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- PDB-5c50: Crystal structure of the complex of human Atg101-Atg13 HORMA domain -

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Basic information

Entry
Database: PDB / ID: 5c50
TitleCrystal structure of the complex of human Atg101-Atg13 HORMA domain
Components
  • Autophagy-related protein 101
  • Autophagy-related protein 13
KeywordsPROTEIN BINDING / complex / autophagy / HORMA domain
Function / homology
Function and homology information


Atg1/ULK1 kinase complex / response to mitochondrial depolarisation / protein localization to phagophore assembly site / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / phagophore assembly site / protein kinase regulator activity / positive regulation of protein targeting to mitochondrion / Macroautophagy / autophagosome assembly ...Atg1/ULK1 kinase complex / response to mitochondrial depolarisation / protein localization to phagophore assembly site / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / phagophore assembly site / protein kinase regulator activity / positive regulation of protein targeting to mitochondrion / Macroautophagy / autophagosome assembly / mitophagy / positive regulation of autophagy / autophagosome / protein serine/threonine kinase activator activity / negative regulation of cell population proliferation / endoplasmic reticulum membrane / protein-containing complex binding / protein kinase binding / mitochondrion / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Autophagy-related protein 101 / Autophagy-related protein 101 / Autophagy-related protein 13 / Autophagy-related protein 13 / Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A / HORMA domain / HORMA domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BENZAMIDINE / Autophagy-related protein 13 / Autophagy-related protein 101
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.63 Å
AuthorsQi, S. / Hurley, J.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM111730 United States
CitationJournal: Structure / Year: 2015
Title: Structure of the Human Atg13-Atg101 HORMA Heterodimer: an Interaction Hub within the ULK1 Complex.
Authors: Qi, S. / Kim, D.J. / Stjepanovic, G. / Hurley, J.H.
History
DepositionJun 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Database references
Revision 1.2Nov 4, 2015Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation ..._pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.name / _software.version
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
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-related protein 101
B: Autophagy-related protein 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0577
Polymers44,4562
Non-polymers6015
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint7 kcal/mol
Surface area17970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.722, 64.447, 94.120
Angle α, β, γ (deg.)90.000, 97.540, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Autophagy-related protein 101


Mass: 22890.082 Da / Num. of mol.: 1 / Fragment: UNP residues 1-198
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATG101, C12orf44, PP894 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9BSB4
#2: Protein Autophagy-related protein 13


Mass: 21566.047 Da / Num. of mol.: 1 / Fragment: UNP residues 12-200
Source method: isolated from a genetically manipulated source
Details: GAMGS is from vector / Source: (gene. exp.) Homo sapiens (human) / Gene: ATG13, KIAA0652 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O75143
#3: Chemical
ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C7H8N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.34 Å3/Da / Density % sol: 47.46 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 19% PEG 3350, 0.5 M benzamidine, and 0.2 M lithium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.07207 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 18, 2015
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07207 Å / Relative weight: 1
ReflectionRedundancy: 5.3 % / Number: 263036 / Rmerge(I) obs: 0.092 / Χ2: 0.92 / D res high: 1.63 Å / D res low: 50 Å / Num. obs: 49908 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
3.515010.0760.8388
2.793.5110.1070.8778.3
2.432.7910.1190.8697
2.212.4310.0950.8554.3
2.052.2110.1060.8744.3
1.932.0510.1260.9464.3
1.841.9310.160.9614.2
1.761.8410.2331.0474.2
1.691.7610.3421.0914.1
1.631.6910.4861.0553.9
ReflectionResolution: 1.63→50 Å / Num. obs: 49908 / % possible obs: 100 % / Redundancy: 5.3 % / Biso Wilson estimate: 24.72 Å2 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.037 / Rrim(I) all: 0.099 / Χ2: 0.919 / Net I/av σ(I): 12.891 / Net I/σ(I): 20.6 / Num. measured all: 263036
Reflection shell

Diffraction-ID: 1 / Rejects: _ / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2
1.63-1.693.90.48649420.8720.2780.5621.055
1.69-1.764.10.34249550.9360.190.3921.091
1.76-1.844.20.23349940.9690.1290.2671.047
1.84-1.934.20.1649850.9820.0880.1830.961
1.93-2.054.30.12649660.9840.0690.1440.946
2.05-2.214.30.10649800.9880.0580.1210.874
2.21-2.434.30.09549770.9880.0520.1090.855
2.43-2.7970.11950020.9910.0470.1290.869
2.79-3.518.30.10749960.9930.040.1150.877
3.51-5080.07651110.9950.030.0820.838

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIXdev_1819refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXDEphasing
PDB_EXTRACT3.15data extraction
Cootmodel building
ARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.63→46.653 Å / SU ML: 0.18 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 21.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1946 2451 4.91 %Random selection
Rwork0.1761 47451 --
obs0.177 49902 99.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 208.61 Å2 / Biso mean: 46.8279 Å2 / Biso min: 14.63 Å2
Refinement stepCycle: final / Resolution: 1.63→46.653 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3048 0 81 197 3326
Biso mean--58.33 38.37 -
Num. residues----383
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063178
X-RAY DIFFRACTIONf_angle_d0.9964293
X-RAY DIFFRACTIONf_chiral_restr0.043484
X-RAY DIFFRACTIONf_plane_restr0.004546
X-RAY DIFFRACTIONf_dihedral_angle_d14.5371184
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6299-1.66120.34011130.29052386249989
1.6612-1.69510.30051090.256326422751100
1.6951-1.7320.29381320.247726792811100
1.732-1.77230.26241490.227425822731100
1.7723-1.81660.24071560.210126212777100
1.8166-1.86570.23541480.202626352783100
1.8657-1.92060.21871280.193226272755100
1.9206-1.98260.21281300.187226642794100
1.9826-2.05350.21111580.189326302788100
2.0535-2.13570.1921300.182826632793100
2.1357-2.23290.20811080.181426682776100
2.2329-2.35060.16751490.171826352784100
2.3506-2.49790.19761340.179726322766100
2.4979-2.69070.19691420.182126552797100
2.6907-2.96140.20351530.192326592812100
2.9614-3.38990.2151440.185126592803100
3.3899-4.27040.16991290.157326882817100
4.2704-46.67240.15831390.142127262865100
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)
13.18311.51441.06412.55111.80132.3474-0.35770.4744-0.4371-0.47780.5466-0.0246-0.19360.6312-0.61760.2562-0.0138-0.00550.2348-0.00930.288638.566525.8634.9429
24.0051-0.03863.4390.2695-0.2763.455-0.06990.20680.1025-0.1252-0.01110.0702-0.27880.11430.18460.1840.0135-0.01850.1070.0060.172736.562138.633523.4799
36.14060.65265.00690.58240.35298.12120.0435-0.17250.0449-0.00090.0126-0.0111-0.14560.0822-0.00190.16090.0077-0.00920.0930.01310.158743.782642.795425.7464
43.94743.5075-4.36117.7214-6.97676.81250.2997-0.13690.16510.146-0.00820.2655-0.6486-0.0284-0.23930.19430.04260.02860.1572-0.03140.214933.076443.330138.4388
53.20461.62161.22783.34593.17333.0169-0.0696-0.1692-0.153-0.05330.07710.0920.0718-0.1720.03260.12480.0010.00730.16970.02220.186730.702431.111736.4763
62.13730.53783.45322.85990.6485.994-0.34670.34320.6264-0.96410.20070.9661.2553-1.42680.34120.7493-0.3984-0.04310.81860.06090.565818.281123.365718.9454
78.18775.46585.46924.80663.3533.68120.5176-0.6984-0.1870.4223-0.3532-0.14660.8082-0.6685-0.20770.13780.0351-0.0010.1621-0.0180.18637.063230.386638.2047
86.82541.8874.20533.76951.15073.3390.0415-0.3289-0.1250.358-0.0842-0.06030.30090.363-0.14020.1960.0020.0140.22610.050.217450.595833.09138.5812
99.2177-3.50424.73146.8508-4.24683.760.12160.3143-0.2252-0.69530.2020.20260.8428-0.3821-0.46320.3904-0.0762-0.07750.392-0.05110.228528.324229.787713.8524
109.3870.99880.22957.15911.21477.36260.05840.13080.4434-0.25430.15130.3256-0.5923-0.3719-0.15330.20120.0066-0.03790.19110.00470.162930.097840.26319.2569
115.83343.584-3.02889.1604-5.5773.54070.021-0.401-0.32430.1427-0.30580.03790.38390.23920.21420.13650.05630.02720.2154-0.00240.209229.41232.612539.2583
125.73182.50573.03865.6123.04382.6614-0.17060.8884-0.3782-0.37210.1823-0.02040.0410.4787-0.00240.1985-0.03510.03070.2736-0.04850.172253.436936.312910.1087
136.2241.85265.2815.82232.54014.6579-0.4978-0.21190.7517-0.02450.07190.1117-0.626-0.23270.80330.2904-0.0314-0.01090.20030.02430.2649.306649.016521.6629
143.56550.593-3.79062.09721.21536.0047-0.01781.08710.7059-0.3985-0.12070.3764-0.8518-0.29690.23580.34040.0003-0.06570.33940.04510.275645.776444.017110.4349
154.9044-1.9244-0.06599.4003-0.10864.7425-0.1581.2057-0.3418-0.8191-0.3071-0.47790.45430.54880.23170.39-0.04090.19280.5926-0.05690.340162.584335.30796.5278
164.00024.70664.24428.7156.44998.613-0.12120.5567-0.5403-0.01560.3646-0.69450.24020.77-0.40730.19120.06050.05010.24280.00590.321867.151734.446221.689
173.2589-2.5487-1.7184.9274-1.35243.40010.09832.1281-0.8157-1.67130.680.91210.7656-0.6371-0.65031.0588-0.2083-0.00790.8237-0.22851.108646.488518.36755.961
187.52583.70664.80715.93813.67944.2625-0.27230.5062-0.2059-0.49230.09450.26410.1801-0.34970.13850.2459-0.07410.0120.2682-0.04450.20545.812232.955616.0138
199.47054.044-5.01419.3707-4.64053.6639-0.3355-0.4124-0.18820.11190.1985-0.20180.43630.24220.11590.20730.0292-0.01710.1927-0.01370.190859.191340.641431.3644
203.48361.29470.88531.66920.83714.4524-0.2170.2626-0.33320.09160.2425-0.51520.39870.5918-0.0290.17610.06440.05680.2820.01660.321668.260934.371922.5475
216.46230.71480.98913.1985-0.01735.3483-0.4870.0854-0.74110.15460.1388-0.25280.34680.12080.14580.42120.05020.13390.1513-00.36358.021326.661621.9232
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 13 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 14 through 44 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 45 through 69 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 70 through 89 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 90 through 105 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 106 through 115 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 116 through 133 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 134 through 161 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 162 through 176 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 177 through 189 )A0
11X-RAY DIFFRACTION11chain 'A' and (resid 190 through 198 )A0
12X-RAY DIFFRACTION12chain 'B' and (resid -1 through 32 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 33 through 42 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 43 through 58 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 59 through 78 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 79 through 103 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 104 through 113 )B0
18X-RAY DIFFRACTION18chain 'B' and (resid 114 through 133 )B0
19X-RAY DIFFRACTION19chain 'B' and (resid 134 through 143 )B0
20X-RAY DIFFRACTION20chain 'B' and (resid 144 through 168 )B0
21X-RAY DIFFRACTION21chain 'B' and (resid 169 through 195 )B0

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