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Basic information

Entry
Database: PDB / ID: 5ifs
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 / eUBX
Function / homology
Function and homology information


positive regulation of protein modification process / regulation of glucose import / positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / vesicle membrane / endosome to lysosome transport via multivesicular body sorting pathway / protein-DNA covalent cross-linking repair / endoplasmic reticulum stress-induced pre-emptive quality control ...positive regulation of protein modification process / regulation of glucose import / positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / vesicle membrane / endosome to lysosome transport via multivesicular body sorting pathway / protein-DNA covalent cross-linking repair / endoplasmic reticulum stress-induced pre-emptive quality control / cellular response to arsenite ion / Derlin-1 retrotranslocation complex / BAT3 complex binding / positive regulation of protein K63-linked deubiquitination / deubiquitinase activator activity / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / aggresome assembly / regulation of protein localization to chromatin / vesicle-fusing ATPase / NADH metabolic process / cellular response to misfolded protein / stress granule disassembly / K48-linked polyubiquitin modification-dependent protein binding / positive regulation of mitochondrial membrane potential / negative regulation of protein localization to chromatin / ubiquitin-modified protein reader activity / retrograde protein transport, ER to cytosol / regulation of aerobic respiration / ATPase complex / regulation of synapse organization / ubiquitin-specific protease binding / positive regulation of ATP biosynthetic process / ERAD pathway / ubiquitin-like protein ligase binding / MHC class I protein binding / autophagosome maturation / RHOH GTPase cycle / polyubiquitin modification-dependent protein binding / HSF1 activation / endomembrane system / translesion synthesis / Protein methylation / endoplasmic reticulum to Golgi vesicle-mediated transport / interstrand cross-link repair / negative regulation of smoothened signaling pathway / ATP metabolic process / Attachment and Entry / endoplasmic reticulum unfolded protein response / endoplasmic reticulum-Golgi intermediate compartment membrane / viral genome replication / lipid droplet / proteasome complex / proteasomal protein catabolic process / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Hh mutants are degraded by ERAD / Defective CFTR causes cystic fibrosis / Hedgehog ligand biogenesis / macroautophagy / intracellular protein transport / Translesion Synthesis by POLH / positive regulation of protein-containing complex assembly / ABC-family proteins mediated transport / establishment of protein localization / ADP binding / cytoplasmic side of plasma membrane / autophagy / Aggrephagy / cytoplasmic stress granule / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of protein catabolic process / activation of cysteine-type endopeptidase activity involved in apoptotic process / KEAP1-NFE2L2 pathway / azurophil granule lumen / double-strand break repair / positive regulation of canonical Wnt signaling pathway / Ovarian tumor domain proteases / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / E3 ubiquitin ligases ubiquitinate target proteins / glucose homeostasis / site of double-strand break / Neddylation / cellular response to heat / ubiquitin-dependent protein catabolic process / regulation of apoptotic process / protein phosphatase binding / proteasome-mediated ubiquitin-dependent protein catabolic process / secretory granule lumen / ficolin-1-rich granule lumen / Attachment and Entry / protein ubiquitination / protein domain specific binding / intracellular membrane-bounded organelle / DNA repair / glutamatergic synapse / lipid binding / DNA damage response / 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 / Barwin-like endoglucanases - #20 / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, CDC48 family ...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 / Barwin-like endoglucanases - #20 / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, CDC48 family / Barwin-like endoglucanases / 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 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Helicase, Ruva Protein; domain 3 / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 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: 2.46 Å
AuthorsRoske, Y. / Arumughan, A. / Heinemann, U. / Wanker, E.
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

Downloads & links

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Assembly

Deposited unit
A: Tether containing UBX domain for GLUT4
B: Transitional endoplasmic reticulum ATPase
C: Tether containing UBX domain for GLUT4
D: Transitional endoplasmic reticulum ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,19613
Polymers159,9194
Non-polymers1,2779
Water7,350408
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12820 Å2
ΔGint-80 kcal/mol
Surface area59350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.844, 132.914, 96.121
Angle α, β, γ (deg.)90.00, 110.15, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A317 - 330
2114C317 - 330
1214A341 - 497
2214C341 - 497
1124B21 - 480
2124D21 - 480

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ACBD

#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: 26451.355 Da / Num. of mol.: 2 / Fragment: UNP residues 317-553
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): Rosetta2 / References: UniProt: Q9BZE9
#2: Protein Transitional endoplasmic reticulum ATPase / TER ATPase / 15S Mg(2+)-ATPase p97 subunit / Valosin-containing protein / VCP


Mass: 53508.168 Da / Num. of mol.: 2
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

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Non-polymers , 6 types, 417 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 2.9 Å3/Da / Density % sol: 57.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 23% PEG3350, 0.3M LiSO4, 0.1M Hepes pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.46→33.8 Å / Num. obs: 58583 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 49.033 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.72
Reflection shell
Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.46-2.522.40.4612.09193.2
2.52-2.590.3982.62198.4
2.59-2.670.3233.2198.8
2.67-2.750.2563.99198.9
2.75-2.840.214.89198.8
2.84-2.940.1695.85198.7
2.94-3.050.1377.18198.6
3.05-3.180.0979.86198.8
3.18-3.320.07412.8198.8
3.32-3.480.05916.03198.7
3.48-3.670.04520.8198.6
3.67-3.890.03625.45198.5
3.89-4.160.02731.29198.6
4.16-4.490.02138.3198.5
4.49-4.920.0241.36198.1
4.92-5.50.02239.07197.1
5.5-6.350.02336.88196.8
6.35-7.780.01941.41197.1
7.78-110.01157.81195.7
110.01161.05190.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CF3

3cf3


Resolution: 2.46→33.77 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.914 / SU B: 9.238 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.429 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25061 2930 5 %RANDOM
Rwork0.20101 ---
obs0.20352 55653 98.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.864 Å2
Baniso -1Baniso -2Baniso -3
1--1.05 Å20 Å2-0.41 Å2
2---0.76 Å20 Å2
3---1.54 Å2
Refinement stepCycle: LAST / Resolution: 2.46→33.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9813 0 79 408 10300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01910095
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0961.9913674
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.34651240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5123.721481
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.985151779
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7981598
X-RAY DIFFRACTIONr_chiral_restr0.0730.21544
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217630
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6964.3634966
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.9496.5286192
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9434.6155129
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.38336.03315053
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1320medium positional0.420.5
22B3452medium positional0.430.5
11A1320medium thermal4.442
22B3452medium thermal6.762
LS refinement shellResolution: 2.46→2.524 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 204 -
Rwork0.289 3862 -
obs--93.21 %

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