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- PDB-4wzg: Structure of human ATG101 -

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Basic information

Entry
Database: PDB / ID: 4wzg
TitleStructure of human ATG101
ComponentsAutophagy-related protein 101
KeywordsPROTEIN BINDING / autophagy / ULK1 complex / HORMA domain / ATG13 binding
Function / homology
Function and homology information


Atg1/ULK1 kinase complex / phagophore assembly site / Macroautophagy / autophagosome assembly / positive regulation of autophagy / negative regulation of cell population proliferation / endoplasmic reticulum membrane / protein kinase binding / protein-containing complex binding / identical protein binding / cytosol
Similarity search - Function
Autophagy-related protein 101 / Autophagy-related protein 101
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Autophagy-related protein 101
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsMichel, M. / Weiergraeber, O.H.
CitationJournal: Autophagy / Year: 2015
Title: The mammalian autophagy initiator complex contains 2 HORMA domain proteins.
Authors: Michel, M. / Schwarten, M. / Decker, C. / Nagel-Steger, L. / Willbold, D. / Weiergraber, O.H.
History
DepositionNov 19, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Jan 13, 2016Group: Database references
Revision 1.3Apr 3, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Autophagy-related protein 101
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1152
Polymers25,0371
Non-polymers781
Water55831
1


  • Idetical with deposited unit
  • defined by software
  • MONOMERIC
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-2 kcal/mol
Surface area11290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.150, 42.620, 67.210
Angle α, β, γ (deg.)90.000, 97.310, 90.000
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-405-

HOH

21A-413-

HOH

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Components

#1: Protein Autophagy-related protein 101


Mass: 25036.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATG101, C12orf44, PP894 / Plasmid: pET11a / Production host: Escherichia coli bl21(de3) (bacteria) / References: UniProt: Q9BSB4
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: PEG3350, MES, NACL, BME / PH range: 5.6-7.0

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryostream
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 21, 2014
RadiationMonochromator: Silicon (1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→42.62 Å / Num. all: 13299 / Num. obs: 13298 / % possible obs: 73.9 % / Redundancy: 4.3 % / Biso Wilson estimate: 40.67 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.039 / Rrim(I) all: 0.045 / Χ2: 1.002 / Net I/σ(I): 16.62 / Num. measured all: 56530
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.9-20.7670.5283.193013222210.52822.8
1.95-20.8110.4573.08156812813950.52830.8
2-2.060.880.3714.01222912325140.42341.7
2.06-2.130.940.3094.61285512426310.34950.8
2.13-2.20.9580.2685.51308211556760.30358.5
2.2-2.270.9670.246.02351511537780.27267.5
2.27-2.360.980.1986.7375111178520.22576.3
2.36-2.450.9880.1617.53372710438890.18485.2
2.45-2.560.990.1379.33431010199660.15594.8
2.56-2.690.9950.09711.6644039899850.1199.6
2.69-2.830.9970.07714.4440279279240.08899.7
2.83-3.010.9980.05817.8736558528520.066100
3.01-3.210.9980.04321.3132508458360.04998.9
3.21-3.470.9980.0427.4832237607550.04599.3
3.47-3.80.9980.03531.9930127197170.0499.7
3.8-4.250.9990.0334.926276536480.03499.2
4.25-4.910.9980.02935.3121435755710.03499.3
4.91-6.010.9990.0336.6919644854820.03499.4
6.01-8.50.9980.0336.5414713933870.03598.5
8.50.9970.02837.257882212190.03399.1

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Processing

Software
NameVersionClassification
XDSJanuary 10, 2014data reduction
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
SHELXDEphasing
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→42.62 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / Phase error: 37.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.22 665 5 %Random selection
Rwork0.198 12630 --
obs0.199 13295 73.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 189.52 Å2 / Biso mean: 59.2244 Å2 / Biso min: 25.47 Å2
Refinement stepCycle: final / Resolution: 1.9→42.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1597 0 4 31 1632
Biso mean--77.52 50.79 -
Num. residues----210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031631
X-RAY DIFFRACTIONf_angle_d0.6252217
X-RAY DIFFRACTIONf_chiral_restr0.025261
X-RAY DIFFRACTIONf_plane_restr0.004282
X-RAY DIFFRACTIONf_dihedral_angle_d13.403571
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9015-2.04830.2941510.2918976X-RAY DIFFRACTION29
2.0483-2.25450.41071010.26991925X-RAY DIFFRACTION57
2.2545-2.58070.29191510.26562869X-RAY DIFFRACTION85
2.5807-3.25120.26611790.23953394X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 12.7649 Å / Origin y: 37.1205 Å / Origin z: 15.0227 Å
111213212223313233
T0.3219 Å2-0.1233 Å20.062 Å2-0.2744 Å2-0.0868 Å2--0.2865 Å2
L2.8235 °2-1.7055 °21.8755 °2-3.2481 °2-1.4713 °2--4.4391 °2
S-0.2713 Å °0.03 Å °0.209 Å °-0.1597 Å °0.0927 Å °-0.2078 Å °0.1787 Å °-0.0097 Å °0.1719 Å °
Refinement TLS groupSelection details: chain A

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