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- PDB-5c18: p97-delta709-728 in complex with ATP-gamma-S -

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Basic information

Entry
Database: PDB / ID: 5c18
Titlep97-delta709-728 in complex with ATP-gamma-S
ComponentsTransitional endoplasmic reticulum ATPase
KeywordsHYDROLASE / AAA ATPase / ERAD / VCP / CDC48
Function / homology
Function and homology information


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 / Derlin-1 retrotranslocation complex / positive regulation of protein K63-linked deubiquitination / protein-DNA covalent cross-linking repair ...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 / Derlin-1 retrotranslocation complex / positive regulation of protein K63-linked deubiquitination / protein-DNA covalent cross-linking repair / deubiquitinase activator activity / ATPase complex / positive regulation of oxidative phosphorylation / cytoplasm protein quality control / regulation of protein localization to chromatin / ubiquitin-modified protein reader activity / 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 / ubiquitin-specific protease binding / regulation of synapse organization / positive regulation of ATP biosynthetic process / ubiquitin-like protein ligase binding / RHOH GTPase cycle / intracellular membrane-bounded organelle / autophagosome maturation / MHC class I protein binding / endoplasmic reticulum to Golgi vesicle-mediated transport / negative regulation of hippo signaling / HSF1 activation / polyubiquitin modification-dependent protein binding / mitophagy / interstrand cross-link repair / ATP metabolic process / protein unfolding / ribosome-associated ubiquitin-dependent protein catabolic process / proteasome complex / Attachment and Entry / endoplasmic reticulum unfolded protein response / Protein methylation / ERAD pathway / negative regulation of smoothened signaling pathway / viral genome replication / translesion synthesis / negative regulation of protein localization to chromatin / macroautophagy / rescue of stalled cytosolic ribosome / lipid droplet / Josephin domain DUBs / establishment of protein localization / proteasomal protein catabolic process / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / positive regulation of protein-containing complex assembly / positive regulation of non-canonical NF-kappaB signal transduction / Hh mutants are degraded by ERAD / ADP binding / Dengue Virus Genome Translation and Replication / Translesion Synthesis by POLH / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / AMPK-induced ERAD and lysosome mediated degradation of PD-L1(CD274) / ABC-family protein mediated transport / autophagy / cytoplasmic stress granule / Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide / positive regulation of protein catabolic process / Aggrephagy / positive regulation of canonical Wnt signaling pathway / double-strand break repair / azurophil granule lumen / Ovarian tumor domain proteases / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / KEAP1-NFE2L2 pathway / site of double-strand break / cellular response to heat / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / secretory granule lumen / protein phosphatase binding / ubiquitin-dependent protein catabolic process / ficolin-1-rich granule lumen / proteasome-mediated ubiquitin-dependent protein catabolic process / regulation of apoptotic process / Attachment and Entry / protein ubiquitination / protein domain specific binding / ubiquitin protein ligase binding / DNA repair / Neutrophil degranulation / DNA damage response / lipid binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm
Similarity search - Function
Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, CDC48 family / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48), N-terminal domain / Cell division protein 48 (CDC48) N-terminal domain / CDC48, domain 2 ...Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, CDC48 family / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48), N-terminal domain / 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 / 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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Transitional endoplasmic reticulum ATPase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.3 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 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)528,38236
Polymers521,5996
Non-polymers6,78330
Water54030
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area54630 Å2
ΔGint-406 kcal/mol
Surface area173560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.330, 180.059, 255.612
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: 86933.094 Da / Num. of mol.: 6 / Mutation: 709-728 deletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VCP / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P55072, vesicle-fusing ATPase
#2: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 3.1 Å3/Da / Density % sol: 60.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 6.5-7% PEG 4000, 0.4-0.6 M potassium acetate, 0.1 M MES pH 5.75

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 3.3→49.18 Å / Num. obs: 97950 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 99.38 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.179 / Rpim(I) all: 0.07 / Net I/σ(I): 10.8 / Num. measured all: 730152
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
3.3-3.367.61.841.23667248260.4970.713100
18.07-49.184.50.0523.929016390.9970.02593.5

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Phasing

PhasingMethod: molecular replacement

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Processing

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

3cf3


Resolution: 3.3→19.99 Å / SU ML: 0.43 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 26.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2488 4867 5 %
Rwork0.211 92511 -
obs0.2129 97378 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 369.42 Å2 / Biso mean: 137.4427 Å2 / Biso min: 39.58 Å2
Refinement stepCycle: final / Resolution: 3.3→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34041 0 546 30 34617
Biso mean--93.44 109.96 -
Num. residues----4338
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00335067
X-RAY DIFFRACTIONf_angle_d0.71847396
X-RAY DIFFRACTIONf_chiral_restr0.0295314
X-RAY DIFFRACTIONf_plane_restr0.0036199
X-RAY DIFFRACTIONf_dihedral_angle_d15.00113600
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3-3.33730.33141520.318230943246100
3.3373-3.37640.32851670.310329743141100
3.3764-3.41740.3631400.313931283268100
3.4174-3.46040.291500.302330483198100
3.4604-3.50570.32041560.300230793235100
3.5057-3.55350.37141640.293730053169100
3.5535-3.6040.34191770.28630663243100
3.604-3.65740.32991290.271830513180100
3.6574-3.71420.34671530.267830853238100
3.7142-3.77470.27551670.26130323199100
3.7747-3.83940.27781750.248130623237100
3.8394-3.90870.29551590.232730843243100
3.9087-3.98330.25921620.223130483210100
3.9833-4.06390.24521820.205430503232100
4.0639-4.15150.23051690.209730493218100
4.1515-4.24720.28141520.220630823234100
4.2472-4.35240.2391880.198130283216100
4.3524-4.46880.22631520.187530923244100
4.4688-4.59870.2481700.186430653235100
4.5987-4.74520.23011540.186930943248100
4.7452-4.91240.24921600.18230743234100
4.9124-5.1060.21181580.189230913249100
5.106-5.33420.24961550.203831123267100
5.3342-5.60950.26761720.223931053277100
5.6095-5.95220.25041510.224631123263100
5.9522-6.39780.26571620.218231183280100
6.3978-7.01620.25051610.213131393300100
7.0162-7.97450.22391670.182131373304100
7.9745-9.84320.20641790.162231753354100
9.8432-19.99050.18381840.1673232341699
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)
15.06011.7911-0.34861.19280.77682.36180.3144-0.39791.06270.4387-0.57021.08080.1057-1.29770.20310.8662-0.13790.28471.4598-0.08871.4687-42.83976.779263.4103
25.38843.27713.09615.21024.48919.0630.266-0.26530.05710.5213-0.37170.17290.3773-0.28170.12570.549-0.03610.19660.70710.14530.5924-18.50584.330561.156
31.1983-0.62190.01361.3632-0.60132.5576-0.12480.3029-0.1612-0.3240.1490.36940.5609-0.7536-0.01640.8288-0.2453-0.01190.71240.090.7649-16.6517-24.689750.9518
41.4529-0.68541.44121.2043-1.06084.16820.05780.51460.2643-0.4655-0.05020.4055-0.1148-0.6885-0.07121.0092-0-0.25541.06030.28130.9793-26.196818.056410.7895
51.6881-0.3603-0.87711.59340.56991.74630.10270.3520.286-0.36790.04150.0980.016-0.3272-0.15240.64790.0269-0.06040.60220.16270.6624-6.405112.107325.3896
63.6951-0.1397-1.13560.79990.41695.4266-0.12750.61-0.3739-0.37010.1069-0.11870.5336-0.14550.04911.0255-0.2170.05420.5470.02430.6388-0.6785-23.062523.6981
71.01221.9025-1.63482.9984-1.72723.8945-0.14330.6720.1562-0.7382-0.1245-0.3993-0.29820.22750.20291.12280.01580.2870.99410.32570.923529.120232.92534.6102
83.2615-0.8333-0.46672.39890.0191.8591-0.07650.20620.0023-0.182-0.1707-0.52790.04230.49130.24270.65180.03070.08780.50590.19830.625627.070420.439226.3587
95.5801-1.2511-0.4272.2771-0.03673.8780.20860.51270.1158-0.3523-0.0106-0.68160.40930.7731-0.19060.89620.05460.23110.7812-0.12420.853631.4155-14.193519.8831
105.06652.0966-0.21582.2156-0.26721.98550.04750.28630.8214-0.0192-0.1889-0.7692-0.98561.07770.11751.0852-0.4337-0.03021.26330.30661.576463.952735.195249.6572
115.9581-1.47582.223.0034-2.61655.377-0.00430.03090.3760.0149-0.2872-0.492-0.40380.53410.22350.5812-0.11520.02190.46150.12570.673739.365723.724652.1885
121.96730.198711.63250.11052.25780.16770.0554-0.4152-0.0226-0.0876-0.62530.44420.7167-0.06440.64810.05850.05210.97330.19321.142852.6545-8.416250.4365
134.74880.59560.40082.7791.54514.5767-0.3294-0.74480.4224-0.03650.2142-0.249-0.72950.10160.11831.2508-0.0759-0.30251.0429-0.01320.731643.879325.2404107.7252
141.49280.69450.46852.0449-0.38941.65930.0685-0.1846-0.02410.2227-0.07160.05910.0525-0.19240.00930.7921-0.0112-0.10360.82730.07830.662130.491614.390284.6942
152.46581.1384-1.11232.6563-1.71763.2520.0443-0.4609-0.32990.5594-0.3451-0.79450.05110.2690.28020.754-0.0363-0.23730.61170.18691.028239.7591-20.937776.8678
162.29390.6416-1.4021.45530.20813.58420.1906-1.20510.13981.0643-0.28670.47320.2708-0.92650.0961.4647-0.2740.24561.7489-0.05230.9746-9.74588.4809106.0177
170.62350.44220.02492.3411-0.69191.48610.0793-0.16530.04740.17710.0230.48810.5972-0.6592-0.07530.9023-0.30920.03471.02690.01320.6176-6.62670.409785.0078
184.9112.605-0.80613.6142-0.92482.6350.1593-0.0015-0.01380.3915-0.0375-0.0428-0.34270.1476-0.13950.7373-0.0011-0.01150.29520.08170.54027.5643-29.281180.6228
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 295 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 296 through 407 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 408 through 769 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 21 through 262 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 263 through 482 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 483 through 770 )B0
7X-RAY DIFFRACTION7chain 'C' and (resid 21 through 262 )C0
8X-RAY DIFFRACTION8chain 'C' and (resid 263 through 482 )C0
9X-RAY DIFFRACTION9chain 'C' and (resid 483 through 770 )C0
10X-RAY DIFFRACTION10chain 'D' and (resid 21 through 262 )D0
11X-RAY DIFFRACTION11chain 'D' and (resid 263 through 425 )D0
12X-RAY DIFFRACTION12chain 'D' and (resid 426 through 769 )D0
13X-RAY DIFFRACTION13chain 'E' and (resid 20 through 209 )E0
14X-RAY DIFFRACTION14chain 'E' and (resid 210 through 482 )E0
15X-RAY DIFFRACTION15chain 'E' and (resid 483 through 769 )E0
16X-RAY DIFFRACTION16chain 'F' and (resid 21 through 295 )F0
17X-RAY DIFFRACTION17chain 'F' and (resid 296 through 482 )F0
18X-RAY DIFFRACTION18chain 'F' and (resid 483 through 769 )F0

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