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- PDB-4uao: Crystal structure of Apical Membrane Antigen 1 from Plasmodium Kn... -

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Basic information

Entry
Database: PDB / ID: 4uao
TitleCrystal structure of Apical Membrane Antigen 1 from Plasmodium Knowlesi in complex with an invasion inhibitory antibody
Components
  • Apical merozoite antigen 1
  • immunoglobulin R31C2 VH and CH1 regions
  • immunoglobulin R31C2 light chain
KeywordsCELL INVASION / Malaria / invasion inhibitory antibody
Function / homology
Function and homology information


immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / membrane / plasma membrane
Similarity search - Function
Apical membrane antigen 1 domain superfamily / Apical membrane antigen 1 / Apical membrane antigen 1 / Apical membrane antigen 1 / Hepatocyte Growth Factor / Hepatocyte Growth Factor / 3-Layer(bba) Sandwich / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type ...Apical membrane antigen 1 domain superfamily / Apical membrane antigen 1 / Apical membrane antigen 1 / Apical membrane antigen 1 / Hepatocyte Growth Factor / Hepatocyte Growth Factor / 3-Layer(bba) Sandwich / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Apical membrane antigen 1 / Apical membrane antigen 1 / Ig kappa chain C region, B allele / Ig gamma-2A chain C region
Similarity search - Component
Biological speciesPlasmodium knowlesi (eukaryote)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsVulliez-Le Normand, B. / Saul, F.A. / Bentley, G.A.
Citation
Journal: Plos One / Year: 2015
Title: Crystal Structure of Plasmodium knowlesi Apical Membrane Antigen 1 and Its Complex with an Invasion-Inhibitory Monoclonal Antibody.
Authors: Vulliez-Le Normand, B. / Faber, B.W. / Saul, F.A. / van der Eijk, M. / Thomas, A.W. / Singh, B. / Kocken, C.H. / Bentley, G.A.
#1: Journal: Clin. Exp. Immunol. / Year: 1982
Title: Rat monoclonal antibodies which inhibit the in vitro multiplication of Plasmodium knowlesi.
Authors: Deans, J.A. / Alderson, T. / Thomas, A.W. / Mitchell, G.H. / Lennox, E.S. / Cohen, S.
History
DepositionAug 11, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Apical merozoite antigen 1
B: immunoglobulin R31C2 light chain
C: immunoglobulin R31C2 VH and CH1 regions


Theoretical massNumber of molelcules
Total (without water)90,1513
Polymers90,1513
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-22 kcal/mol
Surface area33200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.864, 71.807, 90.688
Angle α, β, γ (deg.)90.00, 116.37, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Apical merozoite antigen 1


Mass: 42511.449 Da / Num. of mol.: 1 / Mutation: N107K, S178N, N189E, S240R
Source method: isolated from a genetically manipulated source
Details: fragment 43-387 of B3L5E1. N-terminal residues Glu 41 and Phe 42 are cloning artifacts. C-terminal residue Gly 388 is a cloning artifact, and following residues Leu 389 to His 410 correspond to expression tags.
Source: (gene. exp.) Plasmodium knowlesi (eukaryote) / Gene: PKH_093110 / Plasmid: PPicZalphaA / Production host: Komagataella pastoris (fungus) / Strain (production host): KM71H / References: UniProt: B3L5E1, UniProt: A0A384KGX8*PLUS
#2: Antibody immunoglobulin R31C2 light chain


Mass: 23671.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The sequence for chain B has been deposited to GenBank (KM225619)
Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P01835*PLUS
#3: Antibody immunoglobulin R31C2 VH and CH1 regions


Mass: 23967.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The sequence for chain C has been deposited to GenBank (KM225620)
Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P20760*PLUS
Compound detailsThe Fab light and heavy chains are numbered according to the Kabat convention

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.5 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 8% PEG 6000, 40 mM Hepes pH7.4, 80 mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.1→43.35 Å / Num. obs: 17127 / % possible obs: 97.8 % / Redundancy: 3.1 % / Biso Wilson estimate: 71.32 Å2 / Rmerge(I) obs: 0.152 / Net I/σ(I): 7.8
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.778 / Mean I/σ(I) obs: 1.3 / % possible all: 99.1

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W81, 2GCY, 1D5I, 1IGF

1w81

2gcy

1d5i

1igf


Resolution: 3.1→40.77 Å / Cor.coef. Fo:Fc: 0.8811 / Cor.coef. Fo:Fc free: 0.8245 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.475
RfactorNum. reflection% reflectionSelection details
Rfree0.2662 838 4.9 %RANDOM
Rwork0.1884 ---
obs0.1925 17119 97.57 %-
Displacement parametersBiso mean: 70.7 Å2
Baniso -1Baniso -2Baniso -3
1-24.2978 Å20 Å24.9294 Å2
2---38.9061 Å20 Å2
3---14.6083 Å2
Refine analyzeLuzzati coordinate error obs: 0.511 Å
Refinement stepCycle: 1 / Resolution: 3.1→40.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6004 0 0 0 6004
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016149HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.318342HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2105SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes162HARMONIC2
X-RAY DIFFRACTIONt_gen_planes892HARMONIC5
X-RAY DIFFRACTIONt_it6149HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.05
X-RAY DIFFRACTIONt_other_torsion24.57
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion802SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7237SEMIHARMONIC4
LS refinement shellResolution: 3.1→3.29 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2974 121 4.35 %
Rwork0.236 2663 -
all0.2387 2784 -
obs--97.57 %

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