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- PDB-3srj: PfAMA1 in complex with invasion-inhibitory peptide R1 -

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Basic information

Entry
Database: PDB / ID: 3srj
TitlePfAMA1 in complex with invasion-inhibitory peptide R1
Components
  • Apical membrane antigen 1, AMA1
  • R1 peptide
KeywordsCELL INVASION/inhibitor / AMA1 / Plasmodium falciparum / inhibitory peptide / malaria / CELL INVASION / CELL INVASION-inhibitor complex
Function / homology
Function and homology information


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 / Hepatocyte Growth Factor / Hepatocyte Growth Factor / 3-Layer(bba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Apical membrane antigen 1
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsVulliez-Le Normand, B. / Saul, F.A. / Bentley, G.A.
CitationJournal: Plos Pathog. / Year: 2012
Title: Structural and functional insights into the malaria parasite moving junction complex.
Authors: Vulliez-Le Normand, B. / Tonkin, M.L. / Lamarque, M.H. / Langer, S. / Hoos, S. / Roques, M. / Saul, F.A. / Faber, B.W. / Bentley, G.A. / Boulanger, M.J. / Lebrun, M.
History
DepositionJul 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
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, AMA1
B: Apical membrane antigen 1, AMA1
C: R1 peptide
D: R1 peptide
E: R1 peptide
F: R1 peptide


Theoretical massNumber of molelcules
Total (without water)96,8196
Polymers96,8196
Non-polymers00
Water8,107450
1
A: Apical membrane antigen 1, AMA1
C: R1 peptide
D: R1 peptide


Theoretical massNumber of molelcules
Total (without water)48,4103
Polymers48,4103
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-27 kcal/mol
Surface area14710 Å2
MethodPISA
2
B: Apical membrane antigen 1, AMA1
E: R1 peptide
F: R1 peptide


Theoretical massNumber of molelcules
Total (without water)48,4103
Polymers48,4103
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-26 kcal/mol
Surface area14720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.320, 144.320, 145.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Apical membrane antigen 1, AMA1


Mass: 43665.910 Da / Num. of mol.: 2 / Fragment: AMA1 / Mutation: N162K, T288V, S373D, N422D, S423K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: AMA1, PF11_0344 / Production host: Pichia pastoris (fungus) / References: UniProt: Q7KQK5
#2: Protein/peptide
R1 peptide


Mass: 2371.883 Da / Num. of mol.: 4 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 450 / 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: 2.08 Å3/Da / Density % sol: 40.86 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 15% PEG 4000, 0.1M Tris/HCL, 0.1M sodium acetate, 10% isopropanol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97911 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 17, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.15→40.28 Å / Num. all: 42798 / Num. obs: 42798 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 35.74 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 13.3
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 2.2 / Num. unique all: 4756 / % possible all: 75.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
BUSTER2.9.3refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Z40

1z40


Resolution: 2.15→37.06 Å / Cor.coef. Fo:Fc: 0.9461 / Cor.coef. Fo:Fc free: 0.9173 / SU R Cruickshank DPI: 0.198 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2138 1297 3.03 %RANDOM
Rwork0.1713 ---
all0.1726 42736 --
obs0.1726 42736 94.75 %-
Displacement parametersBiso mean: 41.15 Å2
Baniso -1Baniso -2Baniso -3
1-4.9617 Å20 Å20 Å2
2---8.9993 Å20 Å2
3---4.0376 Å2
Refine analyzeLuzzati coordinate error obs: 0.228 Å
Refinement stepCycle: LAST / Resolution: 2.15→37.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5155 0 0 450 5605
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONo_bond_d0.015342HARMONIC2
X-RAY DIFFRACTIONo_angle_deg1.17246HARMONIC2
X-RAY DIFFRACTIONt_trig_c_planes148HARMONIC2
X-RAY DIFFRACTIONt_gen_planes761HARMONIC5
X-RAY DIFFRACTIONt_it5342HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion3.37
X-RAY DIFFRACTIONt_other_torsion18.82
X-RAY DIFFRACTIONt_chiral_improper_torsion669SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6288SEMIHARMONIC4
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2486 69 3.01 %
Rwork0.2153 2222 -
all0.2162 2291 -
obs--94.75 %

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