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

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Basic information

Entry
Database: PDB / ID: 1.0E+32
TitleStructure of the N-Terminal domain and the D1 AAA domain of membrane fusion ATPase p97
ComponentsP97
KeywordsATPASE / MEMBRANE FUSION
Function / homology
Function and homology information


RHOH GTPase cycle / HSF1 activation / Protein methylation / Translesion Synthesis by POLH / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Ovarian tumor domain proteases / Hedgehog ligand biogenesis / KEAP1-NFE2L2 pathway / ABC-family proteins mediated transport ...RHOH GTPase cycle / HSF1 activation / Protein methylation / Translesion Synthesis by POLH / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Ovarian tumor domain proteases / Hedgehog ligand biogenesis / KEAP1-NFE2L2 pathway / ABC-family proteins mediated transport / Neddylation / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / protein-DNA covalent cross-linking repair / endosome to lysosome transport via multivesicular body sorting pathway / positive regulation of ubiquitin-dependent protein catabolic process / 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 / regulation of protein localization to chromatin / NADH metabolic process / vesicle-fusing ATPase / : / positive regulation of mitochondrial membrane potential / stress granule disassembly / K48-linked polyubiquitin modification-dependent protein binding / 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 / positive regulation of ATP biosynthetic process / ubiquitin-specific protease binding / ubiquitin-like protein ligase binding / autophagosome maturation / polyubiquitin modification-dependent protein binding / translesion synthesis / endoplasmic reticulum to Golgi vesicle-mediated transport / MHC class I protein binding / interstrand cross-link repair / negative regulation of smoothened signaling pathway / ATP metabolic process / : / Neutrophil degranulation / proteasome complex / lipid droplet / viral genome replication / ADP binding / proteasomal protein catabolic process / positive regulation of protein-containing complex assembly / macroautophagy / autophagy / 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 / double-strand break repair / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / site of double-strand break / myelin sheath / cellular response to heat / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein phosphatase binding / protein ubiquitination / protein domain specific binding / DNA repair / lipid binding / glutamatergic synapse / synapse / DNA damage response / ubiquitin protein ligase binding / protein-containing complex binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / Barwin-like endoglucanases - #20 / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, CDC48 family / Barwin-like endoglucanases / Cell division protein 48 (CDC48), N-terminal domain / CDC48, N-terminal subdomain / 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 / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, CDC48 family / Barwin-like endoglucanases / 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 / 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
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.9 Å
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.
History
DepositionJun 5, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 22, 2019Group: Advisory / Data collection ...Advisory / Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status ...pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_residues / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: P97
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4552
Polymers51,0271
Non-polymers4271
Water91951
1
A: P97
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)308,72812
Polymers306,1656
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
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-MP622

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Components

#1: Protein P97


Mass: 51027.477 Da / Num. of mol.: 1
Fragment: N TERMINAL DOMAIN AND D1 AAA DOMAIN, RESIDUES 1-458
Source method: isolated from a genetically manipulated source
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 / Adenosine diphosphate


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


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.56 Å3/Da / Density % 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
IDConc.Common nameCrystal-IDSol-ID
116 mg/mlprotein1drop
23.8-4.2 Msodium formate1reservoir
310 %glycerol1reservoir
45 %PEG6001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 12114 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 19 % / Biso Wilson estimate: 39.9 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 9.7
Reflection shellResolution: 2.9→3 Å / Redundancy: 15 % / Rmerge(I) obs: 0.3 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 30 Å / Redundancy: 19.3 % / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
Rmerge(I) obs: 0.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
SOLVEphasing
CNS0.5refinement
RefinementMethod to determine structure: MIRAS / Resolution: 2.9→15 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 2
Details: RES 337 AND 338 HAVE ZERO OCCUPACIES AND REGIONS BETWEEN 312-317, 432-437 HAVE POOR ELECTRON DENSITI
RfactorNum. reflection% reflectionSelection details
Rfree0.283 1188 10 %RANDOM
Rwork0.224 ---
obs0.224 11808 97 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 33 Å2
Baniso -1Baniso -2Baniso -3
1-14.293 Å2-2.283 Å20 Å2
2--14.293 Å20 Å2
3----28.587 Å2
Refinement stepCycle: LAST / Resolution: 2.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3336 0 27 51 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
LS refinement shellResolution: 2.9→3.03 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 8 /
RfactorNum. reflection
Rfree0.351 106
Rwork0.278 1192

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