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- EMDB-63609: Arabidopsis thaliana CDC48A bound to AMP-PNP (AMPPNP-Up) -

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Basic information

Entry
Database: EMDB / ID: EMD-63609
TitleArabidopsis thaliana CDC48A bound to AMP-PNP (AMPPNP-Up)
Map dataSharpened map from Relion PostProcess. Used for final model refinements.
Sample
  • Complex: Arabidopsis thaliana Cell Division Cycle Protein 48 with AMPPNP
    • Protein or peptide: Cell division control protein 48 homolog A
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
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: 3.2 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_63609.png

Downloads & links

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Map

FileDownload / File: emd_63609.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.)
1.14 Å/pix.
x 320 pix.
= 364. Å		1.14 Å/pix.
x 320 pix.
= 364. Å		1.14 Å/pix.
x 320 pix.
= 364. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1375 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007
Minimum - Maximum-0.0546803 - 0.10837232
Average (Standard dev.)0.000112643414 (±0.0017116517)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 364.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63609_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_63609_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_63609_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_63609_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 Cell Division Cycle Protein 48 with AMPPNP

EntireName: Arabidopsis thaliana Cell Division Cycle Protein 48 with AMPPNP
Components
  • Complex: Arabidopsis thaliana Cell Division Cycle Protein 48 with AMPPNP
    • Protein or peptide: Cell division control protein 48 homolog A
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Arabidopsis thaliana Cell Division Cycle Protein 48 with AMPPNP

SupramoleculeName: Arabidopsis thaliana Cell Division Cycle Protein 48 with AMPPNP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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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Macromolecule #2: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 2 / Number of copies: 12 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 12 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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
2.0 mMAMPPNPAdenylyl-imidodiphosphate
2.0 mMMgCl2Magnesium Chloride
GridModel: C-flat-1.2/1.3 / Material: GOLD / 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
DetailsArabidopsis thaliana CDC48A with AMPPPNP(AMPPNP-Up)

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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: 2 / Number real images: 3379 / 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: 1188006
CTF correctionSoftware - Name: RELION / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 133000
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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