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- PDB-6y09: Crystal structure of Atg16L in complex with GTP-bound Rab33B (Q92L) -

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Basic information

Entry
Database: PDB / ID: 6y09
TitleCrystal structure of Atg16L in complex with GTP-bound Rab33B (Q92L)
Components
  • Autophagy-related protein 16-1
  • Ras-related protein Rab-33B
KeywordsPROTEIN TRANSPORT / ATG16L / autophagy / autophagosome formation / Rab33B
Function / homology
Function and homology information


negative regulation of constitutive secretory pathway / regulation of retrograde vesicle-mediated transport, Golgi to ER / Atg12-Atg5-Atg16 complex / Macroautophagy / negative regulation of dendrite extension / vacuole-isolation membrane contact site / regulation of Golgi organization / Rab protein signal transduction / microautophagy / dendrite arborization ...negative regulation of constitutive secretory pathway / regulation of retrograde vesicle-mediated transport, Golgi to ER / Atg12-Atg5-Atg16 complex / Macroautophagy / negative regulation of dendrite extension / vacuole-isolation membrane contact site / regulation of Golgi organization / Rab protein signal transduction / microautophagy / dendrite arborization / Intra-Golgi traffic / protein localization to Golgi apparatus / regulation of exocytosis / xenophagy / corpus callosum development / protein localization to phagophore assembly site / intra-Golgi vesicle-mediated transport / phagophore assembly site membrane / RAB geranylgeranylation / negative stranded viral RNA replication / endolysosome membrane / TBC/RABGAPs / skeletal system morphogenesis / axonal transport / autophagosome membrane / axoneme / autophagosome assembly / protein-membrane adaptor activity / positive regulation of autophagy / sperm midpiece / autophagosome / hippocampus development / macroautophagy / Golgi lumen / protein transport / presynapse / GTPase binding / defense response to virus / endosome / axon / Golgi membrane / GTPase activity / GTP binding / glutamatergic synapse / Golgi apparatus / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Rab33A/B / Autophagy-related protein 16 / Autophagy-related protein 16 domain / Autophagy protein 16 (ATG16) / small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family ...Rab33A/B / Autophagy-related protein 16 / Autophagy-related protein 16 domain / Autophagy protein 16 (ATG16) / small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / P-loop containing nucleotide triphosphate hydrolases / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Autophagy-related protein 16-1 / Ras-related protein Rab-33B
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPantoom, S. / Wu, Y.W.
CitationJournal: Autophagy / Year: 2021
Title: RAB33B recruits the ATG16L1 complex to the phagophore via a noncanonical RAB binding protein.
Authors: Pantoom, S. / Konstantinidis, G. / Voss, S. / Han, H. / Hofnagel, O. / Li, Z. / Wu, Y.W.
History
DepositionFeb 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ras-related protein Rab-33B
C: Autophagy-related protein 16-1
B: Ras-related protein Rab-33B
D: Autophagy-related protein 16-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,53923
Polymers72,9854
Non-polymers2,55419
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11440 Å2
ΔGint-53 kcal/mol
Surface area29190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.950, 132.420, 155.130
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Ras-related protein Rab-33B


Mass: 21960.377 Da / Num. of mol.: 2 / Mutation: Q92L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB33B / Plasmid: pOPIN / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9H082
#2: Protein Autophagy-related protein 16-1 / APG16-like 1


Mass: 14532.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Atg16l1, Apg16l / Plasmid: pRSF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8C0J2

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Non-polymers , 6 types, 233 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 4.01 Å3/Da / Density % sol: 69.31 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 14% PEG3350, 0.2 M Potassium thiocyanate and 0.1 M Sodium potassium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97714 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97714 Å / Relative weight: 1
ReflectionResolution: 2.4→48.17 Å / Num. obs: 46731 / % possible obs: 99.91 % / Redundancy: 12.9 % / Biso Wilson estimate: 40.26 Å2 / CC1/2: 0.871 / Net I/σ(I): 17.05
Reflection shellResolution: 2.4→2.486 Å / Redundancy: 13.6 % / Mean I/σ(I) obs: 2.67 / Num. unique obs: 4618 / CC1/2: 0.871 / % possible all: 99.87

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Processing

Software
NameVersionClassification
REFMAC1.9_1692refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q8T and 1Z06

3q8t

1z06


Resolution: 2.4→48.168 Å / SU ML: 0.29 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 25.72
RfactorNum. reflection% reflection
Rfree0.2311 2330 5 %
Rwork0.1918 --
obs0.1937 46611 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 173.48 Å2 / Biso mean: 64.2674 Å2 / Biso min: 19.77 Å2
Refinement stepCycle: final / Resolution: 2.4→48.168 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4258 0 157 214 4629
Biso mean--66.77 53.93 -
Num. residues----523
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)
15.50080.03360.22653.54490.76364.88810.0802-0.3061-0.43450.33990.0771-0.32890.29280.351-0.13510.2706-0.0183-0.05190.2251-0.01620.362515.6816180.612543.3638
27.04661.0760.22534.2746-0.47537.2036-0.0903-0.4096-0.60040.40660.0607-0.51560.2930.18630.0440.30840.0525-0.06120.21830.03880.431217.7626177.371345.6177
32.5390.4076-0.64241.7741-0.43451.5774-0.08960.0284-0.0463-0.08850.08180.11480.0697-0.0854-0.0010.26790.0164-0.00470.2933-0.03990.315811.8455188.823735.5285
49.91876.2731-6.32643.9958-4.03444.04190.3059-0.73940.4421.0721-0.3732-0.1283-0.4831-0.12530.12510.4909-0.0001-0.01070.5173-0.05320.343614.3709189.482151.593
52.95451.8488-2.94892.0929-0.79426.954-0.7339-0.3930.12530.02110.4604-0.43510.71210.19780.39191.24380.31940.12831.00810.07370.972620.2029165.0014-22.7504
63.4638-2.0746-4.21525.84264.27163.8819-0.4156-0.1937-0.41350.3174-0.42680.62280.6169-0.05610.73510.3566-0.0499-0.01110.37910.01540.57115.9272167.089638.8617
75.65320.4607-0.20065.379-0.11455.2686-0.1336-0.45810.52710.3190.16150.2629-0.52-0.0637-0.01470.28630.01460.02960.2458-0.040.384811.6388145.878543.8811
88.23721.63983.18438.770.84636.0109-0.17560.40610.7309-0.3579-0.103-0.6833-0.380.26150.39490.3702-0.02920.04070.30020.04730.545822.8882149.731631.9717
93.0271-0.27650.15072.0811-0.31422.151-0.0247-0.06320.0776-0.09670.0157-0.06190.0406-0.00330.00650.20920.0074-0.00660.24530.03530.261415.3844133.302235.1704
104.66282.10284.47319.04941.37444.4175-0.1692-0.8764-0.16310.9427-0.0106-0.09880.2494-0.07460.04690.3622-0.01190.04320.5554-0.00850.299514.0312135.32450.7184
118.75172.3634-3.64123.4864-3.46793.67260.15360.43120.3597-0.2420.0288-0.30730.3265-0.4091-0.25941.36560.16040.16960.6745-0.17271.53740.175162.4034-39.4437
120.4634-0.11621.13630.0333-0.40063.1923-0.1548-0.6998-0.20180.0817-0.0226-0.17930.649-0.79530.05921.44220.14010.23841.09140.10980.86527.2212170.6665-25.7792
131.6466-1.74710.51443.6693-1.9414.2912-0.05460.01580.3902-0.0058-0.3809-0.5939-0.81570.22790.46570.4405-0.10110.01690.4057-0.07770.580321.4334159.608431.5093
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 55 )A30 - 55
2X-RAY DIFFRACTION2chain 'A' and (resid 56 through 89 )A56 - 89
3X-RAY DIFFRACTION3chain 'A' and (resid 90 through 187 )A90 - 187
4X-RAY DIFFRACTION4chain 'A' and (resid 188 through 202 )A188 - 202
5X-RAY DIFFRACTION5chain 'C' and (resid 140 through 173 )C140 - 173
6X-RAY DIFFRACTION6chain 'C' and (resid 174 through 225 )C174 - 225
7X-RAY DIFFRACTION7chain 'B' and (resid 30 through 89 )B30 - 89
8X-RAY DIFFRACTION8chain 'B' and (resid 90 through 104 )B90 - 104
9X-RAY DIFFRACTION9chain 'B' and (resid 105 through 187 )B105 - 187
10X-RAY DIFFRACTION10chain 'B' and (resid 188 through 202 )B188 - 202
11X-RAY DIFFRACTION11chain 'D' and (resid 140 through 144 )D140 - 144
12X-RAY DIFFRACTION12chain 'D' and (resid 145 through 163 )D145 - 163
13X-RAY DIFFRACTION13chain 'D' and (resid 164 through 225 )D164 - 225

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