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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 / cytoplasm / cytosol
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: To Be Published
Title: Plant-specific adaptations of the CDC48 unfoldase
Authors: Huntington B / Sandholu A / Wang J / Zhang J / Zhao L / Qureshi BM / Hameed UFS / Arold ST
History
DepositionMar 3, 2025-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing 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
Contrast
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

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
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 1

Fileemd_63608_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 2

Fileemd_63608_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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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