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- PDB-6tgs: AtNBR1-PB1 domain -

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Basic information

Entry
Database: PDB / ID: 6tgs
TitleAtNBR1-PB1 domain
ComponentsProtein NBR1 homolog
KeywordsSIGNALING PROTEIN / Autophagy
Function / homology
Function and homology information


protein targeting to vacuole involved in autophagy / vacuole / protein polymerization / autophagosome / ubiquitin binding / protein transport / zinc ion binding / cytoplasm
Similarity search - Function
Next to BRCA1, central domain / Ig-like domain from next to BRCA1 gene / PB1 domain / PB1 domain / PB1 domain / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. ...Next to BRCA1, central domain / Ig-like domain from next to BRCA1 gene / PB1 domain / PB1 domain / PB1 domain / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / UBA-like superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / SUCCINIC ACID / Protein NBR1 homolog
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsJakobi, A.J. / Sachse, C.
Funding support Germany, 3items
OrganizationGrant numberCountry
European CommissionPIEF-GA-2012-331285 Germany
European CommissionPCOFUND-GA-2008-229597 Germany
German Research FoundationEXC1074 Germany
CitationJournal: Nat Commun / Year: 2020
Title: Structural basis of p62/SQSTM1 helical filaments and their role in cellular cargo uptake.
Authors: Arjen J Jakobi / Stefan T Huber / Simon A Mortensen / Sebastian W Schultz / Anthimi Palara / Tanja Kuhm / Birendra Kumar Shrestha / Trond Lamark / Wim J H Hagen / Matthias Wilmanns / Terje ...Authors: Arjen J Jakobi / Stefan T Huber / Simon A Mortensen / Sebastian W Schultz / Anthimi Palara / Tanja Kuhm / Birendra Kumar Shrestha / Trond Lamark / Wim J H Hagen / Matthias Wilmanns / Terje Johansen / Andreas Brech / Carsten Sachse /
Abstract: p62/SQSTM1 is an autophagy receptor and signaling adaptor with an N-terminal PB1 domain that forms the scaffold of phase-separated p62 bodies in the cell. The molecular determinants that govern PB1 ...p62/SQSTM1 is an autophagy receptor and signaling adaptor with an N-terminal PB1 domain that forms the scaffold of phase-separated p62 bodies in the cell. The molecular determinants that govern PB1 domain filament formation in vitro remain to be determined and the role of p62 filaments inside the cell is currently unclear. We here determine four high-resolution cryo-EM structures of different human and Arabidopsis PB1 domain assemblies and observed a filamentous ultrastructure of p62/SQSTM1 bodies using correlative cellular EM. We show that oligomerization or polymerization, driven by a double arginine finger in the PB1 domain, is a general requirement for lysosomal targeting of p62. Furthermore, the filamentous assembly state of p62 is required for autophagosomal processing of the p62-specific cargo KEAP1. Our results show that using such mechanisms, p62 filaments can be critical for cargo uptake in autophagy and are an integral part of phase-separated p62 bodies.
History
DepositionNov 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein NBR1 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,96511
Polymers10,0531
Non-polymers91210
Water63135
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-13 kcal/mol
Surface area5880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.128, 79.438, 24.135
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-108-

SO4

21A-225-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Protein NBR1 homolog / AtNBR1 / At4g24690


Mass: 10052.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: NBR1, At4g24690, F22K18.110 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9SB64

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Non-polymers , 6 types, 45 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.19 Å3/Da / Density % sol: 43.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES (pH 6.5), 18-20% (w/v) PEG20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.53→37.9 Å / Num. obs: 12367 / % possible obs: 99.2 % / Redundancy: 2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.02799 / Rpim(I) all: 0.02799 / Rsym value: 0.03958 / Net I/σ(I): 10.45
Reflection shellResolution: 1.53→1.585 Å / Rmerge(I) obs: 0.4132 / Mean I/σ(I) obs: 1.42 / Num. unique obs: 1271 / CC1/2: 0.655 / Rpim(I) all: 0.4132 / Rrim(I) all: 0.5844

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Processing

Software
NameVersionClassification
PHENIX(dev_3500: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: EMD-10499

Resolution: 1.53→37.9 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.22 / Phase error: 31
RfactorNum. reflection% reflection
Rfree0.2549 1227 5.16 %
Rwork0.2204 --
obs0.2221 12367 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.53→37.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms662 0 56 35 753
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007783
X-RAY DIFFRACTIONf_angle_d0.91054
X-RAY DIFFRACTIONf_dihedral_angle_d5.793601
X-RAY DIFFRACTIONf_chiral_restr0.057120
X-RAY DIFFRACTIONf_plane_restr0.005138
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.59130.41221040.36682497X-RAY DIFFRACTION97
1.5913-1.66370.38071510.3312501X-RAY DIFFRACTION99
1.6637-1.75140.35761510.31792479X-RAY DIFFRACTION98
1.7514-1.86110.27911270.28442552X-RAY DIFFRACTION99
1.8611-2.00480.24721260.22582541X-RAY DIFFRACTION99
2.0048-2.20660.28331500.21132447X-RAY DIFFRACTION97
2.2066-2.52580.22931570.20492480X-RAY DIFFRACTION99
2.5258-3.18210.2251210.20782536X-RAY DIFFRACTION99
3.1821-39.73240.23291400.19312509X-RAY DIFFRACTION98

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