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- PDB-4gdl: Crystal Structure of Human Atg12~Atg5 Conjugate in Complex with a... -

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Basic information

Entry
Database: PDB / ID: 4gdl
TitleCrystal Structure of Human Atg12~Atg5 Conjugate in Complex with an N-terminal Fragment of Atg16L1
Components
  • Autophagy protein 5
  • Autophagy-related protein 16-1
  • Ubiquitin-like protein ATG12
KeywordsPROTEIN BINDING / protein-protein conjugate / protein-protein complex / ubiquitin-like protein / autophagy / E3 ligase / ubiquitin-like fold / structural protein / isopeptide bond / Cytoplasm and autophagosomal membranes
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 / glycophagy / 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 / autophagosome maturation / 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 / intracellular membrane-bounded organelle / protein-containing complex / nucleoplasm / membrane / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Ubiquitin-like protein Atg12 / Ubiquitin-like autophagy protein Apg12 / 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 ...Ubiquitin-like protein Atg12 / Ubiquitin-like autophagy protein Apg12 / 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 / Ubiquitin-like domain superfamily / 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
Ubiquitin-like protein ATG12 / Autophagy-related protein 16-1 / Autophagy protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.875 Å
AuthorsOtomo, C. / Metlagel, Z. / Takaesu, G. / Otomo, T.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Structure of the human ATG12~ATG5 conjugate required for LC3 lipidation in autophagy.
Authors: Otomo, C. / Metlagel, Z. / Takaesu, G. / Otomo, T.
History
DepositionJul 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Jan 16, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-like protein ATG12
B: Autophagy protein 5
C: Autophagy-related protein 16-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4524
Polymers47,4293
Non-polymers231
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.601, 58.399, 91.802
Angle α, β, γ (deg.)90.000, 130.040, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ubiquitin-like protein ATG12 / Autophagy-related protein 12 / APG12-like


Mass: 10282.029 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APG12, APG12L, ATG12 / Plasmid: pACYC Duet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O94817
#2: Protein Autophagy protein 5 / / APG5-like / Apoptosis-specific protein


Mass: 32489.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APG5L, ASP, ATG5 / Plasmid: pACYC Duet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9H1Y0
#3: Protein/peptide Autophagy-related protein 16-1 / APG16-like 1


Mass: 4657.435 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APG16L, ATG16L1, UNQ9393/PRO34307 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q676U5
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
Compound detailsTHERE IS AN ISOPEPTIDE LINKAGE BETWEEN RESIDUE GLY140 OF ATG12 AND LYS130 OF ATG5. THE ATG12~ATG5 ...THERE IS AN ISOPEPTIDE LINKAGE BETWEEN RESIDUE GLY140 OF ATG12 AND LYS130 OF ATG5. THE ATG12~ATG5 CONJUGATE WAS GENERATED BY CO-EXPRESSING ATG12 AND ATG5 FROM PACYC DUET-1 AND ATG7 AND ATG10 FROM PCDF DUET-1 IN E. COLI

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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: 2.96 Å3/Da / Density % sol: 58.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PROTEIN: 10 MG/ML in 0.01M HEPES pH 7.0, 0.3 M NaCl, 0.001 M DTT; RESERVOIR: 0.1M BICINE pH9.0, 0.2 M sodium phosphate dibasic, 18% PEG 3350, vapor diffusion, hanging drop, temperature 293K, ...Details: PROTEIN: 10 MG/ML in 0.01M HEPES pH 7.0, 0.3 M NaCl, 0.001 M DTT; RESERVOIR: 0.1M BICINE pH9.0, 0.2 M sodium phosphate dibasic, 18% PEG 3350, vapor diffusion, hanging drop, temperature 293K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.0092 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 6, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0092 Å / Relative weight: 1
ReflectionResolution: 2.875→50 Å / Num. obs: 12548 / % possible obs: 98.6 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.056 / Χ2: 1.044 / Net I/σ(I): 14.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.9-33.70.54111741.042192.4
3-3.124.30.46712531.092198.4
3.12-3.274.50.28712321.139199
3.27-3.444.60.20812531.122199.3
3.44-3.654.60.13812561.092199.6
3.65-3.944.50.09212680.979199.7
3.94-4.334.50.06512440.929199.5
4.33-4.964.50.05512850.971199.7
4.96-6.244.30.04612810.955199.8
6.24-504.40.03113021.118198.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.875→36.224 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7275 / SU ML: 0.32 / σ(F): 1.34 / Phase error: 32.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1263 10.13 %RANDOM
Rwork0.2146 ---
obs0.2186 12465 97.41 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 283.77 Å2 / Biso mean: 138.7687 Å2 / Biso min: 64.41 Å2
Refinement stepCycle: LAST / Resolution: 2.875→36.224 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3226 0 1 0 3227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063316
X-RAY DIFFRACTIONf_angle_d0.514482
X-RAY DIFFRACTIONf_chiral_restr0.037479
X-RAY DIFFRACTIONf_plane_restr0.003566
X-RAY DIFFRACTIONf_dihedral_angle_d9.9141256
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8753-2.99030.42811260.33011081120786
2.9903-3.12640.31261360.3041222135897
3.1264-3.29110.28641410.25061257139898
3.2911-3.49710.29191330.25141253138699
3.4971-3.76690.30621450.23541258140399
3.7669-4.14550.2621410.22071269141099
4.1455-4.74420.20811420.180212671409100
4.7442-5.97290.22651480.20312871435100
5.9729-36.22670.2451510.20061308145999
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)
13.62382.79770.67363.24520.8576.0662-0.93061.63931.6291-1.44870.16031.6733-0.2069-1.65830.82810.87310.55590.15431.56390.51591.5721131.909814.746614.7212
27.2938-3.3147-4.16373.7272-0.75575.89080.38871.6713-0.3986-0.4764-0.57270.9357-0.0244-2.87170.04980.67160.1147-0.29171.8883-0.16961.1547129.99286.065415.7652
36.50544.9979-2.79653.8222-1.81313.27-1.46330.6937-2.0906-1.9661.1251-0.26221.66330.67280.37871.1311-0.12510.02611.3008-0.18781.5979133.6834-2.290912.3846
49.73117.6172-0.51088.88772.84013.3538-0.35541.69750.9582-1.090.86270.3778-1.1970.294-0.60390.97820.2414-0.12241.64640.18381.2002140.042411.938413.0095
53.77525.6888-0.11329.69621.38872.32010.01682.37050.7689-1.86650.8880.5925-0.1597-1.86480.06091.560.3194-0.23462.3461-0.15571.724140.1161-0.37344.6258
67.0139-1.49571.34256.3927-2.9867.10940.27650.2747-1.2077-0.3156-0.07740.91760.7319-0.32630.04750.6411-0.0160.01730.9328-0.22450.9535158.9248-6.763128.9032
74.2388-2.21280.08233.7026-3.84076.36350.30813.5878-0.2294-0.8773-0.03150.21010.26151.0743-0.40281.11550.0125-0.16552.5459-0.20360.9501157.44943.14996.6807
86.8884-0.0631.71234.05081.53652.8113-0.42821.71082.1212-0.30570.12340.0233-0.68170.47770.22670.8807-0.0844-0.06710.95520.40151.0515158.998418.785220.0348
97.7345-4.13514.44353.2343-2.23974.47170.00060.93261.0446-0.1225-0.4194-0.4746-0.15230.85160.74740.7444-0.06130.23671.42810.08180.7622175.84423.717825.6581
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 53:61)A53 - 61
2X-RAY DIFFRACTION2chain 'A' and (resseq 62:91)A62 - 91
3X-RAY DIFFRACTION3chain 'A' and (resseq 92:104)A92 - 104
4X-RAY DIFFRACTION4chain 'A' and (resseq 105:134)A105 - 134
5X-RAY DIFFRACTION5chain 'A' and (resseq 135:140)A135 - 140
6X-RAY DIFFRACTION6chain 'B' and (resseq 3:117)B3 - 117
7X-RAY DIFFRACTION7chain 'B' and (resseq 118:173)B118 - 173
8X-RAY DIFFRACTION8chain 'B' and (resseq 174:274)B174 - 274
9X-RAY DIFFRACTION9chain 'C' and (resseq 10:43)C10 - 43

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