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- PDB-9yw2: Complex structure of human p97 bound to Faf1 and Ufd1 (NTD focused) -

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Basic information

Entry
Database: PDB / ID: 9yw2
TitleComplex structure of human p97 bound to Faf1 and Ufd1 (NTD focused)
Components
  • Glutathione S-transferase class-mu 26 kDa isozyme,FAS-associated factor 1
  • Transitional endoplasmic reticulum ATPase
  • Ubiquitin recognition factor in ER-associated degradation protein 1
KeywordsHYDROLASE / ATPase / p97 / AAA ATPase / ERAD / unfoldase / ubiquitin / segregase / VCP
Function / homology
Function and homology information


UFD1-NPL4 complex / Fas signaling pathway / negative regulation of RIG-I signaling pathway / ooplasm / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / CD95 death-inducing signaling complex / flavin adenine dinucleotide catabolic process / protein kinase regulator activity / VCP-NSFL1C complex / endoplasmic reticulum stress-induced pre-emptive quality control ...UFD1-NPL4 complex / Fas signaling pathway / negative regulation of RIG-I signaling pathway / ooplasm / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / CD95 death-inducing signaling complex / flavin adenine dinucleotide catabolic process / protein kinase regulator activity / VCP-NSFL1C complex / endoplasmic reticulum stress-induced pre-emptive quality control / endosome to lysosome transport via multivesicular body sorting pathway / BAT3 complex binding / cytoplasmic ubiquitin ligase complex / 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 / positive regulation of oxidative phosphorylation / cytoplasm protein quality control / aggresome assembly / ubiquitin-modified protein reader activity / regulation of protein localization to chromatin / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / cellular response to misfolded protein / positive regulation of mitochondrial membrane potential / vesicle-fusing ATPase / K48-linked polyubiquitin modification-dependent protein binding / regulation of aerobic respiration / NAD+ metabolic process / retrograde protein transport, ER to cytosol / stress granule disassembly / perinuclear theca / ATPase complex / negative regulation of type I interferon production / ubiquitin-specific protease binding / regulation of synapse organization / ciliary transition zone / glutathione transferase / regulation of protein catabolic process / positive regulation of ATP biosynthetic process / intracellular membrane-bounded organelle / ubiquitin-like protein ligase binding / RHOH GTPase cycle / glutathione transferase activity / MHC class I protein binding / autophagosome maturation / negative regulation of hippo signaling / HSF1 activation / endoplasmic reticulum to Golgi vesicle-mediated transport / polyubiquitin modification-dependent protein binding / NF-kappaB binding / regulation of cell adhesion / interstrand cross-link repair / ATP metabolic process / Attachment and Entry / translesion synthesis / negative regulation of protein localization to chromatin / Protein methylation / endoplasmic reticulum unfolded protein response / heat shock protein binding / ERAD pathway / proteasomal protein catabolic process / lipid droplet / acrosomal vesicle / ciliary tip / positive regulation of DNA replication / viral genome replication / proteasome complex / Josephin domain DUBs / negative regulation of canonical NF-kappaB signal transduction / skeletal system development / macroautophagy / glutathione metabolic process / ubiquitin binding / negative regulation of smoothened signaling pathway / establishment of protein localization / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / positive regulation of protein-containing complex assembly / ADP binding / Hh mutants are degraded by ERAD / Translesion Synthesis by POLH / positive regulation of non-canonical NF-kappaB signal transduction / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / autophagy / ABC-family protein mediated transport / cytoplasmic stress granule / Aggrephagy / positive regulation of protein catabolic process / azurophil granule lumen / Ovarian tumor domain proteases / nuclear envelope / KEAP1-NFE2L2 pathway / positive regulation of canonical Wnt signaling pathway / double-strand break repair / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / cellular response to heat / E3 ubiquitin ligases ubiquitinate target proteins
Similarity search - Function
FAS-associated factor 1-like, UBX domain / FAF1, UBA-like domain / : / Fas-associated factor 1 / UAS / : / UAS / Ubiquitin fusion degradation protein Ufd1-like / Ufd1-like, Nn domain / : ...FAS-associated factor 1-like, UBX domain / FAF1, UBA-like domain / : / Fas-associated factor 1 / UAS / : / UAS / 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 / Domain present in ubiquitin-regulatory proteins / UBX domain / UBX domain / UBX domain profile. / UBA-like domain / Glutathione S-transferase, C-terminal 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 / CDC48 domain 2-like superfamily / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal / Aspartate decarboxylase-like domain superfamily / Glutathione transferase family / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal 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 / Thioredoxin-like superfamily / 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
Glutathione S-transferase class-mu 26 kDa isozyme / Transitional endoplasmic reticulum ATPase / Ubiquitin recognition factor in ER-associated degradation protein 1 / FAS-associated factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsLiao, Z. / Arkinson, C. / Martin, A.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Cell Rep / Year: 2026
Title: Faf1 accelerates p97-mediated protein unfolding by promoting ubiquitin engagement.
Authors: Zengwei Liao / Connor Arkinson / Andreas Martin /
Abstract: P97/VCP is a protein unfoldase of the AAA+ ATPase family that plays essential roles in numerous processes, including ER-associated degradation and DNA replication. For unfolding of proteins modified ...P97/VCP is a protein unfoldase of the AAA+ ATPase family that plays essential roles in numerous processes, including ER-associated degradation and DNA replication. For unfolding of proteins modified with K48-linked ubiquitin chains, p97 works with the heterodimeric cofactor Ufd1-Npl4, and the cofactor Faf1 was shown to enhance this activity during replisome disassembly by unknown mechanisms. Here, we employ an in vitro reconstituted system with human components for biochemical experiments, FRET-based assays, and cryo-EM structure determination to reveal that Faf1 generally accelerates ubiquitin-dependent substrate processing by promoting the unfolding of an initiator ubiquitin and its engagement by the ATPase. Faf1 thereby uses its p97-bound C-terminal UBX domain to anchor a long helix that braces Ufd1's UT3 domain and stabilizes Ufd1-Npl4 for ubiquitin unfolding. Our findings demonstrate how p97 works simultaneously with several cofactors to facilitate the unfolding of ubiquitinated proteins, indicating more complex regulatory mechanisms than for the simpler yeast Cdc48.
History
DepositionOct 23, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transitional endoplasmic reticulum ATPase
H: Glutathione S-transferase class-mu 26 kDa isozyme,FAS-associated factor 1
I: Ubiquitin recognition factor in ER-associated degradation protein 1


Theoretical massNumber of molelcules
Total (without water)228,6443
Polymers228,6443
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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


Mass: 91177.781 Da / Num. of mol.: 1
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) / Strain (production host): Rosetta2 pLysS / References: UniProt: P55072, vesicle-fusing ATPase
#2: Protein Glutathione S-transferase class-mu 26 kDa isozyme,FAS-associated factor 1 / GST 26 / Sj26 antigen / SjGST / hFAF1 / UBX domain-containing protein 12 / UBX domain-containing protein 3A


Mass: 100807.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAF1, UBXD12, UBXN3A, CGI-03 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 pLysS
References: UniProt: P08515, UniProt: Q9UNN5, glutathione transferase
#3: Protein Ubiquitin recognition factor in ER-associated degradation protein 1 / Ubiquitin fusion degradation protein 1 / UB fusion protein 1


Mass: 36658.621 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 BL21(DE3) (bacteria) / References: UniProt: Q92890
Has protein modificationN

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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: ternary complex of human p97 bound to Faf1 and Ufd1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.6
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMHEPES1
2150 mMpotassium chlorideKCl1
35 mMmagnesium chlorideMgCl21
42 mMAdenosine 5'-O-(3-thio)triphosphateATPgammaS1
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
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 magnification: 165000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2SerialEMimage acquisition
4cryoSPARCCTF correction
7UCSF ChimeraXmodel fitting
8ISOLDEmodel fitting
9Cootmodel fitting
11cryoSPARCinitial Euler assignment
12cryoSPARCfinal Euler assignment
13cryoSPARCclassification
14cryoSPARC3D reconstruction
15PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 943368 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0032653
ELECTRON MICROSCOPYf_angle_d0.7063576
ELECTRON MICROSCOPYf_dihedral_angle_d5.748358
ELECTRON MICROSCOPYf_chiral_restr0.047396
ELECTRON MICROSCOPYf_plane_restr0.005475

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