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- PDB-6rgo: Complex of KlAtg21 with coiled-coil of AgAtg16 -

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Basic information

Entry
Database: PDB / ID: 6rgo
TitleComplex of KlAtg21 with coiled-coil of AgAtg16
Components
  • Autophagy protein 16
  • Autophagy-related protein 21
KeywordsLIPID BINDING PROTEIN / Autophagy / yeast / Atg16 / Atg21 / Atg8 lipidation
Function / homology
Function and homology information


: / : / Atg8-family ligase activity / Atg12-Atg5-Atg16 complex / C-terminal protein lipidation / phagophore / protein lipidation / vacuole-isolation membrane contact site / cytoplasm to vacuole targeting by the Cvt pathway / vesicle organization ...: / : / Atg8-family ligase activity / Atg12-Atg5-Atg16 complex / C-terminal protein lipidation / phagophore / protein lipidation / vacuole-isolation membrane contact site / cytoplasm to vacuole targeting by the Cvt pathway / vesicle organization / autophagosome organization / autophagy of mitochondrion / protein localization to phagophore assembly site / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / phosphatidylinositol-3-phosphate binding / fungal-type vacuole membrane / phagophore assembly site / phosphatidylinositol-4-phosphate binding / phosphatidylinositol-3,5-bisphosphate binding / protein-macromolecule adaptor activity / endosome / identical protein binding / cytosol
Similarity search - Function
Autophagy-related protein 16 domain / Autophagy protein 16 (ATG16) / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Autophagy-related protein 21 / Autophagy protein 16
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
Ashbya gossypii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.701 Å
AuthorsThumm, M. / Neumann, P.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB860 Germany
CitationJournal: Autophagy / Year: 2020
Title: Atg21 organizes Atg8 lipidation at the contact of the vacuole with the phagophore.
Authors: Munzel, L. / Neumann, P. / Otto, F.B. / Krick, R. / Metje-Sprink, J. / Kroppen, B. / Karedla, N. / Enderlein, J. / Meinecke, M. / Ficner, R. / Thumm, M.
History
DepositionApr 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Autophagy-related protein 21
B: Autophagy-related protein 21
C: Autophagy protein 16
D: Autophagy protein 16


Theoretical massNumber of molelcules
Total (without water)99,5484
Polymers99,5484
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-28 kcal/mol
Surface area34860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.447, 123.447, 185.168
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Autophagy-related protein 21


Mass: 43607.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Gene: ATG21, KLLA0E24354g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CLZ2
#2: Protein Autophagy protein 16 /


Mass: 6165.890 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) (fungus)
Strain: ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056 / Gene: ATG16, AFL186W / Production host: Escherichia coli (E. coli) / References: UniProt: Q755K3

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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: 4.09 Å3/Da / Density % sol: 69.94 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein concetration 13 mg/mL, Clostripain for in situ proteolysis (1:2000 ratio). Reservoir: ProComplex (Molecular Dimension) B11: 15 % PEG4000, 0.1 M HEPES pH 7.5. Droplet: 2 microL ...Details: Protein concetration 13 mg/mL, Clostripain for in situ proteolysis (1:2000 ratio). Reservoir: ProComplex (Molecular Dimension) B11: 15 % PEG4000, 0.1 M HEPES pH 7.5. Droplet: 2 microL Protein (mit 1:2000 Clostripain) + 3 microL Reservoir.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.7→46.29 Å / Num. obs: 17917 / % possible obs: 99.6 % / Redundancy: 14.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.23 / Rpim(I) all: 0.062 / Rrim(I) all: 0.239 / Net I/σ(I): 9.4 / Num. measured all: 254489 / Scaling rejects: 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.7-4.0514.41.6976113642310.4760.4521.7582.199.9
9.07-46.2913.30.0451761213270.9990.0130.0474398.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX(1.14_3260: ???)refinement
MOSFLMdata reduction
Aimless0.7.3data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LTG

5ltg


Resolution: 3.701→46.29 Å / SU ML: 0.65 / Cross valid method: THROUGHOUT / σ(F): 0.41 / Phase error: 34.59
RfactorNum. reflection% reflection
Rfree0.3065 1670 4.98 %
Rwork0.2845 --
obs0.2856 17879 99.61 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Refinement stepCycle: LAST / Resolution: 3.701→46.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5698 0 0 0 5698
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015776
X-RAY DIFFRACTIONf_angle_d1.5027797
X-RAY DIFFRACTIONf_dihedral_angle_d11.3293583
X-RAY DIFFRACTIONf_chiral_restr0.086934
X-RAY DIFFRACTIONf_plane_restr0.009993
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7011-3.810.38511380.43222662X-RAY DIFFRACTION100
3.81-3.93290.41931430.40012706X-RAY DIFFRACTION100
3.9329-4.07340.41791410.39542633X-RAY DIFFRACTION100
4.0734-4.23640.33111380.38152681X-RAY DIFFRACTION100
4.2364-4.42910.38671390.34352651X-RAY DIFFRACTION100
4.4291-4.66240.30541380.30742654X-RAY DIFFRACTION100
4.6624-4.95420.25861360.27992652X-RAY DIFFRACTION99
4.9542-5.33620.28421370.27772638X-RAY DIFFRACTION100
5.3362-5.87220.2761460.29612677X-RAY DIFFRACTION100
5.8722-6.71970.30091420.29672645X-RAY DIFFRACTION100
6.7197-8.45770.31911400.26332636X-RAY DIFFRACTION99
8.4577-46.29610.25251320.18762655X-RAY DIFFRACTION99
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)
13.77780.9642-0.26651.029-0.5482.1274-0.3429-0.2597-0.3118-0.11050.2798-0.05840.07540.14710.00691.32860.30370.24111.01750.08411.143656.1311-53.2048-39.4254
22.0719-0.3592-0.63972.45761.60631.98630.29430.09730.3964-0.0674-0.0817-0.7968-0.10880.3384-0.00241.07430.2190.08571.4450.16481.438185.2158-19.9839-8.449
30.3470.327-0.50070.7226-0.24730.7428-0.6381-0.7780.42541.00680.0408-0.28831.0394-0.5866-0.0161.12730.2261-0.15571.42810.00491.642181.0582-45.9851-27.6161
40.38420.5253-0.31240.7991-0.40910.16890.33250.98730.20640.2022-0.5193-0.09820.0463-0.17580.0021.1930.25010.02791.4265-0.23441.489883.8017-37.8051-28.0286
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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