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- PDB-5ifw: Quantitative interaction mapping reveals an extended ubiquitin re... -

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Basic information

Entry
Database: PDB / ID: 5ifw
TitleQuantitative interaction mapping reveals an extended ubiquitin regulatory domain in ASPL that disrupts functional p97 hexamers and induces cell death
Components
  • Tether containing UBX domain for GLUT4
  • Transitional endoplasmic reticulum ATPase
KeywordsSIGNALING PROTEIN / ASPL / p97 / disassembly / hexamer / eUBX
Function / homology
Function and homology information


positive regulation of protein modification process / flavin adenine dinucleotide catabolic process / VCP-NSFL1C complex / endoplasmic reticulum stress-induced pre-emptive quality control / endosome to lysosome transport via multivesicular body sorting pathway / BAT3 complex binding / cellular response to arsenite ion / cytoplasmic ubiquitin ligase complex / protein-DNA covalent cross-linking repair / Derlin-1 retrotranslocation complex ...positive regulation of protein modification process / flavin adenine dinucleotide catabolic process / VCP-NSFL1C complex / endoplasmic reticulum stress-induced pre-emptive quality control / endosome to lysosome transport via multivesicular body sorting pathway / BAT3 complex binding / cellular response to arsenite ion / cytoplasmic ubiquitin ligase complex / protein-DNA covalent cross-linking repair / Derlin-1 retrotranslocation complex / positive regulation of protein K63-linked deubiquitination / deubiquitinase activator activity / positive regulation of oxidative phosphorylation / cytoplasm protein quality control / ATPase complex / aggresome assembly / ubiquitin-modified protein reader activity / regulation of protein localization to chromatin / vesicle membrane / cellular response to misfolded protein / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / positive regulation of mitochondrial membrane potential / vesicle-fusing ATPase / K48-linked polyubiquitin modification-dependent protein binding / regulation of aerobic respiration / NAD+ metabolic process / retrograde protein transport, ER to cytosol / stress granule disassembly / ciliary transition zone / ubiquitin-specific protease binding / regulation of synapse organization / positive regulation of ATP biosynthetic process / intracellular membrane-bounded organelle / ubiquitin-like protein ligase binding / RHOH GTPase cycle / MHC class I protein binding / autophagosome maturation / negative regulation of hippo signaling / endoplasmic reticulum to Golgi vesicle-mediated transport / HSF1 activation / polyubiquitin modification-dependent protein binding / interstrand cross-link repair / ATP metabolic process / Attachment and Entry / endoplasmic reticulum unfolded protein response / ciliary tip / Protein methylation / ERAD pathway / translesion synthesis / endoplasmic reticulum-Golgi intermediate compartment membrane / negative regulation of protein localization to chromatin / endomembrane system / lipid droplet / viral genome replication / proteasome complex / macroautophagy / negative regulation of smoothened signaling pathway / Josephin domain DUBs / Translocation of SLC2A4 (GLUT4) to the plasma membrane / proteasomal protein catabolic process / establishment of protein localization / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / positive regulation of protein-containing complex assembly / intracellular protein transport / ADP binding / Hh mutants are degraded by ERAD / positive regulation of non-canonical NF-kappaB signal transduction / Translesion Synthesis by POLH / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / ABC-family protein mediated transport / cytoplasmic side of plasma membrane / autophagy / cytoplasmic stress granule / positive regulation of canonical Wnt signaling pathway / positive regulation of protein catabolic process / Aggrephagy / azurophil granule lumen / Ovarian tumor domain proteases / glucose homeostasis / KEAP1-NFE2L2 pathway / double-strand break repair / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / cellular response to heat / E3 ubiquitin ligases ubiquitinate target proteins / site of double-strand break / Neddylation / secretory granule lumen / protein phosphatase binding / regulation of apoptotic process / ficolin-1-rich granule lumen / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / ciliary basal body / Attachment and Entry / protein ubiquitination / protein domain specific binding / DNA repair / ubiquitin protein ligase binding
Similarity search - Function
TUG ubiquitin-like domain / : / TUG ubiquitin-like domain / Vcp-like ATPase; Chain A, domain 2 - #10 / UBX domain / UBX domain / UBX domain profile. / Vcp-like ATPase; Chain A, domain 2 / Vps4 C terminal oligomerisation domain / Barwin-like endoglucanases - #20 ...TUG ubiquitin-like domain / : / TUG ubiquitin-like domain / Vcp-like ATPase; Chain A, domain 2 - #10 / UBX domain / UBX domain / UBX domain profile. / Vcp-like ATPase; Chain A, domain 2 / Vps4 C terminal oligomerisation domain / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, CDC48 family / Cell division protein 48 (CDC48), N-terminal domain / : / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain / CDC48, domain 2 / Cell division protein 48 (CDC48), domain 2 / Cell division protein 48 (CDC48) domain 2 / CDC48 domain 2-like superfamily / Aspartate decarboxylase-like domain superfamily / Helicase, Ruva Protein; domain 3 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Ubiquitin-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Roll / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Transitional endoplasmic reticulum ATPase / Tether containing UBX domain for GLUT4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.4 Å
AuthorsRoske, Y. / Heinemann, U.
CitationJournal: Nat Commun / Year: 2016
Title: Quantitative interaction mapping reveals an extended UBX domain in ASPL that disrupts functional p97 hexamers.
Authors: Arumughan, A. / Roske, Y. / Barth, C. / Forero, L.L. / Bravo-Rodriguez, K. / Redel, A. / Kostova, S. / McShane, E. / Opitz, R. / Faelber, K. / Rau, K. / Mielke, T. / Daumke, O. / Selbach, M. ...Authors: Arumughan, A. / Roske, Y. / Barth, C. / Forero, L.L. / Bravo-Rodriguez, K. / Redel, A. / Kostova, S. / McShane, E. / Opitz, R. / Faelber, K. / Rau, K. / Mielke, T. / Daumke, O. / Selbach, M. / Sanchez-Garcia, E. / Rocks, O. / Panakova, D. / Heinemann, U. / Wanker, E.E.
History
DepositionFeb 26, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references
Revision 1.2Jan 10, 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: Tether containing UBX domain for GLUT4
B: Transitional endoplasmic reticulum ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,6614
Polymers110,8062
Non-polymers8542
Water43224
1
A: Tether containing UBX domain for GLUT4
B: Transitional endoplasmic reticulum ATPase
hetero molecules

A: Tether containing UBX domain for GLUT4
B: Transitional endoplasmic reticulum ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,3218
Polymers221,6124
Non-polymers1,7094
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+11
Buried area16930 Å2
ΔGint-82 kcal/mol
Surface area85900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.344, 208.361, 99.129
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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Components

#1: Protein Tether containing UBX domain for GLUT4 / Alveolar soft part sarcoma chromosomal region candidate gene 1 protein / Alveolar soft part sarcoma ...Alveolar soft part sarcoma chromosomal region candidate gene 1 protein / Alveolar soft part sarcoma locus / Renal papillary cell carcinoma protein 17 / UBX domain-containing protein 9


Mass: 21356.389 Da / Num. of mol.: 1 / Fragment: UNP residues 317-504
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASPSCR1, ASPL, RCC17, TUG, UBXD9, UBXN9 / Plasmid: pQLinkG / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: Q9BZE9
#2: Protein Transitional endoplasmic reticulum ATPase / TER ATPase / 15S Mg(2+)-ATPase p97 subunit / Valosin-containing protein / VCP


Mass: 89449.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VCP / Plasmid: pQLinkG / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: P55072, vesicle-fusing ATPase
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 3.54 Å3/Da / Density % sol: 65.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 2M Ammonium sulfate, 0.1M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 3.4→33.9 Å / Num. obs: 20794 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 56.207 Å2 / Rmerge(I) obs: 0.168 / Net I/σ(I): 10.8
Reflection shell
Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
3.4-3.495.10.8442.161100
3.49-3.580.6672.691100
3.58-3.690.4963.561100
3.69-3.80.4484.091100
3.8-3.930.355.01199.8
3.93-4.060.2836.211100
4.06-4.220.2067.99199.9
4.22-4.390.1799.531100
4.39-4.580.14611.271100
4.58-4.810.13611.771100
4.81-5.070.12912.271100
5.07-5.380.13911.571100
5.38-5.750.1411.061100
5.75-6.210.13711.45199.9
6.21-6.80.11713.741100
6.8-7.60.08218.59199.7
7.6-8.780.04429.51100
8.78-10.750.02939.44199.8
10.75-15.210.02743.03199.8
15.210.02539.22186.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CF1

3cf1


Resolution: 3.4→33.887 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 25.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2614 1040 5 %
Rwork0.229 --
obs0.2307 20785 99.88 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→33.887 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6960 0 54 24 7038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037137
X-RAY DIFFRACTIONf_angle_d0.8649664
X-RAY DIFFRACTIONf_dihedral_angle_d14.2352748
X-RAY DIFFRACTIONf_chiral_restr0.0541093
X-RAY DIFFRACTIONf_plane_restr0.0041271
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4001-3.57920.35021460.30142778X-RAY DIFFRACTION100
3.5792-3.80310.29611460.26842778X-RAY DIFFRACTION100
3.8031-4.09630.311470.24952796X-RAY DIFFRACTION100
4.0963-4.50770.23551480.20042802X-RAY DIFFRACTION100
4.5077-5.1580.24151480.2062805X-RAY DIFFRACTION100
5.158-6.49110.25871490.23382844X-RAY DIFFRACTION100
6.4911-33.88890.2271560.20712942X-RAY DIFFRACTION99

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