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- PDB-6hd3: Common mode of remodeling AAA ATPases p97/CDC48 by their disassem... -

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Basic information

Entry
Database: PDB / ID: 6hd3
TitleCommon mode of remodeling AAA ATPases p97/CDC48 by their disassembly cofactors ASPL/PUX1
ComponentsCell division control protein 48 homolog A
KeywordsPLANT PROTEIN / ATPase / Arabidopsis thaliana / CDC48 / hexamer
Function / homology
Function and homology information


pollen germination / : / pollen tube growth / negative regulation of defense response / phragmoplast / : / plasmodesma / cell wall / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex ...pollen germination / : / pollen tube growth / negative regulation of defense response / phragmoplast / : / plasmodesma / cell wall / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / retrograde protein transport, ER to cytosol / autophagosome maturation / polyubiquitin modification-dependent protein binding / cytosolic ribosome / response to cadmium ion / lipid droplet / protein destabilization / spindle / nuclear envelope / hydrolase activity / cell division / nucleolus / Golgi apparatus / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Cell division control protein 48 homolog A
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHeinemann, U. / Roske, Y. / Banchenko, S. / Arumughan, A. / Petrovic, S.
CitationJournal: Structure / Year: 2019
Title: Common Mode of Remodeling AAA ATPases p97/CDC48 by Their Disassembling Cofactors ASPL/PUX1.
Authors: Banchenko, S. / Arumughan, A. / Petrovic, S. / Schwefel, D. / Wanker, E.E. / Roske, Y. / Heinemann, U.
History
DepositionAug 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 11, 2019Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Jan 17, 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: Cell division control protein 48 homolog A
C: Cell division control protein 48 homolog A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,4827
Polymers107,3422
Non-polymers1,1395
Water1,72996
1
A: Cell division control protein 48 homolog A
C: Cell division control protein 48 homolog A
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)1,301,78084
Polymers1,288,10824
Non-polymers13,67260
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_885-y+3,x-y+3,z1
crystal symmetry operation3_585-x+y,-x+3,z1
crystal symmetry operation4_795-x+2,-y+4,z1
crystal symmetry operation5_465y-1,-x+y+1,z1
crystal symmetry operation6_765x-y+2,x+1,z1
crystal symmetry operation7_466y-1,x+1,-z+11
crystal symmetry operation8_796x-y+2,-y+4,-z+11
crystal symmetry operation9_766-x+2,-x+y+1,-z+11
crystal symmetry operation10_886-y+3,-x+3,-z+11
crystal symmetry operation11_556-x+y,y,-z+11
crystal symmetry operation12_586x,x-y+3,-z+11
Buried area125690 Å2
ΔGint-513 kcal/mol
Surface area438680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.266, 146.266, 173.133
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number177
Space group name H-MP622

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Components

#1: Protein Cell division control protein 48 homolog A / AtCDC48a


Mass: 53671.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CDC48A, CDC48, At3g09840, F8A24.11 / Plasmid: pQlinkH / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / Variant (production host): DE3 / References: UniProt: P54609
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 50.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.9 / Details: 1.8M Na/K phosphate pH 6.9; 50mM KCL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.8→47.9 Å / Num. obs: 27532 / % possible obs: 99.6 % / Redundancy: 12.84 % / CC1/2: 0.998 / Rrim(I) all: 0.0242 / Net I/σ(I): 11.44
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 0.98 / Num. unique obs: 2673 / CC1/2: 0.628 / Rrim(I) all: 0.258 / % possible all: 99.3

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S3S

1s3s


Resolution: 2.8→47.88 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.888 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.371
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1377 5 %RANDOM
Rwork0.219 ---
obs0.221 27531 99.7 %-
Displacement parametersBiso max: 191.66 Å2 / Biso mean: 95.37 Å2 / Biso min: 24.43 Å2
Baniso -1Baniso -2Baniso -3
1-16.5246 Å20 Å20 Å2
2--16.5246 Å20 Å2
3----33.0493 Å2
Refine analyzeLuzzati coordinate error obs: 0.49 Å
Refinement stepCycle: final / Resolution: 2.8→47.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6925 0 69 96 7090
Biso mean--87.66 59.06 -
Num. residues----885
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2600SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1240HARMONIC5
X-RAY DIFFRACTIONt_it7109HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion936SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8098SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7109HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg9606HARMONIC3.20.79
X-RAY DIFFRACTIONt_omega_torsion2.5
X-RAY DIFFRACTIONt_other_torsion21.95
LS refinement shellResolution: 2.8→2.9 Å / Rfactor Rfree error: 0 / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.3468 141 5 %
Rwork0.2839 2681 -
all0.2869 2822 -
obs--99.12 %
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)
12.43791.34650.30812.53530.16820.74330.11360.0132-0.1540.1548-0.02990.00950.056-0.1462-0.0837-0.34160.0093-0.0053-0.3311-0.0350.4874-39.3043-25.815963.0104
23.11710.2995-0.48012.4913-0.29920.99990.07920.2428-0.1767-0.31220.05890.3148-0.0166-0.2436-0.1382-0.10250.0316-0.0231-0.0442-0.0284-0.2195-44.4889-15.120226.9928
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A15 - 471
2X-RAY DIFFRACTION2{ C|* }C25 - 463

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