[English] 日本語
Yorodumi
- PDB-4eoy: Plasmodium falciparum Atg8 in complex with Plasmodium falciparum ... -

+
Open data


ID or keywords:

Loading...

-
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


Macroautophagy / Atg8-family conjugating enzyme activity / apicoplast / glycophagy / nucleophagy / autophagy of mitochondrion / phosphatidylethanolamine binding / phagophore assembly site / cellular response to nitrogen starvation / autophagosome membrane ...Macroautophagy / Atg8-family conjugating enzyme activity / apicoplast / glycophagy / nucleophagy / autophagy of mitochondrion / phosphatidylethanolamine binding / phagophore assembly site / cellular response to nitrogen starvation / autophagosome membrane / autophagosome assembly / autophagosome maturation / mitophagy / protein transport / cytoplasmic vesicle / metal ion binding / membrane / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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


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


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


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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more