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- PDB-5nuv: Structure of the WD40-domain of human ATG16L1 -

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Basic information

Entry
Database: PDB / ID: 5nuv
TitleStructure of the WD40-domain of human ATG16L1
ComponentsAutophagy-related protein 16-1
KeywordsPROTEIN BINDING / ATG16L1 / WD40 / seven-bladed beta-propeller
Function / homology
Function and homology information


Atg12-Atg5-Atg16 complex / C-terminal protein lipidation / vacuole-isolation membrane contact site / ubiquitin-like protein transferase activity / microautophagy / xenophagy / corpus callosum development / protein localization to phagophore assembly site / phagophore assembly site membrane / negative stranded viral RNA replication ...Atg12-Atg5-Atg16 complex / C-terminal protein lipidation / vacuole-isolation membrane contact site / ubiquitin-like protein transferase activity / microautophagy / xenophagy / corpus callosum development / protein localization to phagophore assembly site / phagophore assembly site membrane / negative stranded viral RNA replication / endolysosome membrane / Macroautophagy / axoneme / autophagosome membrane / autophagosome assembly / autophagosome / positive regulation of autophagy / protein-membrane adaptor activity / sperm midpiece / hippocampus development / macroautophagy / protein transport / GTPase binding / defense response to virus / identical protein binding / cytosol
Similarity search - Function
Autophagy-related protein 16 / Autophagy-related protein 16 domain / Autophagy protein 16 (ATG16) / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats ...Autophagy-related protein 16 / Autophagy-related protein 16 domain / Autophagy protein 16 (ATG16) / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
(R,R)-2,3-BUTANEDIOL / Autophagy-related protein 16-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsBajagic, M. / Scrima, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
Helmholtz AssociationVH-NG-727 Germany
CitationJournal: Protein Sci. / Year: 2017
Title: Structure of the WD40-domain of human ATG16L1.
Authors: Bajagic, M. / Archna, A. / Busing, P. / Scrima, A.
History
DepositionMay 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.3Jan 17, 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

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Assembly

Deposited unit
A: Autophagy-related protein 16-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5792
Polymers33,4891
Non-polymers901
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint1 kcal/mol
Surface area11940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.550, 38.220, 45.620
Angle α, β, γ (deg.)90.000, 105.740, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-979-

HOH

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Components

#1: Protein Autophagy-related protein 16-1 / APG16-like 1


Mass: 33489.051 Da / Num. of mol.: 1 / Mutation: E354A/K355A/Y607P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATG16L1, APG16L, UNQ9393/PRO34307 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q676U5
#2: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 1.97 Å3/Da / Density % sol: 37.45 %
Crystal growTemperature: 303 K / Method: vapor diffusion / pH: 6.3 / Details: 1.61 M (NH4)2SO4, 0.09 M NaCl, 0.1 M MES pH 6.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.55→43.909 Å / Num. obs: 38280 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.736 % / Biso Wilson estimate: 19.43 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.073 / Χ2: 0.981 / Net I/σ(I): 15.62
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.55-1.656.6820.732.4564880.8270.79299.6
1.65-1.756.8050.4893.7951090.9230.5399.9
1.75-1.856.7010.3095.8840320.9650.33699.8
1.85-1.956.3370.28.7732630.9830.21899.9
1.95-26.4760.14911.5714170.9880.163100
2-2.27.0790.1215.2744200.9930.1399.8
2.2-2.46.9930.09118.9530930.9960.09899.8
2.4-2.66.7910.07721.8921750.9970.083100
2.6-2.86.260.05925.4916340.9970.06499.8
2.8-36.6310.05329.7712200.9980.05899.7
3-3.27.1480.04535.719390.9990.04999.9
3.2-3.47.0690.03841.437350.9990.041100
3.4-3.67.0370.03444.875750.9990.03799.5
3.6-3.86.8870.03345.944780.9990.036100
3.8-46.8520.03447.273710.9990.037100
4-66.3380.03247.6116140.9990.03599.7
6-107.0380.03650.635570.9990.03999.3
10-43.9095.7940.03448.621600.9990.03797.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIX1.10_2155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CNX

2cnx


Resolution: 1.55→43.909 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.12
RfactorNum. reflection% reflection
Rfree0.197 1914 5 %
Rwork0.1649 --
obs0.1666 38278 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.55 Å2 / Biso mean: 29.9829 Å2 / Biso min: 8.67 Å2
Refinement stepCycle: final / Resolution: 1.55→43.909 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2295 0 16 220 2531
Biso mean--43.8 36.72 -
Num. residues----301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092373
X-RAY DIFFRACTIONf_angle_d1.1083223
X-RAY DIFFRACTIONf_chiral_restr0.066372
X-RAY DIFFRACTIONf_plane_restr0.007407
X-RAY DIFFRACTIONf_dihedral_angle_d9.6431419
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5501-1.58880.32381350.2782574270999
1.5888-1.63180.31291350.24625592694100
1.6318-1.67980.27821360.216825932729100
1.6798-1.7340.22571350.20425632698100
1.734-1.7960.24121350.196225722707100
1.796-1.86790.22661360.184725842720100
1.8679-1.95290.19991360.16325662702100
1.9529-2.05590.19131370.153926062743100
2.0559-2.18470.20121370.158326032740100
2.1847-2.35340.20471360.167925852721100
2.3534-2.59020.20931370.167326112748100
2.5902-2.96490.20471380.160526172755100
2.9649-3.73520.1781390.149326342773100
3.7352-43.92650.16171420.150226972839100
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)
11.72730.66540.2690.8789-0.77171.5414-0.05420.31090.0272-0.2557-0.0534-0.053-0.1613-0.1012-0.00390.19670.0566-0.02840.1746-0.0380.15155.367334.79872.6029
20.74020.146-0.01791.23620.020.5929-0.00450.27650.063-0.26810.0396-0.0422-0.2235-0.01260.02150.24080.1354-0.04510.4764-0.05190.223246.967238.75381.1791
30.89490.1266-0.22390.8646-0.43050.806-0.03870.0363-0.0596-0.11920.13650.3141-0.0622-0.81690.13280.00350.0799-0.10.5839-0.08890.175539.896432.008510.83
41.1629-0.305-0.08320.4477-0.69391.39780.08080.1048-0.4402-0.0024-0.18340.16880.3935-0.63670.02540.1754-0.04820.00340.5019-0.07240.209842.9225.494919.3894
50.3763-0.01080.10680.5397-0.09630.2622-0.1320.1599-0.2294-0.23590.14740.10610.2381-0.5912-0.01760.177-0.2370.06110.6282-0.0710.214239.074424.386624.7648
60.9373-0.58580.0250.8665-0.64860.8068-0.0156-0.0433-0.260.1191-0.09790.20270.3621-0.1671-0.00810.1934-0.03890.05010.1277-0.03120.190252.847821.77824.9498
71.3825-0.19010.21811.15280.01940.81090.0589-0.2038-0.38890.1222-0.06390.06580.4906-0.23560.0120.2268-0.0590.01940.09390.00750.199857.012319.58521.892
80.60080.24190.04460.29790.05320.30640.0796-0.0477-0.21140.05140.0081-0.13620.28520.09580.0050.20460.0224-0.01750.0854-0.01350.213566.169720.214420.0917
90.2368-0.06890.16540.1318-0.28380.6177-0.0337-0.19880.29630.1628-0.0907-0.115-0.21030.0256-0.04010.1343-0.00020.00650.0815-0.01070.190964.296834.775218.1382
101.1375-0.10890.25270.2584-0.24420.93560.04810.1688-0.0541-0.1646-0.0308-0.2017-0.05550.0762-0.09910.14660.01090.01470.0611-0.02530.146164.481328.15039.0143
111.48950.6351-0.02890.31340.00241.65270.09760.20220.0272-0.2541-0.1127-0.2691-0.13250.3458-0.00530.17820.00620.00490.14890.00570.182369.777232.07587.4207
121.26480.43210.09460.3074-0.2070.6242-0.09120.24170.0422-0.20010.0002-0.0375-0.3108-0.0468-0.0150.18710.0332-0.00220.1104-0.02840.131859.489634.78053.293
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 307 through 341 )A307 - 341
2X-RAY DIFFRACTION2chain 'A' and (resid 342 through 362 )A342 - 362
3X-RAY DIFFRACTION3chain 'A' and (resid 363 through 404 )A363 - 404
4X-RAY DIFFRACTION4chain 'A' and (resid 405 through 427 )A405 - 427
5X-RAY DIFFRACTION5chain 'A' and (resid 428 through 447 )A428 - 447
6X-RAY DIFFRACTION6chain 'A' and (resid 448 through 475 )A448 - 475
7X-RAY DIFFRACTION7chain 'A' and (resid 476 through 507 )A476 - 507
8X-RAY DIFFRACTION8chain 'A' and (resid 508 through 526 )A508 - 526
9X-RAY DIFFRACTION9chain 'A' and (resid 527 through 539 )A527 - 539
10X-RAY DIFFRACTION10chain 'A' and (resid 540 through 557 )A540 - 557
11X-RAY DIFFRACTION11chain 'A' and (resid 558 through 579 )A558 - 579
12X-RAY DIFFRACTION12chain 'A' and (resid 580 through 607 )A580 - 607

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