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- EMDB-73536: Complex structure of human p97 bound to Faf1 and Ufd1 (NTD focused) -

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Entry
Database: EMDB / ID: EMD-73536
TitleComplex structure of human p97 bound to Faf1 and Ufd1 (NTD focused)
Map data
Sample
  • Complex: ternary complex of human p97 bound to Faf1 and Ufd1
    • Protein or peptide: Transitional endoplasmic reticulum ATPase
    • Protein or peptide: Glutathione S-transferase class-mu 26 kDa isozyme,FAS-associated factor 1
    • Protein or peptide: Ubiquitin recognition factor in ER-associated degradation protein 1
KeywordsATPase / p97 / AAA ATPase / ERAD / unfoldase / ubiquitin / segregase / VCP / HYDROLASE
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsLiao Z / Arkinson C / Martin A
Funding support United States, 1 items
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, 2025-
Header (metadata) releaseApr 22, 2026-
Map releaseApr 22, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73536.png

Downloads & links

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Map

FileDownload / File: emd_73536.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.16 Å/pix.
x 256 pix.
= 297.19 Å		1.16 Å/pix.
x 256 pix.
= 297.19 Å		1.16 Å/pix.
x 256 pix.
= 297.19 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1609 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0564
Minimum - Maximum-0.7781446 - 0.9377602
Average (Standard dev.)-0.0018085041 (±0.0097000785)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 297.1904 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Map sharpened using DeepEMhancer

Fileemd_73536_additional_1.map
AnnotationMap sharpened using DeepEMhancer
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Half map: #1

Fileemd_73536_half_map_1.map
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Half map: #2

Fileemd_73536_half_map_2.map
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Sample components

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Entire : ternary complex of human p97 bound to Faf1 and Ufd1

EntireName: ternary complex of human p97 bound to Faf1 and Ufd1
Components
  • Complex: ternary complex of human p97 bound to Faf1 and Ufd1
    • Protein or peptide: Transitional endoplasmic reticulum ATPase
    • Protein or peptide: Glutathione S-transferase class-mu 26 kDa isozyme,FAS-associated factor 1
    • Protein or peptide: Ubiquitin recognition factor in ER-associated degradation protein 1

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Supramolecule #1: ternary complex of human p97 bound to Faf1 and Ufd1

SupramoleculeName: ternary complex of human p97 bound to Faf1 and Ufd1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Transitional endoplasmic reticulum ATPase

MacromoleculeName: Transitional endoplasmic reticulum ATPase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: vesicle-fusing ATPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 91.177781 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MASGADSKGD DLSTAILKQK NRPNRLIVDE AINEDNSVVS LSQPKMDELQ LFRGDTVLLK GKKRREAVCI VLSDDTCSDE KIRMNRVVR NNLRVRLGDV ISIQPCPDVK YGKRIHVLPI DDTVEGITGN LFEVYLKPYF LEAYRPIRKG DIFLVRGGMR A VEFKVVET ...String:
MASGADSKGD DLSTAILKQK NRPNRLIVDE AINEDNSVVS LSQPKMDELQ LFRGDTVLLK GKKRREAVCI VLSDDTCSDE KIRMNRVVR NNLRVRLGDV ISIQPCPDVK YGKRIHVLPI DDTVEGITGN LFEVYLKPYF LEAYRPIRKG DIFLVRGGMR A VEFKVVET DPSPYCIVAP DTVIHCEGEP IKREDEEESL NEVGYDDIGG CRKQLAQIKE MVELPLRHPA LFKAIGVKPP RG ILLYGPP GTGKTLIARA VANETGAFFF LINGPEIMSK LAGESESNLR KAFEEAEKNA PAIIFIDELD AIAPKREKTH GEV ERRIVS QLLTLMDGLK QRAHVIVMAA TNRPNSIDPA LRRFGRFDRE VDIGIPDATG RLEILQIHTK NMKLADDVDL EQVA NETHG HVGADLAALC SEAALQAIRK KMDLIDLEDE TIDAEVMNSL AVTMDDFRWA LSQSNPSALR ETVVEVPQVT WEDIG GLED VKRELQELVQ YPVEHPDKFL KFGMTPSKGV LFYGPPGCGK TLLAKAIANE CQANFISIKG PELLTMWFGE SEANVR EIF DKARQAAPCV LFFDELDSIA KARGGNIGDG GGAADRVINQ ILTEMDGMST KKNVFIIGAT NRPDIIDPAI LRPGRLD QL IYIPLPDEKS RVAILKANLR KSPVAKDVDL EFLAKMTNGF SGADLTEICQ RACKLAIRES IESEIRRERE RQTNPSAM E VEEDDPVPEI RRDHFEEAMR FARRSVSDND IRKYEMFAQT LQQSRGFGSF RFPSGNQGGA GPSQGSGGGT GGSVYTEDN DDDLYGVDKL AAALEHHHHH H

UniProtKB: Transitional endoplasmic reticulum ATPase

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Macromolecule #2: Glutathione S-transferase class-mu 26 kDa isozyme,FAS-associated ...

MacromoleculeName: Glutathione S-transferase class-mu 26 kDa isozyme,FAS-associated factor 1
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: glutathione transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 100.807102 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSPILGYWKI KGLVQPTRLL LEYLEEKYEE HLYERDEGDK WRNKKFELGL EFPNLPYYID GDVKLTQSMA IIRYIADKHN MLGGCPKER AEISMLEGAV LDIRYGVSRI AYSKDFETLK VDFLSKLPEM LKMFEDRLCH KTYLNGDHVT HPDFMLYDAL D VVLYMDPM ...String:
MSPILGYWKI KGLVQPTRLL LEYLEEKYEE HLYERDEGDK WRNKKFELGL EFPNLPYYID GDVKLTQSMA IIRYIADKHN MLGGCPKER AEISMLEGAV LDIRYGVSRI AYSKDFETLK VDFLSKLPEM LKMFEDRLCH KTYLNGDHVT HPDFMLYDAL D VVLYMDPM CLDAFPKLVC FKKRIEAIPQ IDKYLKSSKY IAWPLQGWQA TFGGGDHPPK SDLEVLFQGP LGMASNMDRE MI LADFQAC TGIENIDEAI TLLEQNNWDL VAAINGVIPQ ENGILQSEYG GETIPGPAFN PASHPASAPT SSSSSAFRPV MPS RQIVER QPRMLDFRVE YRDRNVDVVL EDTCTVGEIK QILENELQIP VSKMLLKGWK TGDVEDSTVL KSLHLPKNNS LYVL TPDLP PPSSSSHAGA LQESLNQNFM LIITHREVQR EYNLNFSGSS TIQEVKRNVY DLTSIPVRHQ LWEGWPTSAT DDSMC LAES GLSYPCHRLT VGRRSSPAQT REQSEEQITD VHMVSDSDGD DFEDATEFGV DDGEVFGMAS SALRKSPMMP ENAENE GDA LLQFTAEFSS RYGDCHPVFF IGSLEAAFQE AFYVKARDRK LLAIYLHHDE SVLTNVFCSQ MLCAESIVSY LSQNFIT WA WDLTKDSNRA RFLTMCNRHF GSVVAQTIRT QKTDQFPLFL IIMGKRSSNE VLNVIQGNTT VDELMMRLMA AMEIFTAQ Q QEDIKDEDER EARENVKREQ DEAYRLSLEA DRAKREAHER EMAEQFRLEQ IRKEQEEERE AIRLSLEQAL PPEPKEENA EPVSKLRIRT PSGEFLERRF LASNKLQIVF DFVASKGFPW DEYKLLSTFP RRDVTQLDPN KSLLEVKLFP QETLFLEAKE

UniProtKB: Glutathione S-transferase class-mu 26 kDa isozyme, FAS-associated factor 1

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Macromolecule #3: Ubiquitin recognition factor in ER-associated degradation protein 1

MacromoleculeName: Ubiquitin recognition factor in ER-associated degradation protein 1
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.658621 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSSHHHHHHS SGLVPRGSHM FSFNMFDHPI PRVFQNRFST QYRCFSVSML AGPNDRSDVE KGGKIIMPPS ALDQLSRLNI TYPMLFKLT NKNSDRMTHC GVLEFVADEG ICYLPHWMMQ NLLLEEGGLV QVESVNLQVA TYSKFQPQSP DFLDITNPKA V LENALRNF ...String:
MSSHHHHHHS SGLVPRGSHM FSFNMFDHPI PRVFQNRFST QYRCFSVSML AGPNDRSDVE KGGKIIMPPS ALDQLSRLNI TYPMLFKLT NKNSDRMTHC GVLEFVADEG ICYLPHWMMQ NLLLEEGGLV QVESVNLQVA TYSKFQPQSP DFLDITNPKA V LENALRNF ACLTTGDVIA INYNEKIYEL RVMETKPDKA VSIIECDMNV DFDAPLGYKE PERQVQHEES TEGEADHSGY AG ELGFRAF SGSGNRLDGK KKGVEPSPSP IKPGDIKRGI PNYEFKLGKI TFIRNSRPLV KKVEEDEAGG RFVAFSGEGQ SLR KKGRKP

UniProtKB: Ubiquitin recognition factor in ER-associated degradation protein 1

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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

Concentration4 mg/mL
BufferpH: 7.6
Component:
ConcentrationNameFormula
50.0 mMHEPES
150.0 mMpotassium chlorideKCl
5.0 mMmagnesium chlorideMgCl2
2.0 mMAdenosine 5'-O-(3-thio)triphosphateATPgammaS
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / 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 / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000
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

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 943368
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL
Output model

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

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