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- PDB-1e32: Structure of the N-Terminal domain and the D1 AAA domain of membr... -

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Entry
Database: PDB / ID: 1e32
TitleStructure of the N-Terminal domain and the D1 AAA domain of membrane fusion ATPase p97
ComponentsP97
KeywordsATPASE / MEMBRANE FUSION
Function / homologyAAA+ lid domain / Cell division protein 48 (CDC48), domain 2 / CDC48, N-terminal subdomain / AAA+ ATPase domain / ATPase, AAA-type, core / ATPase, AAA-type, conserved site / CDC48, domain 2 / Aspartate decarboxylase-like domain superfamily / Vps4 oligomerisation, C-terminal / P-loop containing nucleoside triphosphate hydrolase ...AAA+ lid domain / Cell division protein 48 (CDC48), domain 2 / CDC48, N-terminal subdomain / AAA+ ATPase domain / ATPase, AAA-type, core / ATPase, AAA-type, conserved site / CDC48, domain 2 / Aspartate decarboxylase-like domain superfamily / Vps4 oligomerisation, C-terminal / P-loop containing nucleoside triphosphate hydrolase / CDC48 domain 2-like superfamily / ATPase family associated with various cellular activities (AAA) / Cell division protein 48 (CDC48), N-terminal domain / AAA ATPase, CDC48 family / Josephin domain DUBs / Protein methylation / AAA-protein family signature. / Translesion Synthesis by POLH / HSF1 activation / ABC-family proteins mediated transport / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Hedgehog ligand biogenesis / Vps4 C terminal oligomerisation domain / Ovarian tumor domain proteases / Neutrophil degranulation / flavin adenine dinucleotide catabolic process / ATPase complex / positive regulation of Lys63-specific deubiquitinase activity / positive regulation of protein K63-linked deubiquitination / VCP-NSFL1C complex / endoplasmic reticulum stress-induced pre-emptive quality control / mitotic spindle disassembly / deubiquitinase activator activity / K48-linked polyubiquitin modification-dependent protein binding / cellular response to arsenite ion / endosome to lysosome transport via multivesicular body sorting pathway / ER-associated misfolded protein catabolic process / positive regulation of oxidative phosphorylation / Derlin-1 retrotranslocation complex / ERAD pathway / VCP-NPL4-UFD1 AAA ATPase complex / BAT3 complex binding / NADH metabolic process / vesicle-fusing ATPase / aggresome assembly / retrograde protein transport, ER to cytosol / stress granule disassembly / positive regulation of ATP biosynthetic process / protein N-linked glycosylation via asparagine / positive regulation of mitochondrial membrane potential / regulation of aerobic respiration / autophagosome maturation / protein hexamerization / ubiquitin-specific protease binding / ubiquitin-like protein ligase binding / regulation of synapse organization / MHC class I protein binding / lipid droplet / polyubiquitin modification-dependent protein binding / positive regulation of protein complex assembly / viral genome replication / ATP metabolic process / proteasome complex / ubiquitin-dependent ERAD pathway / ADP binding / double-strand break repair / proteasomal protein catabolic process / macroautophagy / site of double-strand break / positive regulation of protein catabolic process / autophagy / cytoplasmic stress granule / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of canonical Wnt signaling pathway / activation of cysteine-type endopeptidase activity involved in apoptotic process / translesion synthesis / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitin-dependent protein catabolic process / cellular response to heat / endoplasmic reticulum to Golgi vesicle-mediated transport / protein homooligomerization / protein phosphatase binding / ATPase activity / protein ubiquitination / lipid binding / protein-containing complex binding / synapse / intracellular membrane-bounded organelle / myelin sheath / glutamatergic synapse / cellular response to DNA damage stimulus / endoplasmic reticulum membrane / protein domain specific binding / signaling receptor binding / ubiquitin protein ligase binding / endoplasmic reticulum / perinuclear region of cytoplasm / protein-containing complex / nucleoplasm / ATP binding
Function and homology information
Specimen sourceMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / 2.9 Å resolution
AuthorsZhang, X. / Shaw, A. / Bates, P.A. / Gorman, M.A. / Kondo, H. / Dokurno, P. / Leonard M, G. / Sternberg, J.E. / Freemont, P.S.
CitationJournal: Mol.Cell / Year: 2000
Title: Structure of the Aaa ATPase P97
Authors: Zhang, X. / Shaw, A. / Bates, P.A. / Newman, R.H. / Gowen, B. / Orlova, E. / Gorman, M.A. / Kondo, H. / Dokurno, P. / Lally, J. / Leonard, G. / Meyer, H. / Van Heel, M. / Freemont, P.S.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 5, 2000 / Release: May 31, 2001
RevisionDateData content typeGroupProviderType
1.0May 31, 2001Structure modelrepositoryInitial release
1.1May 8, 2011Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: P97
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4552
Polyers51,0271
Non-polymers4271
Water91951
1
A: P97
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)308,72812
Polyers306,1656
Non-polymers2,5636
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
MethodPQS
Unit cell
γ
α
β
Length a, b, c (Å)146.000, 146.000, 84.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP 6 2 2

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Components

#1: Protein/peptide P97


Mass: 51027.477 Da / Num. of mol.: 1
Fragment: N TERMINAL DOMAIN AND D1 AAA DOMAIN, RESIDUES 1-458
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ER2566 / References: UniProt: Q01853
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Formula: H2O / Water

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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: 2.56 / Density percent sol: 55 %
Crystal growpH: 6
Details: 3.8-4.2 M NAFORMATE, 10% GLYCEROL, 5% PEG600, PH 5.5-6.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 6 / PH range high: 5.5
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
116 mg/mlprotein1drop
23.8-4.2 Msodium formate1reservoir
310 %glycerol1reservoir
45 %PEG6001reservoir

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Data collection

DiffractionMean temperature: 1 kelvins
SourceSource: SYNCHROTRON / Type: EMBL/DESY, HAMBURG BEAMLINE X11 / Synchrotron site: EMBL/DESY, Hamburg / Beamline: X11 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Collection date: Sep 15, 1999
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 39.9 Å2 / D resolution high: 2.9 Å / D resolution low: 3 Å / Number obs: 12114 / Observed criterion sigma I: 2 / Rmerge I obs: 0.09 / Rsym value: 0.09 / NetI over sigmaI: 9.7 / Redundancy: 19 % / Percent possible obs: 99.8
Reflection shellRmerge I obs: 0.3 / Highest resolution: 2.9 Å / Lowest resolution: 3 Å / Redundancy: 15 % / Percent possible all: 1
Reflection
*PLUS
D resolution low: 3 Å / Rmerge I obs: 0.09 / Redundancy: 19.3 %
Reflection shell
*PLUS
Rmerge I obs: 0.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
SOLVEphasing
CNS0.5refinement
RefineMethod to determine structure: MIRAS
Details: RES 337 AND 338 HAVE ZERO OCCUPACIES AND REGIONS BETWEEN 312-317, 432-437 HAVE POOR ELECTRON DENSITI
R Free selection details: RANDOM / Data cutoff high absF: 10000 / Cross valid method: THROUGHTOUT / Sigma F: 2
Solvent computationSolvent model details: FLAT MODEL / Solvent model param bsol: 33 / Solvent model param ksol: 0.33
Displacement parametersB iso mean: 33 Å2 / Aniso B11: 14.293 Å2 / Aniso B12: -2.283 Å2 / Aniso B13: 0 Å2 / Aniso B22: 14.293 Å2 / Aniso B23: 0 Å2 / Aniso B33: -28.587 Å2
Least-squares processR factor R free: 0.283 / R factor R free error: 0.008 / R factor R work: 0.224 / R factor obs: 0.224 / Highest resolution: 2.9 Å / Lowest resolution: 15 Å / Number reflection R free: 1188 / Number reflection obs: 11808 / Percent reflection R free: 1 / Percent reflection obs: 97
Refine hist #LASTHighest resolution: 2.9 Å / Lowest resolution: 15 Å
Number of atoms included #LASTProtein: 3336 / Nucleic acid: 0 / Ligand: 27 / Solvent: 51 / Total: 3414
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0075
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.53
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS shellHighest resolution: 2.9 Å / R factor R free: 0.351 / R factor R free error: 0.034 / R factor R work: 0.278 / Lowest resolution: 3.03 Å / Number reflection R free: 106 / Number reflection R work: 1192 / Total number of bins used: 8

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