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- EMDB-63612: Arabidopsis thaliana CDC48A-NPL4-UFD1B (AtCNU) complex -

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Basic information

Entry
Database: EMDB / ID: EMD-63612
TitleArabidopsis thaliana CDC48A-NPL4-UFD1B (AtCNU) complex
Map dataSharpened map from Relion PostProcess. Used for final model refinements.
Sample
  • Complex: Ternary Complex of Arabidopsis thaliana CDC48A with NPL4 and UFD1
    • Protein or peptide: Cell division control protein 48 homolog A
    • Protein or peptide: NPL4-like protein 2
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Keywordsp97/VCP/CDC48 / AAA+ ATPase / Ubiquitin-proteasome / Unfoldase / 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 / proteasome-mediated ubiquitin-dependent protein catabolic process / cell division / nucleolus / Golgi apparatus / ATP hydrolysis activity / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Nuclear pore localisation protein Npl4, ubiquitin-like domain / Nuclear pore localisation protein NPL4 / Nuclear pore localisation protein NPL4, C-terminal / Nuclear protein localization protein 4 / NPL4 family / AAA ATPase, CDC48 family / Cell division protein 48 (CDC48), N-terminal domain / : / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain ...Nuclear pore localisation protein Npl4, ubiquitin-like domain / Nuclear pore localisation protein NPL4 / Nuclear pore localisation protein NPL4, C-terminal / Nuclear protein localization protein 4 / NPL4 family / 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 / MPN domain / MPN domain profile. / 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 / Ubiquitin-like domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
NPL4-like protein 2 / 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_63612.png

Downloads & links

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Map

FileDownload / File: emd_63612.map.gz / Format: CCP4 / Size: 178 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.)
1.17 Å/pix.
x 360 pix.
= 422.399 Å		1.17 Å/pix.
x 360 pix.
= 422.399 Å		1.17 Å/pix.
x 360 pix.
= 422.399 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.17333 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.050015908 - 0.07893134
Average (Standard dev.)0.00006719155 (±0.001024008)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 422.39877 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63612_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_63612_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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Additional map: Unsharpened map from Relion Refine3D

Fileemd_63612_additional_2.map
AnnotationUnsharpened map from Relion Refine3D
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 1

Fileemd_63612_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_63612_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 : Ternary Complex of Arabidopsis thaliana CDC48A with NPL4 and UFD1

EntireName: Ternary Complex of Arabidopsis thaliana CDC48A with NPL4 and UFD1
Components
  • Complex: Ternary Complex of Arabidopsis thaliana CDC48A with NPL4 and UFD1
    • Protein or peptide: Cell division control protein 48 homolog A
    • Protein or peptide: NPL4-like protein 2
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Ternary Complex of Arabidopsis thaliana CDC48A with NPL4 and UFD1

SupramoleculeName: Ternary Complex of Arabidopsis thaliana CDC48A with NPL4 and UFD1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: Equimolar concentrations of CDC48A, NPL4, and UFD1B were incubated with AMPPNP, crosslinked with glutaraldehyde, and purified through SEC with a buffer containing ATP.
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 / 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: NPL4-like protein 2

MacromoleculeName: NPL4-like protein 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 46.634145 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GPLGSMMMLR IRSRDGLERV TAEGAHITVS QLKTLIADQL QIPLHKQTLS TNRDLLLAKT PADLLAFTDL TDPNLPLSSL NLGHGSMLY LAYDGERSIP GAPPVTPAGS FGRKMTVDDL IARQMRVTRQ ETSHCDSVSF DRDAANAFQH YVNESLAFAV K RGGFMYGT ...String:
GPLGSMMMLR IRSRDGLERV TAEGAHITVS QLKTLIADQL QIPLHKQTLS TNRDLLLAKT PADLLAFTDL TDPNLPLSSL NLGHGSMLY LAYDGERSIP GAPPVTPAGS FGRKMTVDDL IARQMRVTRQ ETSHCDSVSF DRDAANAFQH YVNESLAFAV K RGGFMYGT VTEEGQVEVD FIYEPPQQGT EANLILMRDA DEEKRVDAIA MGLGMRRVGF IFNQTVVQDK TEYTLSNAEV LQ AAELHAE SELKEWVTAV VKLEVNEDGG ADVHFEAFQM SDMCIRLFKE EWFETEIMPD DDPKLSKMKK EVVVGVKDLK EVD NDFFLV LVRILDHQGP LSSTFPIENR SSRATMRALK THLDRAKSLP LVKKMSDFHL LLFVAQFLDV SSDVPALAEC VRLQ SPVPE GYALLIESMA NTC

UniProtKB: NPL4-like protein 2

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Macromolecule #3: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 6 / 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 #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 6 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 6 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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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

Concentration1.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPESHEPES
150.0 mMNaClSodium Chloride
1.0 mMTCEPTCEP
100.0 uMATPAdenosine triphosphate
2.0 mMMgCl2Magnesium Chloride

Details: Buffer for complex formation: 20 mM HEPES, 150 mM NaCl, 1 mM TCEP, 2 mM MgCl2, 2 mM AMPPNP. Buffer for SEC:20 mM HEPES, 150 mM NaCl, 1 mM TCEP, 2 mM MgCl2, 100 uM ATP.
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
DetailsEquimolar concentrations of CDC48A, NPL4, and UFD1B were incubated with 2 mM AMPPNP, crosslinked with 0.025% glutaraldehyde, and purified through SEC with a buffer containing 100 uM ATP.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 15984 / Average exposure time: 3.0 sec. / Average electron dose: 66.0 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: 2.6 µm / Nominal defocus min: 0.8 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: 3421602
CTF correctionSoftware - Name: RELION / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 199000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Software - details: NU-Refinement / Details: NU-Refinement with C6 symmetry relaxation
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationNumber classes: 4 / Software - Name: RELION / Software - details: Class3D w/o image alignments / Details: 3D Classification without alignment
FSC plot (resolution estimation)

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