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- PDB-4eoy: Plasmodium falciparum Atg8 in complex with Plasmodium falciparum ... -

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Basic information

Entry
Database: PDB / ID: 4eoy
TitlePlasmodium falciparum Atg8 in complex with Plasmodium falciparum Atg3 peptide
Components
  • Autophagy-related protein 3
  • Microtubule-associated protein 1 light chain 3
KeywordsTRANSPORT PROTEIN / Ubiquitin fold
Function / homology
Function and homology information


cytoplasmic ubiquitin ligase complex / Macroautophagy / Atg8-family ligase activity / apicoplast / response to xenobiotic stimulus => GO:0009410 / nucleophagy / autophagy of mitochondrion / cellular response to nitrogen starvation / autophagosome assembly / autophagy ...cytoplasmic ubiquitin ligase complex / Macroautophagy / Atg8-family ligase activity / apicoplast / response to xenobiotic stimulus => GO:0009410 / nucleophagy / autophagy of mitochondrion / cellular response to nitrogen starvation / autophagosome assembly / autophagy / protein transport / cytoplasmic vesicle / membrane / metal ion binding / cytosol
Similarity search - Function
Ubiquitin-like-conjugating enzyme Atg3/Atg10 / Autophagocytosis associated protein, active-site domain / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Autophagy-related protein 3, putative / Autophagy-related protein
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsHain, A.U.P. / Bosch, J.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: Structural characterization and inhibition of the Plasmodium Atg8-Atg3 interaction.
Authors: Hain, A.U. / Weltzer, R.R. / Hammond, H. / Jayabalasingham, B. / Dinglasan, R.R. / Graham, D.R. / Colquhoun, D.R. / Coppens, I. / Bosch, J.
History
DepositionApr 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Microtubule-associated protein 1 light chain 3
B: Microtubule-associated protein 1 light chain 3
C: Microtubule-associated protein 1 light chain 3
D: Autophagy-related protein 3
E: Autophagy-related protein 3
F: Autophagy-related protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,40117
Polymers47,9146
Non-polymers48711
Water5,963331
1
A: Microtubule-associated protein 1 light chain 3
D: Autophagy-related protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1466
Polymers15,9712
Non-polymers1754
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-34 kcal/mol
Surface area8200 Å2
MethodPISA
2
B: Microtubule-associated protein 1 light chain 3
E: Autophagy-related protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0904
Polymers15,9712
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-10 kcal/mol
Surface area8130 Å2
MethodPISA
3
C: Microtubule-associated protein 1 light chain 3
F: Autophagy-related protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1667
Polymers15,9712
Non-polymers1945
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-29 kcal/mol
Surface area8200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.300, 111.080, 57.090
Angle α, β, γ (deg.)90.00, 92.58, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999985, 0.002748, 0.004684), (0.002841, -0.47031, 0.882497), (0.004628, 0.882497, 0.470296)8.62898, -41.51017, 25.63575
3given(-0.9999, -0.010841, -0.009058), (0.013418, -0.528177, -0.849028), (0.00442, -0.849065, 0.528269)18.1398, 28.33306, 23.36422

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Components

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Protein / Protein/peptide , 2 types, 6 molecules ABCDEF

#1: Protein Microtubule-associated protein 1 light chain 3


Mass: 14964.341 Da / Num. of mol.: 3 / Mutation: C32I, C119S, C122S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: PF10_0193 / Plasmid: MBP-pRSF-5 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: Q8IJK2
#2: Protein/peptide Autophagy-related protein 3


Mass: 1007.098 Da / Num. of mol.: 3 / Fragment: UNP residues 103-110 / Source method: obtained synthetically / Details: peptide
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: C0H519

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Non-polymers , 5 types, 342 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 331 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES pH 6.5, 0.1 M Ca(OAc)2, 20% w/v PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL12-211.0332
SYNCHROTRONALS 5.0.120.9774
Detector
TypeIDDetectorDate
PSI PILATUS 6M1PIXELFeb 20, 2012
ADSC QUANTUM 3152CCDFeb 26, 2012
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Liquid nitrogen-cooled double crystalSINGLE WAVELENGTHMx-ray1
2Asymmetric curved crystalSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.03321
20.97741
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.904
11-h,-k,l20.096
ReflectionResolution: 2.22→31.06 Å / Num. all: 21538 / Num. obs: 17965 / % possible obs: 83.4 % / Observed criterion σ(F): 20402 / Observed criterion σ(I): -3 / Redundancy: 2.07 % / Biso Wilson estimate: 29.081 Å2 / Rmerge(I) obs: 0.215 / Net I/σ(I): 7.28
Reflection shellResolution: 2.18→2.24 Å / Redundancy: 2.18 % / Rmerge(I) obs: 0.918 / Mean I/σ(I) obs: 1.6 / Num. unique all: 1605 / % possible all: 45

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXPhasermodel building
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
PHENIXPhaserphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 20 models (15 PDB 5 predicted) as ensemble using phenix.automr

Resolution: 2.22→20 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.884 / SU B: 20.949 / SU ML: 0.255 / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.343 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27965 801 5.1 %RANDOM
Rwork0.20463 ---
obs0.20839 14961 77.37 %-
all-21538 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.76 Å2
Baniso -1Baniso -2Baniso -3
1--10.8 Å20 Å2-8.64 Å2
2---9.05 Å2-0 Å2
3---19.85 Å2
Refinement stepCycle: LAST / Resolution: 2.22→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3289 0 23 331 3643
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.023386
X-RAY DIFFRACTIONr_bond_other_d0.0020.022370
X-RAY DIFFRACTIONr_angle_refined_deg1.1971.9814562
X-RAY DIFFRACTIONr_angle_other_deg1.14135774
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7715390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.7224165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.54415638
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1751521
X-RAY DIFFRACTIONr_chiral_restr0.0650.2486
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213663
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02686
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.22→2.341 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.427 30 -
Rwork0.255 509 -
obs--18.55 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.6085-0.4529-0.36530.07950.06050.0645-0.02060.1256-0.15520.0032-0.01810.01940.0224-0.03830.03870.0989-0.0265-0.02050.0385-0.0380.09362.9804-26.668325.6401
20.18940.08770.06040.2096-0.17220.25740.0017-0.03330.0248-0.0491-0.02830.00530.0530.00720.02650.07280.004-0.02710.00920.01040.11099.2597-25.953841.778
33.08730.19290.85848.14892.48421.7348-0.29640.15190.13050.18650.2105-0.29410.1432-0.09910.08590.0929-0.03660.01150.0961-0.00420.090416.5375-27.336550.8152
40.5469-0.16410.18220.1611-0.24570.3954-0.066-0.04010.0946-0.00420.0118-0.02910.0028-0.00790.05420.0698-0.0051-0.01810.00580.00470.11431.7463-16.817436.6756
514.95164.288-8.14251.88161.713529.60950.31560.3956-0.08090.0131-0.027-0.087-0.6546-1.0981-0.28860.07970.0227-0.00110.0431-0.00520.150512.4823-8.449442.4588
60.666-0.1421-0.01590.2263-0.0310.0161-0.03750.001-0.0146-0.05510.00750.0007-0.00210.00280.030.08750.0035-0.03090.0050.0140.08491.96551.396318.0692
75.74562.8382-4.95172.5916-3.71865.6295-0.07020.06770.1279-0.0920.19860.09030.1259-0.2333-0.12840.143-0.0037-0.03340.0349-0.03150.1146-7.758715.572924.4125
80.99770.0008-0.25950.89180.33710.1960.0088-0.0639-0.0358-0.00510.0134-0.07660.00380.0203-0.02220.08130.0013-0.03330.01260.01710.08817.011-1.891726.9553
98.9846.80237.84725.1665.9446.85550.0617-0.29880.03260.0293-0.1370.00150.022-0.2490.07540.06990.0196-0.01160.1995-0.01850.1735-3.5853-0.539937.2527
100.7158-0.1609-0.75030.57750.07430.806-0.02310.00570.00680.00630.0232-0.00420.0062-0.0078-00.0733-0.0151-0.03710.00490.00180.121614.455127.371348.0243
110.90480.1926-0.12850.2237-0.24850.2950.0084-0.01270.0279-0.01530.00970.02230.02010.0061-0.01810.07460.0015-0.01840.0319-0.00390.08898.23913.11755.9169
125.5227-0.82910.764.65456.36169.362-0.23660.23840.0427-0.09460.03170.1317-0.22460.12810.20490.1354-0.0138-0.03170.03290.04060.07150.97546.097461.777
130.82860.39340.07880.37980.1720.10290.00970.02560.02410.0023-0.00460.0210.0005-0.0054-0.00510.0803-0.0114-0.02360.02970.00640.091415.852712.721645.5118
145.8206-9.71353.09616.2176-5.40529.1348-0.15720.2530.00620.2361-0.4232-0.03050.3363-0.08170.58040.0826-0.0132-0.01540.0491-0.02250.08685.01753.454241.5344
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 30
2X-RAY DIFFRACTION2A31 - 77
3X-RAY DIFFRACTION3A78 - 83
4X-RAY DIFFRACTION4A84 - 120
5X-RAY DIFFRACTION5A121 - 124
6X-RAY DIFFRACTION6B2 - 30
7X-RAY DIFFRACTION6B31 - 77
8X-RAY DIFFRACTION7B78 - 83
9X-RAY DIFFRACTION8B84 - 120
10X-RAY DIFFRACTION9B121 - 124
11X-RAY DIFFRACTION10C2 - 30
12X-RAY DIFFRACTION11C31 - 77
13X-RAY DIFFRACTION12C78 - 83
14X-RAY DIFFRACTION13C84 - 120
15X-RAY DIFFRACTION14C121 - 124

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