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- PDB-9yrc: p97Ufd1-Npl4 complex processing poly-ubiquitinated substrate in t... -

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Basic information

Entry
Database: PDB / ID: 9yrc
Titlep97Ufd1-Npl4 complex processing poly-ubiquitinated substrate in the presence of ATP
Components
  • Nuclear protein localization protein 4 homolog
  • Transitional endoplasmic reticulum ATPase
  • Ubiquitin
  • Ubiquitin recognition factor in ER-associated degradation protein 1
KeywordsTRANSLOCASE / p97 / VCP / AAA+ ATPase
Function / homology
Function and homology information


UFD1-NPL4 complex / negative regulation of RIG-I signaling pathway / flavin adenine dinucleotide catabolic process / VCP-NSFL1C complex / endoplasmic reticulum stress-induced pre-emptive quality control / endosome to lysosome transport via multivesicular body sorting pathway / cytoplasmic ubiquitin ligase complex / BAT3 complex binding / cellular response to arsenite ion / protein-DNA covalent cross-linking repair ...UFD1-NPL4 complex / negative regulation of RIG-I signaling pathway / flavin adenine dinucleotide catabolic process / VCP-NSFL1C complex / endoplasmic reticulum stress-induced pre-emptive quality control / endosome to lysosome transport via multivesicular body sorting pathway / cytoplasmic ubiquitin ligase complex / BAT3 complex binding / cellular response to arsenite ion / protein-DNA covalent cross-linking repair / Derlin-1 retrotranslocation complex / positive regulation of protein K63-linked deubiquitination / deubiquitinase activator activity / cytoplasm protein quality control / positive regulation of oxidative phosphorylation / aggresome assembly / ubiquitin-modified protein reader activity / regulation of protein localization to chromatin / cellular response to misfolded protein / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / positive regulation of mitochondrial membrane potential / vesicle-fusing ATPase / K48-linked polyubiquitin modification-dependent protein binding / nuclear outer membrane-endoplasmic reticulum membrane network / K63-linked polyubiquitin modification-dependent protein binding / regulation of aerobic respiration / retrograde protein transport, ER to cytosol / NAD+ metabolic process / stress granule disassembly / negative regulation of type I interferon production / ciliary transition zone / ATPase complex / ubiquitin-specific protease binding / regulation of synapse organization / Golgi organization / positive regulation of ATP biosynthetic process / ubiquitin-like protein ligase binding / RHOH GTPase cycle / MHC class I protein binding / polyubiquitin modification-dependent protein binding / autophagosome maturation / ribosomal large subunit export from nucleus / endoplasmic reticulum to Golgi vesicle-mediated transport / negative regulation of hippo signaling / HSF1 activation / interstrand cross-link repair / ATP metabolic process / translesion synthesis / Attachment and Entry / endoplasmic reticulum unfolded protein response / Protein methylation / ERAD pathway / negative regulation of protein localization to chromatin / proteasomal protein catabolic process / lipid droplet / ciliary tip / proteasome complex / viral genome replication / Josephin domain DUBs / skeletal system development / intracellular membrane-bounded organelle / ubiquitin binding / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / macroautophagy / negative regulation of smoothened signaling pathway / establishment of protein localization / positive regulation of protein-containing complex assembly / Hh mutants are degraded by ERAD / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Translesion Synthesis by POLH / ADP binding / positive regulation of non-canonical NF-kappaB signal transduction / ABC-family proteins mediated transport / modification-dependent protein catabolic process / autophagy / protein tag activity / cytoplasmic stress granule / Aggrephagy / azurophil granule lumen / positive regulation of protein catabolic process / Ovarian tumor domain proteases / KEAP1-NFE2L2 pathway / positive regulation of canonical Wnt signaling pathway / double-strand break repair / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / E3 ubiquitin ligases ubiquitinate target proteins / cellular response to heat / site of double-strand break / ribosome biogenesis / ATPase binding / Neddylation / ribosomal large subunit assembly / secretory granule lumen / protein phosphatase binding / regulation of apoptotic process / ficolin-1-rich granule lumen / cytosolic large ribosomal subunit / ubiquitin-dependent protein catabolic process
Similarity search - Function
Nuclear pore localisation protein Npl4, ubiquitin-like domain / Nuclear pore localisation protein NPL4 / Ubiquitin fusion degradation protein Ufd1-like / Ufd1-like, Nn domain / : / : / Ubiquitin fusion degradation protein UFD1, N-terminal subdomain 1 / Ubiquitin fusion degradation protein UFD1, N-terminal subdomain 2 / NPL4, zinc-binding putative / NPL4 family, putative zinc binding region ...Nuclear pore localisation protein Npl4, ubiquitin-like domain / Nuclear pore localisation protein NPL4 / Ubiquitin fusion degradation protein Ufd1-like / Ufd1-like, Nn domain / : / : / Ubiquitin fusion degradation protein UFD1, N-terminal subdomain 1 / Ubiquitin fusion degradation protein UFD1, N-terminal subdomain 2 / NPL4, zinc-binding putative / NPL4 family, putative zinc binding region / Nuclear pore localisation protein NPL4, C-terminal / Nuclear protein localization protein 4 / NPL4 family / Zinc finger domain / 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 / Zinc finger RanBP2 type profile. / CDC48 domain 2-like superfamily / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / Aspartate decarboxylase-like domain superfamily / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / MPN domain / AAA ATPase, AAA+ lid domain / AAA+ lid domain / MPN domain profile. / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / 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
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Ubiquitin-ribosomal protein eL40A fusion protein / Transitional endoplasmic reticulum ATPase / Nuclear protein localization protein 4 homolog / Ubiquitin recognition factor in ER-associated degradation protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsLi, H. / Rapoport, T.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Sci Rep / Year: 2026
Title: The deubiquitinating enzyme Otu1 releases substrates from the conserved initiation complex of the Cdc48/p97 ATPase for proteasomal degradation.
Authors: Li, H. / Guan, H. / Rapoport, T.A.
History
DepositionOct 16, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transitional endoplasmic reticulum ATPase
B: Transitional endoplasmic reticulum ATPase
C: Transitional endoplasmic reticulum ATPase
D: Transitional endoplasmic reticulum ATPase
E: Transitional endoplasmic reticulum ATPase
F: Transitional endoplasmic reticulum ATPase
G: Nuclear protein localization protein 4 homolog
H: Ubiquitin recognition factor in ER-associated degradation protein 1
I: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)653,26920
Polymers647,9309
Non-polymers5,33911
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: immunoprecipitation, IP experiments verifies the hexameric assembly of p97.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 4 types, 9 molecules ABCDEFGHI

#1: Protein
Transitional endoplasmic reticulum ATPase / TER ATPase / 15S Mg(2+)-ATPase p97 subunit / Valosin-containing protein / VCP


Mass: 89435.828 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VCP, HEL-220, HEL-S-70 / Production host: Escherichia coli (E. coli) / References: UniProt: P55072, vesicle-fusing ATPase
#2: Protein Nuclear protein localization protein 4 homolog / Protein NPL4


Mass: 68202.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NPLOC4, KIAA1499, NPL4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TAT6
#3: Protein Ubiquitin recognition factor in ER-associated degradation protein 1 / Ubiquitin fusion degradation protein 1 / UB fusion protein 1


Mass: 34544.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UFD1, UFD1L / Production host: Escherichia coli (E. coli) / References: UniProt: Q92890
#4: Protein Ubiquitin


Mass: 8568.769 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPL40A, UBI1, YIL148W / Production host: Escherichia coli (E. coli) / References: UniProt: P0CH08

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Non-polymers , 2 types, 11 molecules

#5: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: p97-Ufd1-Npl4 complex processing poly-ubiquitinated substrate in the presence of ATP
Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightValue: 0.8 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.19.2_4158model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 65959 / Symmetry type: POINT
RefinementHighest resolution: 2.97 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00528650
ELECTRON MICROSCOPYf_angle_d0.76738752
ELECTRON MICROSCOPYf_dihedral_angle_d7.5653902
ELECTRON MICROSCOPYf_chiral_restr0.0474314
ELECTRON MICROSCOPYf_plane_restr0.0055064

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