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- EMDB-63608: Arabidopsis thaliana CDC48A, nucleotide-free (Apo) -

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Basic information

Entry
Database: EMDB / ID: EMD-63608
TitleArabidopsis thaliana CDC48A, nucleotide-free (Apo)
Map dataSharpened map from Relion PostProcess. Used for final model refinements.
Sample
  • Complex: Arabidopsis thaliana CDC48A, nucleotide-free (Apo)
    • Protein or peptide: Cell division control protein 48 homolog A
KeywordsTargeted protein degradation / plant protein quality control / AAA+ ATPase / cryo-EM / adaptation / ubiquitin-proteasome system / PLANT PROTEIN
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
Cell division control protein 48 homolog A
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsHuntington B / Arold ST
Funding support Saudi Arabia, 2 items
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 3, 2025-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63608.png

Downloads & links

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Map

FileDownload / File: emd_63608.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map from Relion PostProcess. Used for final model refinements.
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 320 pix.
= 332.8 Å		1.04 Å/pix.
x 320 pix.
= 332.8 Å		1.04 Å/pix.
x 320 pix.
= 332.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.004
Minimum - Maximum-0.029720299 - 0.05270368
Average (Standard dev.)0.00008109617 (±0.0010323644)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 332.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63608_msk_1.map
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Additional map: EMReady post-processed map for initial model building

Fileemd_63608_additional_1.map
AnnotationEMReady post-processed map for initial model building
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Half map: Half Map 1

Fileemd_63608_half_map_1.map
AnnotationHalf Map 1
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Histogram

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Half map: Half Map 2

Fileemd_63608_half_map_2.map
AnnotationHalf Map 2
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Sample components

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Entire : Arabidopsis thaliana CDC48A, nucleotide-free (Apo)

EntireName: Arabidopsis thaliana CDC48A, nucleotide-free (Apo)
Components
  • Complex: Arabidopsis thaliana CDC48A, nucleotide-free (Apo)
    • Protein or peptide: Cell division control protein 48 homolog A

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Supramolecule #1: Arabidopsis thaliana CDC48A, nucleotide-free (Apo)

SupramoleculeName: Arabidopsis thaliana CDC48A, nucleotide-free (Apo) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Cell division control protein 48 homolog A

MacromoleculeName: Cell division control protein 48 homolog A / type: protein_or_peptide / ID: 1 / Details: GST Tag / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 89.922844 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GPLGSMSTPA ESSDSKSKKD FSTAILERKK SPNRLVVDEA INDDNSVVSL HPATMEKLQL FRGDTILIKG KKRKDTVCIA LADETCEEP KIRMNKVVRS NLRVRLGDVI SVHQCPDVKY GKRVHILPVD DTVEGVTGNL FDAYLKPYFL EAYRPVRKGD L FLVRGGMR ...String:
GPLGSMSTPA ESSDSKSKKD FSTAILERKK SPNRLVVDEA INDDNSVVSL HPATMEKLQL FRGDTILIKG KKRKDTVCIA LADETCEEP KIRMNKVVRS NLRVRLGDVI SVHQCPDVKY GKRVHILPVD DTVEGVTGNL FDAYLKPYFL EAYRPVRKGD L FLVRGGMR SVEFKVIETD PAEYCVVAPD TEIFCEGEPV KREDEERLDD VGYDDVGGVR KQMAQIRELV ELPLRHPQLF KS IGVKPPK GILLYGPPGS GKTLIARAVA NETGAFFFCI NGPEIMSKLA GESESNLRKA FEEAEKNAPS IIFIDEIDSI APK REKTNG EVERRIVSQL LTLMDGLKSR AHVIVMGATN RPNSIDPALR RFGRFDREID IGVPDEIGRL EVLRIHTKNM KLAE DVDLE RISKDTHGYV GADLAALCTE AALQCIREKM DVIDLEDDSI DAEILNSMAV TNEHFHTALG NSNPSALRET VVEVP NVSW NDIGGLENVK RELQETVQYP VEHPEKFEKF GMSPSKGVLF YGPPGCGKTL LAKAIANECQ ANFISVKGPE LLTMWF GES EANVREIFDK ARQSAPCVLF FDELDSIATQ RGGGSGGDGG GAADRVLNQL LTEMDGMNAK KTVFIIGATN RPDIIDS AL LRPGRLDQLI YIPLPDEDSR LNIFKAALRK SPIAKDVDIG ALAKYTQGFS GADITEICQR ACKYAIRENI EKDIEKEK R RSENPEAMEE DGVDEVSEIK AAHFEESMKY ARRSVSDADI RKYQAFAQTL QQSRGFGSEF RFENSAGSGA TTGVADPFA TSAAAAGDDD DLYN

UniProtKB: Cell division control protein 48 homolog A

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.0 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPESHEPES
150.0 mMNaClSodium Chloride
1.0 mMTCEPTCEP
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 1263 / Average exposure time: 5.6 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 210000
CTF correctionSoftware - Name: RELION / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: CryoSPARC Ab initio
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 73000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationNumber classes: 6 / Details: 3D Classification without Alignment
FSC plot (resolution estimation)

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