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- PDB-9m4n: Structure of AtCDC48 -

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Basic information

Entry
Database: PDB / ID: 9m4n
TitleStructure of AtCDC48
ComponentsCell division control protein 48 homolog A
KeywordsPLANT PROTEIN / AAA ATPase / Hexamer / ATP-dependent chaperone / Protein unfollding
Function / homology
Function and homology information


pollen germination / pollen tube growth / negative regulation of defense response / phragmoplast / plant-type cell wall / plasmodesma / lipid droplet / cytosolic ribosome / protein destabilization / spindle ...pollen germination / pollen tube growth / negative regulation of defense response / phragmoplast / plant-type cell wall / plasmodesma / lipid droplet / cytosolic ribosome / protein destabilization / spindle / nuclear envelope / protein transport / cell division / nucleolus / Golgi apparatus / ATP hydrolysis activity / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 ...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 / 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Cell division control protein 48 homolog A
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 Å
AuthorsSandholu, A.S. / Zhang, J. / Brandon, Z.H. / Hameed, U.F.S. / Arold, S.T.
Funding support Saudi Arabia, 2items
OrganizationGrant numberCountry
Other privateURF/1/4039-01-01 Saudi Arabia
Other privateURF/1/4080-01-01 Saudi Arabia
CitationJournal: Plant Commun / Year: 2026
Title: Cryo-EM structural analyses reveal plant-specific adaptations of the CDC48 unfoldase.
Authors: Brandon Huntington / Anandsukeerthi Sandholu / Jun Wang / Junrui Zhang / Lingyun Zhao / Bilal M Qureshi / Umar F Shahul Hameed / Stefan T Arold /
Abstract: Targeted protein degradation through the CDC48 unfoldase enables the maintenance and rapid adaptation of proteomes across eukaryotes. However, the substantial differences among animals, fungi, and ...Targeted protein degradation through the CDC48 unfoldase enables the maintenance and rapid adaptation of proteomes across eukaryotes. However, the substantial differences among animals, fungi, and plants presumably drove extensive adaptation of CDC48-mediated degradation. Although animal and fungal CDC48 systems have shown structural and functional preservation, comparable analysis has been lacking for plants. We determined the structural and functional characteristics of Arabidopsis thaliana CDC48A in multiple states and in complex with the target-identifying cofactors UFD1 and NPL4. Our analysis revealed several features that distinguish AtCDC48A from its animal and yeast counterparts despite 80% sequence identity. Key findings include that AtCDC48A exhibits distinct domain dynamics and engages AtNPL4 in a unique manner. Moreover, AtNPL4 and AtUFD1 do not form an obligate heterodimer; instead, AtNPL4 can independently bind to AtCDC48A and mediate target degradation, although their combined action is synergistic. An evolutionary analysis indicates that these Arabidopsis features are conserved across plants and represent the ancestral state of eukaryotic CDC48 systems. Collectively, our findings suggest that plant CDC48 retains a more modular and combinatorial mode of cofactor usage, highlighting a specific adaptation of targeted protein degradation in plants.
History
DepositionMar 4, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell division control protein 48 homolog A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,5663
Polymers86,7111
Non-polymers8542
Water1629
1
A: Cell division control protein 48 homolog A
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)525,39318
Polymers520,2676
Non-polymers5,12612
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 area41860 Å2
ΔGint-97 kcal/mol
Surface area185570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.467, 144.467, 162.963
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 Cell division control protein 48 homolog A / AtCDC48a


Mass: 86711.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CDC48A, CDC48, At3g09840, F8A24.11 / Production host: Escherichia coli (E. coli) / References: UniProt: P54609
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.92 Å3/Da / Density % sol: 57.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100mM HEPES, 20mM magnesium chloride hexahydrate, 22% poly acrylic acid 5100, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980118 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980118 Å / Relative weight: 1
ReflectionResolution: 3.45→47.29 Å / Num. obs: 13805 / % possible obs: 100 % / Redundancy: 31.8 % / Biso Wilson estimate: 85.93 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.62 / Rpim(I) all: 0.15 / Rrim(I) all: 0.64 / Net I/σ(I): 8.4
Reflection shellResolution: 3.45→3.73 Å / Redundancy: 32.5 % / Rmerge(I) obs: 3.77 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 13799 / CC1/2: 0.32 / Rpim(I) all: 0.92 / Rrim(I) all: 3.88

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.45→47.29 Å / SU ML: 0.85 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 51.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3838 701 5.08 %
Rwork0.3461 --
obs0.3482 13799 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.45→47.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5132 0 55 9 5196
Refine LS restraintsType: f_plane_restr / Dev ideal: 0.006 / Number: 925
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.45-3.720.4761360.46422547X-RAY DIFFRACTION100
3.72-4.090.45331250.41382572X-RAY DIFFRACTION100
4.09-4.680.38931480.35672564X-RAY DIFFRACTION100
4.68-5.90.41381400.36092620X-RAY DIFFRACTION100

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