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- PDB-5c19: p97 variant 2 in the apo state -

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Basic information

Entry
Database: PDB / ID: 5c19
Titlep97 variant 2 in the apo state
ComponentsTransitional endoplasmic reticulum ATPase
KeywordsHYDROLASE / AAA ATPase / ERAD / VCP / CDC48
Function / homology
Function and homology information


positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / 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 / BAT3 complex binding / Derlin-1 retrotranslocation complex ...positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / 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 / BAT3 complex binding / Derlin-1 retrotranslocation complex / positive regulation of protein K63-linked deubiquitination / deubiquitinase activator activity / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / aggresome assembly / NADH metabolic process / regulation of protein localization to chromatin / vesicle-fusing ATPase / 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 / ERAD pathway / 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 / ubiquitin-like protein ligase binding / autophagosome maturation / RHOH GTPase cycle / polyubiquitin modification-dependent protein binding / HSF1 activation / translesion synthesis / endoplasmic reticulum to Golgi vesicle-mediated transport / MHC class I protein binding / Protein methylation / negative regulation of smoothened signaling pathway / interstrand cross-link repair / Attachment and Entry / : / ATP metabolic process / endoplasmic reticulum unfolded protein response / proteasome complex / lipid droplet / viral genome replication / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / ADP binding / proteasomal protein catabolic process / Hh mutants are degraded by ERAD / positive regulation of protein-containing complex assembly / Defective CFTR causes cystic fibrosis / Hedgehog ligand biogenesis / macroautophagy / Translesion Synthesis by POLH / ABC-family proteins mediated transport / establishment of protein localization / autophagy / Aggrephagy / cytoplasmic stress granule / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of canonical Wnt signaling pathway / 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 / Ovarian tumor domain proteases / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / E3 ubiquitin ligases ubiquitinate target proteins / site of double-strand break / cellular response to heat / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein phosphatase binding / regulation of apoptotic process / secretory granule lumen / ficolin-1-rich granule lumen / Attachment and Entry / protein ubiquitination / protein domain specific binding / DNA repair / intracellular membrane-bounded organelle / glutamatergic synapse / lipid binding / DNA damage response / ubiquitin protein ligase binding / Neutrophil degranulation / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / RNA binding
Similarity search - Function
Vps4 C terminal oligomerisation domain / 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 ...Vps4 C terminal oligomerisation domain / 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. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Transitional endoplasmic reticulum ATPase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.2 Å
AuthorsHaenzelmann, P. / Schindelin, H.
CitationJournal: Structure / Year: 2016
Title: Structural Basis of ATP Hydrolysis and Intersubunit Signaling in the AAA+ ATPase p97.
Authors: Hanzelmann, P. / Schindelin, H.
History
DepositionJun 13, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 20, 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: Transitional endoplasmic reticulum ATPase
B: Transitional endoplasmic reticulum ATPase
C: Transitional endoplasmic reticulum ATPase
D: Transitional endoplasmic reticulum ATPase
E: Transitional endoplasmic reticulum ATPase
F: Transitional endoplasmic reticulum ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)536,56518
Polymers535,4126
Non-polymers1,15312
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area43600 Å2
ΔGint-331 kcal/mol
Surface area176400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.665, 165.780, 243.992
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 89235.352 Da / Num. of mol.: 6 / Mutation: N750D, R753D, M757D, Q760D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VCP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P55072, vesicle-fusing ATPase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4

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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: 2.6 Å3/Da / Density % sol: 52.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 12% PEG 4000, 0.15 M ammonium sulfate, 0.1 M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 4.2→49.13 Å / Num. obs: 41484 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 130.75 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.259 / Rpim(I) all: 0.107 / Net I/σ(I): 7.3 / Num. measured all: 277534
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
4.2-4.3771.1971.83240046130.680.484100
15.14-49.135.30.04430.650759620.9970.02196.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.3.8data scaling
MxCuBEdata collection
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CF3

3cf3


Resolution: 4.2→49.129 Å / SU ML: 0.67 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 32.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3023 2071 5 %
Rwork0.2369 39342 -
obs0.2402 41413 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 533.82 Å2 / Biso mean: 181.0739 Å2 / Biso min: 34.63 Å2
Refinement stepCycle: final / Resolution: 4.2→49.129 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32717 0 60 0 32777
Biso mean--126.51 --
Num. residues----4191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00233297
X-RAY DIFFRACTIONf_angle_d0.59744983
X-RAY DIFFRACTIONf_chiral_restr0.0385073
X-RAY DIFFRACTIONf_plane_restr0.0035960
X-RAY DIFFRACTIONf_dihedral_angle_d12.1412814
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.2001-4.29780.37711370.322925902727100
4.2978-4.40520.3781350.304825732708100
4.4052-4.52420.32571370.280726042741100
4.5242-4.65730.32791360.267425742710100
4.6573-4.80750.34061360.272325932729100
4.8075-4.97910.32161370.261125932730100
4.9791-5.17830.34681380.269326212759100
5.1783-5.41370.3311360.265125862722100
5.4137-5.69870.371380.265826222760100
5.6987-6.05510.34821370.278325992736100
6.0551-6.52170.34511380.253226372775100
6.5217-7.17620.35051390.243826402779100
7.1762-8.21040.27551400.209526462786100
8.2104-10.32840.21161410.174326832824100
10.3284-49.13240.24181460.18672781292799
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)
14.22692.80340.86783.63822.12796.37510.6277-1.6028-0.41130.5296-0.9018-0.3050.46410.03190.23011.04190.0015-0.15341.55110.0581.2841120.145214.606524.884
23.98790.8712-0.50293.3802-3.21867.785-0.0498-0.3820.48520.2214-0.27630.1935-0.86920.38790.28020.91280.09720.01840.9386-0.06421.302197.51714.24239.257
30.8707-0.4175-0.64911.97490.23493.48130.0117-0.0922-0.48160.0861-0.1628-0.30440.40510.60880.0920.86410.1709-0.08691.080.28141.618396.9426-22.19794.2012
43.1978-1.5062-2.86011.34140.93912.55280.4049-2.652-0.1634-1.92460.1783-1.29620.2932-0.1412-0.77962.13820.18510.6473.2310.36782.059167.224914.987454.9019
53.64330.16250.22063.3087-2.03242.06920.1189-1.7954-0.15820.868-0.2564-0.0263-0.42290.48780.03541.11070.08990.1441.62390.11661.180166.049116.641629.5566
65.4606-1.2773-0.24131.41170.39781.15150.2275-0.4628-0.2425-0.0742-0.0360.04610.3798-0.1352-0.21510.8993-0.0843-0.17570.85950.27271.195663.9721-21.601320.5483
77.6011-2.05872.86713.9839-0.92356.390.4266-0.56020.158-0.07740.02930.3195-0.28260.2945-0.39790.9408-0.0151-0.05570.9004-0.01781.709413.858927.027317.7472
84.1768-2.0938-2.83246.86651.16522.5802-0.7599-1.626-0.88610.6672-0.5456-0.45681.1431.59580.11531.0607-0.0218-0.10191.77110.59731.741840.009718.292717.4705
99.83140.72622.44770.35921.44013.2786-0.0281-0.5819-0.9412-0.332-0.1408-0.1410.06510.03480.28341.0406-0.13690.03550.9424-0.03341.590839.064620.74342.3541
101.9805-1.97241.89461.8789-1.98144.10830.0489-0.5478-0.14940.3141-0.01950.2753-0.1489-0.2093-0.22991.0041-0.10920.18941.1049-0.03322.304237.2057-9.6245.0199
116.59221.74961.85331.3714-0.79851.88990.036-0.3156-0.1375-0.30890.10470.04850.5996-0.3151-0.20851.283-0.1238-0.07230.88920.06411.958936.9951-20.46751.496
126.752-3.79013.90794.9383-2.26173.46140.29981.10392.2426-1.5027-0.5806-0.71931.1853-0.29770.79081.2793-0.45-0.04771.47490.26451.79724.9297-24.7895-10.5783
136.8432-0.408-2.04774.1312.74567.60560.11910.622-0.3755-0.4828-0.10370.3448-0.1403-1.4230.34981.3626-0.2254-0.47371.4110.12631.432232.324626.3496-24.5904
146.0179-2.2478-1.26674.20252.56326.9868-0.61441.37631.2951-0.81540.1661-0.5312-0.70250.945-0.74681.1371-0.18950.10311.006-0.19050.803849.772331.2008-17.1897
155.3499-1.0373-2.60473.18142.05862.923-0.16570.048-1.2686-0.0785-0.03270.67050.7604-0.80390.14991.14890.00080.08511.17450.09651.175241.159920.071-26.6356
164.3751-0.806-2.26851.61552.20084.1884-0.49411.48261.8318-1.51370.5704-1.4318-0.4137-0.9416-0.44741.86720.0075-0.18732.03680.36091.977946.56827.1878-58.5304
172.590.21250.12333.2626-0.23070.9016-0.24320.6265-0.588-0.2270.1530.4928-0.3936-0.5869-0.15771.3930.0569-0.37741.2876-0.03152.049935.2787-3.2877-30.8969
183.871.56910.39865.1195-0.03834.59510.0780.0263-1.2311-0.22950.28190.48140.4193-0.8025-0.02141.08780.0682-0.43481.0501-0.03332.212640.8512-12.9044-22.0688
193.7386-0.8545-2.0264.4713-1.26551.68-0.43591.5718-1.3345-0.2355-0.08271.6582-0.5646-1.9271-0.07192.0786-0.1506-0.71441.5847-0.5391.448536.4113-15.0321-55.727
203.68342.61440.72224.9023-0.21620.2829-0.26341.6222-1.9617-1.25440.8605-0.80910.18890.31163.20771.66170.0989-0.31251.26510.00862.298338.0916-23.4933-45.1831
215.6222-0.0647-1.75850.91470.30650.6255-0.82870.4552-2.3491-1.29940.11130.33931.13640.2723-0.40972.6557-0.474-0.15411.73550.79121.946767.501629.5936-72.984
223.74240.9313-2.5950.1387-0.70921.55550.57671.04480.66120.5516-0.3519-0.5868-0.8952-0.16720.05372.0565-0.2515-0.2581.83920.60261.410882.734833.8283-67.5431
233.8726-0.6015-1.69854.00970.46382.30080.07340.39130.2785-0.3251-0.195-0.6312-0.0887-0.10420.06461.2938-0.03660.00250.98640.13191.260373.699623.8917-43.3819
244.81160.369-0.34953.2312-1.19251.2590.28140.97690.3925-0.6980.13510.3714-0.0551-0.7643-0.56851.75990.2575-0.31311.1729-0.09730.786666.4693-3.5793-49.303
254.6468-2.1263-3.20521.60452.53444.68770.43010.6321-0.6306-0.5817-0.14090.3660.36390.283-0.10381.1540.0809-0.26321.0603-0.10020.637173.845-17.9223-52.1848
263.6842-0.11422.56641.9121-0.3941.70020.51721.79111.44560.00010.2389-0.5339-0.10991.8666-0.4791.88590.21120.52292.65670.0413.0334128.626725.1048-34.7811
273.7925-2.91251.04933.3516-1.15934.92030.42660.11860.9076-0.7164-0.4977-1.30030.68360.2490.0691.15990.01060.16080.6712-0.01821.2984101.533118.9986-25.4247
282.5234-1.24041.75491.38210.20972.9939-0.34280.3463-0.11250.0540.0066-0.10860.28780.35160.40751.13950.08010.19080.88470.11141.3445100.1166-16.5095-30.6031
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 225 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 226 through 448 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 449 through 774 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 21 through 150 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 151 through 448 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 449 through 772 )B0
7X-RAY DIFFRACTION7chain 'C' and (resid 21 through 209 )C0
8X-RAY DIFFRACTION8chain 'C' and (resid 210 through 262 )C0
9X-RAY DIFFRACTION9chain 'C' and (resid 263 through 448 )C0
10X-RAY DIFFRACTION10chain 'C' and (resid 449 through 585 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 586 through 683 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 684 through 769 )C0
13X-RAY DIFFRACTION13chain 'D' and (resid 197 through 269 )D0
14X-RAY DIFFRACTION14chain 'D' and (resid 270 through 318 )D0
15X-RAY DIFFRACTION15chain 'D' and (resid 319 through 407 )D0
16X-RAY DIFFRACTION16chain 'D' and (resid 408 through 448 )D0
17X-RAY DIFFRACTION17chain 'D' and (resid 449 through 569 )D0
18X-RAY DIFFRACTION18chain 'D' and (resid 570 through 649 )D0
19X-RAY DIFFRACTION19chain 'D' and (resid 650 through 706 )D0
20X-RAY DIFFRACTION20chain 'D' and (resid 707 through 772 )D0
21X-RAY DIFFRACTION21chain 'E' and (resid 21 through 104 )E0
22X-RAY DIFFRACTION22chain 'E' and (resid 105 through 225 )E0
23X-RAY DIFFRACTION23chain 'E' and (resid 226 through 448 )E0
24X-RAY DIFFRACTION24chain 'E' and (resid 449 through 586 )E0
25X-RAY DIFFRACTION25chain 'E' and (resid 587 through 763 )E0
26X-RAY DIFFRACTION26chain 'F' and (resid 21 through 209 )F0
27X-RAY DIFFRACTION27chain 'F' and (resid 210 through 448 )F0
28X-RAY DIFFRACTION28chain 'F' and (resid 449 through 763 )F0

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