qu7
TitleCrystal structure of the Plasmodium falciparum Apical membrane antigen (AMA1) in complex with single domain i-body WD34
Components
  • Apical membrane 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 membrane antigen 1
Function and homology information
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 14, 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 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: Apical membrane antigen 1
A: single domain i-body WD34
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6455
Polymers55,2662
Non-polymers3793
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-23 kcal/mol
Surface area17680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.651, 38.462, 227.355
Angle α, β, γ (deg.)90.000, 90.180, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2

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Components

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Protein , 2 types, 2 molecules EA

#1: Protein Apical membrane antigen 1 / Merozoite surface antigen


Mass: 41462.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: AMA-1, PF83 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P22621
#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)

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Non-polymers , 4 types, 68 molecules

#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.83 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1MSodium HEPES pH7.5 70% v/v MPD

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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 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.6→38.45 Å / Num. obs: 19822 / % possible obs: 100 % / Redundancy: 4.8 % / Biso Wilson estimate: 34.06 Å2 / CC1/2: 0.994 / Net I/σ(I): 6.8
Reflection shellResolution: 2.6→2.693 Å / Num. unique obs: 2335 / CC1/2: 0.864

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→38.45 Å / SU ML: 0.261 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.9909
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2348 1010 5.15 %
Rwork0.2132 18598 -
obs0.2143 19608 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.95 Å2
Refinement stepCycle: LAST / Resolution: 2.6→38.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2905 0 24 65 2994
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00282997
X-RAY DIFFRACTIONf_angle_d0.60294079
X-RAY DIFFRACTIONf_chiral_restr0.0448446
X-RAY DIFFRACTIONf_plane_restr0.005530
X-RAY DIFFRACTIONf_dihedral_angle_d12.86421075
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.740.26341220.24872671X-RAY DIFFRACTION99.93
2.74-2.910.31081470.2472595X-RAY DIFFRACTION100
2.91-3.130.25691500.2362617X-RAY DIFFRACTION99.82
3.13-3.450.23581190.20612661X-RAY DIFFRACTION99.93
3.45-3.950.20391630.19622620X-RAY DIFFRACTION99.96
3.95-4.970.19561480.18062672X-RAY DIFFRACTION99.89
4.97-38.450.25321610.22982762X-RAY DIFFRACTION99.9
Refinement TLS params.Method: refined / Origin x: -31.0160550045 Å / Origin y: -6.6041637606 Å / Origin z: -40.7436801463 Å
111213212223313233
T0.260880556551 Å20.0146250334475 Å20.0271787532271 Å2-0.26588220804 Å2-0.0100537422245 Å2--0.331682356707 Å2
L1.93265769579 °2-0.333190331649 °20.537488285235 °2-1.10100701922 °2-0.263667545032 °2--1.28120084285 °2
S-0.0381927189974 Å °-0.342292420291 Å °0.00607039452183 Å °0.24587764691 Å °0.0408655808053 Å °-0.0496212038567 Å °-0.0203007971813 Å °0.0499983219918 Å °-0.00913683813334 Å °
Refinement TLS groupSelection details: all

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