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- PDB-6hd0: Common mode of remodeling AAA ATPases p97/CDC48 by their disassem... -

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Basic information

Entry
Database: PDB / ID: 6hd0
TitleCommon mode of remodeling AAA ATPases p97/CDC48 by their disassembly cofactors ASPL/PUX1
Components
  • Plant UBX domain-containing protein 1
  • Transitional endoplasmic reticulum ATPase
KeywordsGENE REGULATION / ATPase / PUX1 / UBX / p97 / disassembly
Function / homology
Function and homology information


protein-containing complex disassembly / positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / cytoplasm protein quality control / endosome to lysosome transport via multivesicular body sorting pathway / endoplasmic reticulum stress-induced pre-emptive quality control / cellular response to arsenite ion / Derlin-1 retrotranslocation complex ...protein-containing complex disassembly / positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / cytoplasm protein quality control / endosome to lysosome transport via multivesicular body sorting pathway / endoplasmic reticulum stress-induced pre-emptive quality control / cellular response to arsenite ion / Derlin-1 retrotranslocation complex / BAT3 complex binding / protein-DNA covalent cross-linking repair / positive regulation of protein K63-linked deubiquitination / deubiquitinase activator activity / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / ubiquitin-modified protein reader activity / regulation of protein localization to chromatin / aggresome assembly / vesicle-fusing ATPase / NADH metabolic process / cellular response to misfolded protein / stress granule disassembly / negative regulation of protein localization to chromatin / positive regulation of mitochondrial membrane potential / retrograde protein transport, ER to cytosol / K48-linked polyubiquitin modification-dependent protein binding / organ growth / regulation of aerobic respiration / regulation of synapse organization / ubiquitin-specific protease binding / positive regulation of ATP biosynthetic process / ATPase complex / MHC class I protein binding / ubiquitin-like protein ligase binding / RHOH GTPase cycle / polyubiquitin modification-dependent protein binding / autophagosome maturation / HSF1 activation / negative regulation of hippo signaling / endoplasmic reticulum to Golgi vesicle-mediated transport / proteasomal protein catabolic process / translesion synthesis / Protein methylation / interstrand cross-link repair / ERAD pathway / negative regulation of smoothened signaling pathway / ATP metabolic process / endoplasmic reticulum unfolded protein response / Attachment and Entry / proteasome complex / viral genome replication / lipid droplet / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / macroautophagy / Hh mutants are degraded by ERAD / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Translesion Synthesis by POLH / establishment of protein localization / positive regulation of protein-containing complex assembly / ABC-family proteins mediated transport / ADP binding / activation of cysteine-type endopeptidase activity involved in apoptotic process / autophagy / Aggrephagy / cytoplasmic stress granule / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of protein catabolic process / azurophil granule lumen / KEAP1-NFE2L2 pathway / Ovarian tumor domain proteases / positive regulation of canonical Wnt signaling pathway / double-strand break repair / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / site of double-strand break / cellular response to heat / ATPase binding / ubiquitin-dependent protein catabolic process / protein phosphatase binding / secretory granule lumen / proteasome-mediated ubiquitin-dependent protein catabolic process / regulation of apoptotic process / ficolin-1-rich granule lumen / Attachment and Entry / protein ubiquitination / protein domain specific binding / intracellular membrane-bounded organelle / DNA repair / lipid binding / glutamatergic synapse / ubiquitin protein ligase binding / DNA damage response / Neutrophil degranulation / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum
Similarity search - Function
Plant UBX domain-containing protein 1 / 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 / Barwin-like endoglucanases / AAA ATPase, CDC48 family ...Plant UBX domain-containing protein 1 / 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 / Barwin-like endoglucanases / 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 / 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 / Plant UBX domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Arabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.728 Å
AuthorsHeinemann, U. / Roske, Y. / Banchenko, S.
CitationJournal: Structure / Year: 2019
Title: Common Mode of Remodeling AAA ATPases p97/CDC48 by Their Disassembling Cofactors ASPL/PUX1.
Authors: Banchenko, S. / Arumughan, A. / Petrovic, S. / Schwefel, D. / Wanker, E.E. / Roske, Y. / Heinemann, U.
History
DepositionAug 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 11, 2019Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Jan 17, 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
B: Transitional endoplasmic reticulum ATPase
G: Plant UBX domain-containing protein 1
T: Transitional endoplasmic reticulum ATPase
U: Transitional endoplasmic reticulum ATPase
V: Transitional endoplasmic reticulum ATPase
A: Transitional endoplasmic reticulum ATPase
C: Transitional endoplasmic reticulum ATPase
D: Plant UBX domain-containing protein 1
E: Plant UBX domain-containing protein 1
F: Plant UBX domain-containing protein 1
K: Plant UBX domain-containing protein 1
I: Plant UBX domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)494,89518
Polymers492,33212
Non-polymers2,5636
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, RALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33720 Å2
ΔGint-111 kcal/mol
Surface area140450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.120, 185.120, 122.426
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21T
31U
41V
51A
61C
12D
22G
32F
42E
52K
62I

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114B23 - 462
2114T23 - 462
3114U23 - 462
4114V23 - 462
5114A23 - 462
6114C23 - 462
1124D108 - 182
2124G108 - 182
3124F108 - 182
4124E108 - 182
5124K108 - 182
6124I108 - 182

NCS ensembles :
ID
1
2

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Components

#1: Protein
Transitional endoplasmic reticulum ATPase / TER ATPase / 15S Mg(2+)-ATPase p97 subunit / Valosin-containing protein / VCP


Mass: 53508.168 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VCP / Plasmid: pQlinkH / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / Variant (production host): DE3 / References: UniProt: P55072, vesicle-fusing ATPase
#2: Protein
Plant UBX domain-containing protein 1 / PUX1 / CDC48-interacting UBX-domain protein 1


Mass: 28547.164 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PUX1, At3g27310, K17E12.13 / Plasmid: pQlinkH / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / Variant (production host): DE3 / References: UniProt: Q9LK22
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
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: 3.5 Å3/Da / Density % sol: 64.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 6% (v/v) PEG1500, 0.2M sodium acetate, 0.1M Hepes pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
Reflection twinOperator: -k,-h,-l / Fraction: 0.47
ReflectionResolution: 3.728→48.98 Å / Num. obs: 28980 / % possible obs: 90.7 % / Redundancy: 5.3 % / CC1/2: 0.983 / Rmerge(I) obs: 0.306 / Rpim(I) all: 0.148 / Rrim(I) all: 0.34 / Net I/σ(I): 6.2
Reflection shellResolution: 3.88→4.03 Å / Mean I/σ(I) obs: 0.75 / Num. unique obs: 668 / CC1/2: 0.324 / Rrim(I) all: 0.2686 / % possible all: 98.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0238refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S3S, 5IFS

1s3s

5ifs


Resolution: 3.728→48.98 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.854 / SU B: 62.234 / SU ML: 0.446 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.234
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2529 2606 9 %RANDOM
Rwork0.2077 ---
obs0.2117 26254 58.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 281.57 Å2 / Biso mean: 123.914 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1--50.75 Å20 Å20 Å2
2---50.75 Å20 Å2
3---101.5 Å2
Refinement stepCycle: final / Resolution: 3.728→48.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24272 0 162 0 24434
Biso mean--75.77 --
Num. residues----3086
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01324889
X-RAY DIFFRACTIONr_bond_other_d0.0020.01723814
X-RAY DIFFRACTIONr_angle_refined_deg1.1681.64833703
X-RAY DIFFRACTIONr_angle_other_deg1.041.5855251
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.18753073
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.58921.8881361
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.257154441
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.93415210
X-RAY DIFFRACTIONr_chiral_restr0.0330.23295
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0227627
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025017
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11B6768MEDIUM POSITIONAL0.490.5
12T6768MEDIUM POSITIONAL0.460.5
13U6768MEDIUM POSITIONAL0.430.5
14V6768MEDIUM POSITIONAL0.450.5
15A6768MEDIUM POSITIONAL0.460.5
16C6768MEDIUM POSITIONAL0.390.5
11B6768MEDIUM THERMAL12.952
12T6768MEDIUM THERMAL16.942
13U6768MEDIUM THERMAL11.652
14V6768MEDIUM THERMAL10.292
15A6768MEDIUM THERMAL12.012
16C6768MEDIUM THERMAL11.072
21D1193MEDIUM POSITIONAL0.470.5
22G1193MEDIUM POSITIONAL0.440.5
23F1193MEDIUM POSITIONAL0.370.5
24E1193MEDIUM POSITIONAL0.420.5
25K1193MEDIUM POSITIONAL0.410.5
26I1193MEDIUM POSITIONAL0.50.5
21D1193MEDIUM THERMAL12.022
22G1193MEDIUM THERMAL34.882
23F1193MEDIUM THERMAL14.92
24E1193MEDIUM THERMAL22.682
25K1193MEDIUM THERMAL40.032
26I1193MEDIUM THERMAL19.432
LS refinement shellResolution: 3.728→3.825 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.372 18 -
Rwork0.271 138 -
obs--4.26 %
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)
10.11380.0603-0.22370.4885-0.88622.1410.03660.318-0.01080.29090.06740.11980.091-0.4988-0.10411.0855-0.1546-0.00570.944-0.12020.624982.7248-107.644-18.8364
22.1577-0.48280.56121.8109-1.86612.0656-0.0236-0.10970.04680.21270.26760.25220.1431-0.2539-0.2441.0533-0.20850.01970.93510.01730.302797.0949-83.02-11.9028
30.10140.0924-0.23641.1128-1.73292.8964-0.1019-0.06840.2157-0.4610.27870.03450.8194-0.0594-0.17680.92810.18010.03460.90710.07360.6399146.1527-107.4966-21.6469
42.25090.47361.70031.12890.45711.33210.0462-0.0418-0.2460.24090.04670.0689-0.0021-0.1139-0.09290.998-0.0195-0.02290.93290.11950.3465132.2145-83.3384-12.6976
51.19771.56010.02642.11140.04690.0341-0.10480.1836-0.0649-0.2390.1221-0.31130.0394-0.152-0.01740.8905-0.22690.04310.80660.22910.8801147.01422.6562-17.584
63.0348-0.4822-0.77233.21282.01921.35690.056-0.1208-0.03340.37840.1955-0.39510.11250.1344-0.25151.0173-0.0817-0.04151.0155-0.05440.1669132.8684-22.2595-11.2272
71.9565-0.0239-0.11581.26450.50530.24340.08790.2106-0.10240.0210.1846-0.398-0.0471-0.0637-0.27250.84580.1822-0.03290.92420.12860.58483.53932.2047-20.3974
81.55640.2404-0.80110.98690.42112.60030.2842-0.14710.03580.0567-0.01190.0213-0.03170.109-0.27231.0231-0.03320.03440.7993-0.0360.364798.0054-21.8936-12.0434
90.8213-0.0405-1.00570.06880.06441.82580.2876-0.1358-0.0463-0.1006-0.0211-0.14190.1071-0.2278-0.26650.6365-0.146-0.1391.1628-0.10080.605351.9434-52.6378-19.8608
102.19170.2277-0.93533.0861-1.53991.08020.1454-0.24660.29770.27140.09390.2496-0.16710.0198-0.23930.84580.010.07931.134-0.09040.269880.0321-52.325-11.6773
111.7963-0.04990.00572.97731.47150.73210.0851-0.0819-0.2221-0.7887-0.0696-0.0711-0.4007-0.1062-0.01540.6486-0.00840.01611.24010.07420.5675178.198-52.5307-20.7028
121.76170.45440.82963.22381.82161.2410.2084-0.3691-0.37320.16580.0654-0.28080.08550.0068-0.27380.69450.0332-0.1081.12980.05180.2677150.0209-53.3778-12.2185
138.7453-3.7177-2.33984.72482.08121.0024-0.0499-0.2549-0.17670.24730.0528-0.00520.10910.042-0.00290.8963-0.3469-0.15550.592-0.18590.6401154.249819.74391.2142
143.97660.3853-3.70061.3004-0.00763.56380.30650.15480.37220.3755-0.04340.3129-0.0303-0.1564-0.26311.03810.2977-0.05210.75050.04070.787771.953417.4806-2.9737
153.9351-0.2322-2.276310.8994-2.07081.76840.3889-0.3421-0.15340.4724-0.37920.4216-0.32250.3496-0.00960.3099-0.0309-0.17711.0929-0.0730.6288196.9149-50.5986-3.3854
169.24854.09712.31353.12580.75810.6365-0.051-0.5466-0.44830.13750.1304-0.1796-0.0664-0.2341-0.07940.97110.3741-0.0380.50630.09370.6257158.6031-121.882-3.9213
173.8847-2.49781.61731.6142-1.05510.75430.5603-0.0505-1.0388-0.32350.01790.7674-0.03110.1778-0.57820.9758-0.71280.16040.6024-0.00371.531276.4603-124.65350.1052
180.26741.3525-0.08197.2571-0.42550.03910.0892-0.06990.12310.383-0.02140.19650.0335-0.0116-0.06790.37030.03960.03020.9687-0.01640.746432.9459-56.3457-3.1738
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 200
2X-RAY DIFFRACTION2A201 - 462
3X-RAY DIFFRACTION3B23 - 200
4X-RAY DIFFRACTION4B201 - 462
5X-RAY DIFFRACTION5T23 - 200
6X-RAY DIFFRACTION6T201 - 462
7X-RAY DIFFRACTION7U23 - 200
8X-RAY DIFFRACTION8U201 - 462
9X-RAY DIFFRACTION9V23 - 200
10X-RAY DIFFRACTION10V201 - 462
11X-RAY DIFFRACTION11C23 - 200
12X-RAY DIFFRACTION11C23 - 200
13X-RAY DIFFRACTION12C201 - 462
14X-RAY DIFFRACTION13D108 - 182
15X-RAY DIFFRACTION14G108 - 182
16X-RAY DIFFRACTION15E108 - 182
17X-RAY DIFFRACTION16F108 - 182
18X-RAY DIFFRACTION17K108 - 182
19X-RAY DIFFRACTION18I108 - 182

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