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- PDB-7pux: Structure of p97 N-D1(L198W) in complex with Fragment TROLL2 -

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Basic information

Entry
Database: PDB / ID: 7pux
TitleStructure of p97 N-D1(L198W) in complex with Fragment TROLL2
ComponentsTransitional endoplasmic reticulum ATPase
KeywordsHYDROLASE / p97 / VCP / fragment screening
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 / cytoplasmic ubiquitin ligase complex / cellular response to arsenite ion / protein-DNA covalent cross-linking repair / Derlin-1 retrotranslocation complex / positive regulation of protein K63-linked deubiquitination ...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 / cytoplasmic ubiquitin ligase complex / cellular response to arsenite ion / protein-DNA covalent cross-linking repair / Derlin-1 retrotranslocation complex / positive regulation of protein K63-linked deubiquitination / deubiquitinase activator activity / cytoplasm protein quality control / positive regulation of oxidative phosphorylation / aggresome assembly / ubiquitin-modified protein reader activity / regulation of protein localization to chromatin / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / cellular response to misfolded protein / positive regulation of mitochondrial membrane potential / vesicle-fusing ATPase / K48-linked polyubiquitin modification-dependent protein binding / NAD+ metabolic process / regulation of aerobic respiration / retrograde protein transport, ER to cytosol / stress granule disassembly / ATPase complex / ubiquitin-specific protease binding / regulation of synapse organization / ciliary transition zone / 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 / HSF1 activation / negative regulation of hippo signaling / endoplasmic reticulum to Golgi vesicle-mediated transport / polyubiquitin modification-dependent protein binding / interstrand cross-link repair / ATP metabolic process / translesion synthesis / Attachment and Entry / Protein methylation / negative regulation of protein localization to chromatin / endoplasmic reticulum unfolded protein response / ERAD pathway / proteasomal protein catabolic process / lipid droplet / ciliary tip / proteasome complex / viral genome replication / Josephin domain DUBs / macroautophagy / negative regulation of smoothened signaling pathway / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / establishment of protein localization / positive regulation of protein-containing complex assembly / Hh mutants are degraded by ERAD / Hedgehog ligand biogenesis / Translesion Synthesis by POLH / Defective CFTR causes cystic fibrosis / ADP binding / positive regulation of non-canonical NF-kappaB signal transduction / ABC-family protein mediated transport / autophagy / cytoplasmic stress granule / Aggrephagy / positive regulation of protein catabolic process / azurophil granule lumen / Ovarian tumor domain proteases / KEAP1-NFE2L2 pathway / 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 / cellular response to heat / 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 / Attachment and Entry / proteasome-mediated ubiquitin-dependent protein catabolic process / ciliary basal body / protein ubiquitination / protein domain specific binding / DNA repair / DNA damage response / Neutrophil degranulation / ubiquitin protein ligase binding / lipid binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / glutamatergic synapse / endoplasmic reticulum / ATP hydrolysis activity
Similarity search - Function
Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / 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 ...Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / 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 / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Roll / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
(1S)-2-amino-1-(4-bromophenyl)ethan-1-ol / ADENOSINE-5'-DIPHOSPHATE / FORMIC ACID / DI(HYDROXYETHYL)ETHER / Transitional endoplasmic reticulum ATPase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsBothe, S. / Schindelin, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)GK 2243 Germany
Citation
Journal: Commun Chem / Year: 2022
Title: Fragment screening using biolayer interferometry reveals ligands targeting the SHP-motif binding site of the AAA+ ATPase p97
Authors: Bothe, S. / Hanzelmann, P. / Bohler, S. / Kehrein, J. / Zehe, M. / Wiedemann, C. / Hellmich, U.A. / Brenk, R. / Schindelin, H. / Sotriffer, C.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionOct 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transitional endoplasmic reticulum ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,89821
Polymers52,3891
Non-polymers1,50920
Water4,594255
1
A: Transitional endoplasmic reticulum ATPase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)323,386126
Polymers314,3336
Non-polymers9,053120
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Buried area42010 Å2
ΔGint-130 kcal/mol
Surface area110810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.234, 146.234, 84.397
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number177
Space group name H-MP622
Space group name HallP62
Symmetry operation#1: x,y,z
#2: x-y,x,z
#3: y,-x+y,z
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z
#9: y,x,-z
#10: -y,-x,-z
#11: -x+y,y,-z
#12: x,x-y,-z

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 52388.875 Da / Num. of mol.: 1 / Mutation: L198W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VCP / Production host: Escherichia coli BL21(DE3) / References: UniProt: P55072, vesicle-fusing ATPase

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Non-polymers , 6 types, 275 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-6LY / (1S)-2-amino-1-(4-bromophenyl)ethan-1-ol


Mass: 216.075 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10BrNO / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.49 Å3/Da / Density % sol: 50.53 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Natriumformiat (pH 6.0) 4.0 M Glycerol (v/v) 10 % PEG 600 (v/v) 5 %

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.73→47.87 Å / Num. obs: 42850 / % possible obs: 96.12 % / Redundancy: 26.47 % / Biso Wilson estimate: 26.19 Å2 / CC1/2: 0.9989 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.027 / Rrim(I) all: 0.14 / Net I/σ(I): 16.684
Reflection shellResolution: 1.73→1.83 Å / Rmerge(I) obs: 2.498 / Mean I/σ(I) obs: 1.63 / Num. unique obs: 2143 / CC1/2: 0.6201 / Rpim(I) all: 0.492 / Rrim(I) all: 2.547 / % possible all: 25.31

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DYG

5dyg


Resolution: 1.73→47.87 Å / SU ML: 0.188 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.0693
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2353 2155 5.02 %
Rwork0.192 40749 -
obs0.1942 42904 77.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.26 Å2
Refinement stepCycle: LAST / Resolution: 1.73→47.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3487 0 94 255 3836
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063755
X-RAY DIFFRACTIONf_angle_d0.88525074
X-RAY DIFFRACTIONf_chiral_restr0.0513571
X-RAY DIFFRACTIONf_plane_restr0.0051667
X-RAY DIFFRACTIONf_dihedral_angle_d14.54871484
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.770.3187340.2867662X-RAY DIFFRACTION19.17
1.77-1.820.323560.2741009X-RAY DIFFRACTION29.12
1.82-1.860.3072590.25231298X-RAY DIFFRACTION37.47
1.86-1.920.30641020.2551698X-RAY DIFFRACTION49.17
1.92-1.980.23841130.23222056X-RAY DIFFRACTION59.57
1.98-2.050.2781290.22932515X-RAY DIFFRACTION72.12
2.05-2.130.23271730.21723079X-RAY DIFFRACTION88.61
2.13-2.230.24211930.20593346X-RAY DIFFRACTION96.35
2.23-2.350.25721790.193501X-RAY DIFFRACTION99.97
2.35-2.50.24881630.1923535X-RAY DIFFRACTION99.97
2.5-2.690.22332040.18883522X-RAY DIFFRACTION100
2.69-2.960.24951780.19923529X-RAY DIFFRACTION100
2.96-3.390.23921900.18043566X-RAY DIFFRACTION100
3.39-4.270.20692000.16133592X-RAY DIFFRACTION100
4.27-47.870.2321820.19783841X-RAY DIFFRACTION99.93

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