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- PDB-6zay: Crystal structure of Atg16L in complex with GDP-bound Rab33B -

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Basic information

Entry
Database: PDB / ID: 6zay
TitleCrystal structure of Atg16L in complex with GDP-bound Rab33B
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 / Intra-Golgi traffic ...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 / Intra-Golgi traffic / dendrite arborization / xenophagy / protein localization to Golgi apparatus / corpus callosum development / regulation of exocytosis / protein localization to phagophore assembly site / phagophore assembly site membrane / RAB geranylgeranylation / intra-Golgi vesicle-mediated transport / negative stranded viral RNA replication / endolysosome membrane / TBC/RABGAPs / skeletal system morphogenesis / axonal transport / autophagosome membrane / axoneme / autophagosome assembly / protein-membrane adaptor activity / sperm midpiece / positive regulation of autophagy / autophagosome / small monomeric GTPase / hippocampus development / macroautophagy / Golgi lumen / protein transport / presynapse / G protein activity / GTPase binding / defense response to virus / endosome / Golgi membrane / axon / 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 Rab domain 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 Rab domain 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 / WD domain, G-beta repeat / G-protein beta WD-40 repeat / P-loop containing nucleotide triphosphate hydrolases / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / 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'-DIPHOSPHATE / 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
DepositionJun 6, 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)75,31023
Polymers73,0154
Non-polymers2,29519
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11080 Å2
ΔGint-75 kcal/mol
Surface area29470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.010, 132.110, 154.370
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: 21975.348 Da / Num. of mol.: 2
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, 198 molecules

#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-MG / MAGNESIUM ION


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


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 3.88 Å3/Da / Density % sol: 68.3 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / pH: 6.2
Details: 22% PEG3350, 0.2M potassium thiocyanate and 0.1M 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-F / Detector: PIXEL / Date: Jun 29, 2013
RadiationMonochromator: si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97714 Å / Relative weight: 1
ReflectionResolution: 2.4→49.572 Å / Num. obs: 46452 / % possible obs: 99.96 % / Redundancy: 13.1 % / Biso Wilson estimate: 38.92 Å2 / Rmerge(I) obs: 0.1169 / Net I/σ(I): 16.22
Reflection shellResolution: 2.4→2.486 Å / Redundancy: 13.7 % / Num. unique obs: 4577 / CC1/2: 0.971 / % possible all: 99.89

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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: 1Z06 and 3Q8T

1z06

3q8t


Resolution: 2.4→49.572 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2114 2317 5.01 %
Rwork0.1851 --
obs0.1865 46278 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 193.21 Å2 / Biso mean: 69.6901 Å2 / Biso min: 22.12 Å2
Refinement stepCycle: final / Resolution: 2.4→49.572 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4252 0 141 179 4572
Biso mean--75.88 56.03 -
Num. residues----522
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)
15.2335-0.2883-0.71573.6298-0.74343.84070.12950.3703-0.5874-0.3020.01210.46390.2222-0.3495-0.09810.31920.016-0.09930.26130.00060.5001-15.713448.1911-43.0456
28.1099-5.63796.6678.4098-7.05689.10570.8878-0.2316-1.2429-0.2034-0.02341.72311.0916-0.5136-0.76010.5156-0.0381-0.03690.37510.01260.8816-23.853442.2333-35.1159
32.9703-1.26911.33533.934-1.77067.9709-0.0160.0738-0.3415-0.07250.05720.11380.3815-0.01270.010.3455-0.0224-0.00060.2359-0.04710.5576-10.836344.7977-42.7768
43.7706-1.5221-1.79612.45291.23794.4592-0.1556-0.2249-0.12430.22110.1498-0.43140.2130.359-0.00470.2461-0.0382-0.04060.31280.04930.4215-7.893455.3006-33.6887
53.6475-0.3985-0.61411.1873-0.32081.49010.0490.07780.26870.00770.04380.1496-0.1031-0.062-0.07610.2648-0.02520.01190.27170.00740.4457-16.346161.6481-37.1715
69.4188-6.7267-5.78234.90874.15433.52310.4920.88930.3426-1.4903-0.37030.3625-0.6562-0.3863-0.22740.5436-0.0609-0.00140.51780.06520.4161-13.549157.1797-51.7232
74.3868-1.427-3.35642.90982.11333.0411-0.80380.2593-0.3782-0.9262-0.02620.71040.10560.09790.92191.4136-0.15940.1120.8559-0.0910.9359-20.375932.652724.3
83.24171.9574-3.46035.591-4.03043.5892-0.33530.1822-0.3606-0.355-0.2951-0.23270.97310.00670.69890.36090.0630.0010.3849-0.04750.5805-6.191134.3821-37.1237
97.3167-0.28431.37355.63260.47273.094-0.09390.56790.8192-0.2604-0.0285-0.2735-0.56730.09040.11740.32070.03250.00780.27720.03350.5486-12.871711.4994-42.2648
105.6607-5.52990.41415.82640.69632.71610.2888-0.7340.4755-0.24080.1986-1.4511-0.65060.4777-0.98680.4708-0.03130.06570.4523-0.06510.7834-4.808517.9325-34.4462
118.115-5.1767-5.66624.97815.12755.3409-0.08250.59950.1411-0.3935-0.4251-0.2025-0.5065-0.12950.47950.56720.02980.03610.39540.0950.492-12.00314.8367-48.42
129.8701-4.2525-4.70845.53415.94796.4680.05791.6120.6434-0.7609-0.64930.1855-0.3741-0.86590.43320.5448-0.00570.07550.47550.05040.5873-15.322112.6461-50.49
139.0952-4.13035.23459.3979-3.65933.2668-0.461-0.70370.15410.97710.11840.2541-0.3335-0.68970.22170.41870.01530.01250.3708-0.01980.7441-22.758218.0941-31.0389
147.219-1.25164.67956.725-2.90733.7676-0.4556-0.42910.22660.17930.690.7842-0.7138-0.6533-0.25040.31530.0544-0.00580.43490.00730.4733-20.71498.0255-39.417
153.8661-1.16911.66262.8021-0.41121.87360.0721-0.057-0.16050.0570.00540.35370.0399-0.1403-0.08280.2243-0.00890.01160.2683-0.02480.3709-17.0281-0.3888-33.277
168.499-4.03326.49543.4175-2.7098.80770.35420.3941-0.4682-0.3077-0.0097-0.08850.33460.2964-0.32280.28150.02010.04270.37890.01420.4728-9.59232.3132-46.4349
170.4767-0.1242-0.56860.03680.13821.0241-1.1355-0.33550.0294-0.21690.1811-0.94350.1363-0.46020.83861.8725-0.02730.14191.0058-0.05371.1622-9.399436.666320.516
182.86042.03772.16177.67275.76683.831-0.30750.25920.3778-0.8084-0.3130.6892-1.0816-0.30920.62160.46650.0832-0.05340.47390.11220.7885-22.756324.8851-39.565
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 67 )A56 - 67
3X-RAY DIFFRACTION3chain 'A' and (resid 68 through 104 )A68 - 104
4X-RAY DIFFRACTION4chain 'A' and (resid 105 through 135 )A105 - 135
5X-RAY DIFFRACTION5chain 'A' and (resid 136 through 187 )A136 - 187
6X-RAY DIFFRACTION6chain 'A' and (resid 188 through 202 )A188 - 202
7X-RAY DIFFRACTION7chain 'C' and (resid 140 through 171 )C140 - 171
8X-RAY DIFFRACTION8chain 'C' and (resid 172 through 225 )C172 - 225
9X-RAY DIFFRACTION9chain 'B' and (resid 30 through 55 )B30 - 55
10X-RAY DIFFRACTION10chain 'B' and (resid 56 through 67 )B56 - 67
11X-RAY DIFFRACTION11chain 'B' and (resid 68 through 77 )B68 - 77
12X-RAY DIFFRACTION12chain 'B' and (resid 78 through 89 )B78 - 89
13X-RAY DIFFRACTION13chain 'B' and (resid 90 through 103 )B90 - 103
14X-RAY DIFFRACTION14chain 'B' and (resid 104 through 115 )B104 - 115
15X-RAY DIFFRACTION15chain 'B' and (resid 116 through 176 )B116 - 176
16X-RAY DIFFRACTION16chain 'B' and (resid 177 through 202 )B177 - 202
17X-RAY DIFFRACTION17chain 'D' and (resid 140 through 175 )D140 - 175
18X-RAY DIFFRACTION18chain 'D' and (resid 176 through 225 )D176 - 225

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