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- PDB-5npv: Structure of human ATG5-ATG16L1(ATG5BD) complex (I4) -

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Basic information

Entry
Database: PDB / ID: 5npv
TitleStructure of human ATG5-ATG16L1(ATG5BD) complex (I4)
Components
  • Autophagy protein 5
  • Autophagy-related protein 16-1
KeywordsCELL CYCLE / autophagy / ATG16L1 / ATG5
Function / homology
Function and homology information


otolith development / regulation of autophagosome maturation / response to fluoride / regulation of cytokine production involved in immune response / positive regulation of viral translation / Atg8-family ligase activity / Atg12-Atg5-Atg16 complex / antigen processing and presentation of endogenous antigen / C-terminal protein lipidation / phagophore ...otolith development / regulation of autophagosome maturation / response to fluoride / regulation of cytokine production involved in immune response / positive regulation of viral translation / Atg8-family ligase activity / Atg12-Atg5-Atg16 complex / antigen processing and presentation of endogenous antigen / C-terminal protein lipidation / phagophore / negative regulation of autophagic cell death / vacuole-isolation membrane contact site / positive regulation of stress granule assembly / cellular response to nitrosative stress / ubiquitin-like protein transferase activity / negative regulation of defense response to virus / ventricular cardiac muscle cell development / microautophagy / mitochondria-associated endoplasmic reticulum membrane contact site / regulation of cilium assembly / aggrephagy / transferase complex / mucus secretion / response to fungus / xenophagy / negative thymic T cell selection / corpus callosum development / protein localization to phagophore assembly site / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / cellular response to nitrogen starvation / regulation of release of sequestered calcium ion into cytosol / negative stranded viral RNA replication / endolysosome membrane / response to iron(II) ion / negative regulation of phagocytosis / negative regulation of cardiac muscle cell apoptotic process / positive regulation of mucus secretion / negative regulation of type I interferon production / chaperone-mediated autophagy / Macroautophagy / Receptor Mediated Mitophagy / heart contraction / axoneme / autophagosome membrane / mitophagy / autophagosome assembly / negative regulation of reactive oxygen species metabolic process / autophagosome / blood vessel remodeling / positive regulation of autophagy / protein-membrane adaptor activity / cardiac muscle cell apoptotic process / negative regulation of protein ubiquitination / sperm midpiece / PINK1-PRKN Mediated Mitophagy / negative regulation of innate immune response / post-translational protein modification / establishment of localization in cell / Negative regulators of DDX58/IFIH1 signaling / hippocampus development / macroautophagy / autophagy / vasodilation / phagocytic vesicle membrane / protein transport / GTPase binding / chromatin organization / defense response to virus / protein ubiquitination / response to xenobiotic stimulus / axon / protein-containing complex / membrane / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Autophagy protein Apg5, helix rich domain / Ubiquitin-like (UB roll) - #620 / : / : / : / Autophagy protein ATG5, alpha-helical bundle region / Autophagy protein ATG5, UblA domain / Autophagy-related protein 5 / Autophagy protein Atg5, helix rich domain / Autophagy protein Atg5, UblA domain ...Autophagy protein Apg5, helix rich domain / Ubiquitin-like (UB roll) - #620 / : / : / : / Autophagy protein ATG5, alpha-helical bundle region / Autophagy protein ATG5, UblA domain / Autophagy-related protein 5 / Autophagy protein Atg5, helix rich domain / Autophagy protein Atg5, UblA domain / Autophagy protein ATG5, UblB domain / Autophagy-related protein 16 / Autophagy-related protein 16 domain / Autophagy protein 16 (ATG16) / Serum Albumin; Chain A, Domain 1 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / 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 / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Autophagy-related protein 16-1 / Autophagy protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsArchna, A. / Scrima, A.
Funding support Germany, 2items
OrganizationGrant numberCountry
Helmholtz Gemeinschaft Deutscher ForschungszentrenVH-NG-727 Germany
Helmholtz Gemeinschaft Deutscher ForschungszentrenVH-GS-202 Germany
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Identification, biochemical characterization and crystallization of the central region of human ATG16L1.
Authors: Archna, A. / Scrima, A.
History
DepositionApr 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 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

Downloads & links

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Assembly

Deposited unit
A: Autophagy protein 5
B: Autophagy-related protein 16-1
C: Autophagy protein 5
D: Autophagy-related protein 16-1


Theoretical massNumber of molelcules
Total (without water)135,9564
Polymers135,9564
Non-polymers00
Water19811
1
A: Autophagy protein 5
B: Autophagy-related protein 16-1


Theoretical massNumber of molelcules
Total (without water)67,9782
Polymers67,9782
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-18 kcal/mol
Surface area14430 Å2
MethodPISA
2
C: Autophagy protein 5
D: Autophagy-related protein 16-1


Theoretical massNumber of molelcules
Total (without water)67,9782
Polymers67,9782
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-17 kcal/mol
Surface area14010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.580, 143.580, 62.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Autophagy protein 5 / / APG5-like / Apoptosis-specific protein


Mass: 33187.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATG5, APG5L, ASP / Plasmid: pET15b-derived / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H1Y0
#2: Protein Autophagy-related protein 16-1 / APG16-like 1


Mass: 34789.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATG16L1, APG16L, UNQ9393/PRO34307 / Plasmid: pCOLA-derived / Production host: Escherichia coli (E. coli) / References: UniProt: Q676U5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.76 / Details: 0.1 M MES pH 5.76, 0.378 M KCl, 21.7 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 26, 2015 / Details: VariMax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.1→45.404 Å / Num. obs: 11680 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 5.51 % / Biso Wilson estimate: 49.15 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.167 / Rrim(I) all: 0.185 / Χ2: 0.895 / Net I/σ(I): 11.45
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3.1-3.25.5470.7232.2210690.6710.799100
3.2-3.35.5330.4533.659100.7740.501100
3.3-3.45.5990.3614.88300.8340.398100
3.4-3.55.4340.3525.147380.8780.39100
3.5-45.4880.2716.7426490.9580.399.6
4-65.5470.11814.3838400.9910.13199.6
6-105.5380.06122.9612840.9980.068100
10-45.4044.9560.02549.093600.9990.02894.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GDK

4gdk


Resolution: 3.1→45.404 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.23
RfactorNum. reflection% reflection
Rfree0.2781 581 4.98 %
Rwork0.2529 --
obs0.2543 11670 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 113.54 Å2 / Biso mean: 40.39 Å2 / Biso min: 13.27 Å2
Refinement stepCycle: final / Resolution: 3.1→45.404 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4623 0 0 11 4634
Biso mean---34.4 -
Num. residues----569
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034751
X-RAY DIFFRACTIONf_angle_d0.4896447
X-RAY DIFFRACTIONf_chiral_restr0.036701
X-RAY DIFFRACTIONf_plane_restr0.004813
X-RAY DIFFRACTIONf_dihedral_angle_d10.2362823
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1-3.41190.33711440.338627622906100
3.4119-3.90530.24981450.268827512896100
3.9053-4.91940.28261450.2282751289699
4.9194-45.40880.26381470.2212825297299
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)
14.44770.57490.64672.8140.06872.5037-0.26520.82090.804-0.32720.599-0.2448-0.1517-0.30050.06140.31640.03620.03980.3316-0.14280.1618-28.4621-51.5868-1.2153
22.6077-0.14180.24541.09840.61351.00310.1340.45990.192-0.09620.0454-1.2856-0.36590.36230.08280.5187-0.1254-0.12770.5602-0.2581.1967-8.3233-49.05123.6355
32.7964-0.23631.47653.1587-1.30353.36110.1798-0.437-0.5341.67460.1949-0.5025-0.4087-0.37110.33620.5779-0.0241-0.36530.3356-0.15860.6015-16.4734-57.907519.4199
43.2213-2.41381.6862.5817-3.24596.01720.5103-0.0812-1.33520.40620.8295-0.27441.4249-0.0275-0.40170.47880.1869-0.30490.3465-0.14640.8129-19.2501-71.3069.1597
58.7437-6.49231.26837.38380.09331.87130.88621.5867-0.369-1.7304-0.3518-0.31550.1620.94730.10870.3749-0.0171-0.0040.577-0.08160.5113-31.4428-62.0067-12.4819
63.39511.4181-1.98543.5612-1.62453.42510.13450.56190.0568-0.06460.15470.1356-0.1693-0.8459-0.10690.3811-0.05830.00120.3558-0.10030.2096-44.3232-76.6564-5.3587
72.95721.382-0.00453.9629-0.81370.81270.01670.0787-0.0769-0.64070.0549-0.00780.4129-0.2175-0.18730.4752-0.0373-0.01490.3489-0.02320.3432-48.8279-87.2323-3.8543
80.1351-0.2566-0.11428.54890.97511.72410.5712-0.5921-0.56171.1047-0.40621.3320.3955-0.2904-0.20260.5799-0.2368-0.28950.39770.00760.6425-51.1278-96.686716.9953
91.6647-1.6993-1.68653.5912.30966.4058-0.2681-0.2278-0.16130.0539-0.1158-0.68831.1930.17560.72240.6662-0.0509-0.14270.43650.06050.828-37.8688-96.784614.2607
100.4959-1.4036-1.29257.24351.70094.9930.2929-0.8541-0.38310.52290.2579-2.38430.80670.8550.21770.64860.0858-0.32270.36740.06070.8956-33.0925-86.704713.1144
112.6882-0.5235-0.62883.2648-0.09641.71540.40040.27910.50310.33620.1703-0.5263-0.79360.5083-0.18910.4832-0.157-0.10690.34410.07350.2983-42.3815-87.84979.6559
124.22930.59390.23853.0487-0.84690.25980.6398-1.3462-0.0591.4792-0.6679-0.0691-0.046-0.19910.13970.7667-0.2585-0.1540.30770.1010.3583-39.8943-73.402411.8847
137.03682.6297-2.93766.82932.30453.2386-0.49461.08480.6983-1.24150.62821.1252-0.7944-0.8350.33310.4616-0.0559-0.1230.5267-0.17270.3315-42.9839-62.8855-13.3292
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 103 )A4 - 103
2X-RAY DIFFRACTION2chain 'A' and (resid 104 through 186 )A104 - 186
3X-RAY DIFFRACTION3chain 'A' and (resid 187 through 273 )A187 - 273
4X-RAY DIFFRACTION4chain 'B' and (resid 10 through 28 )B10 - 28
5X-RAY DIFFRACTION5chain 'B' and (resid 29 through 47 )B29 - 47
6X-RAY DIFFRACTION6chain 'C' and (resid 4 through 53 )C4 - 53
7X-RAY DIFFRACTION7chain 'C' and (resid 54 through 173 )C54 - 173
8X-RAY DIFFRACTION8chain 'C' and (resid 174 through 187 )C174 - 187
9X-RAY DIFFRACTION9chain 'C' and (resid 188 through 222 )C188 - 222
10X-RAY DIFFRACTION10chain 'C' and (resid 223 through 250 )C223 - 250
11X-RAY DIFFRACTION11chain 'C' and (resid 251 through 273 )C251 - 273
12X-RAY DIFFRACTION12chain 'D' and (resid 10 through 32 )D10 - 32
13X-RAY DIFFRACTION13chain 'D' and (resid 33 through 48 )D33 - 48

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