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- EMDB-58599: CryoEM structure of substrate engaged p97 in complex with Ufd1/Np... -

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Entry
Database: EMDB / ID: EMD-58599
TitleCryoEM structure of substrate engaged p97 in complex with Ufd1/Npl4 and C-terminal FAF1- State IV
Map data
Sample
  • Cell: Substrate engaged p97 in complex with Ufd1/Npl4 and only-C-term FAF1
    • Protein or peptide: Polyubiquitin-B
    • Protein or peptide: Nuclear protein localization protein 4 homolog
    • Protein or peptide: Ubiquitin recognition factor in ER-associated degradation protein 1
    • Protein or peptide: Transitional endoplasmic reticulum ATPase
    • Protein or peptide: FAS-associated factor 1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: MAGNESIUM ION
KeywordsComplex / ATPase / Protein unfolding / Cell cycle / TRANSLOCASE
Function / homology
Function and homology information


UFD1-NPL4 complex / Fas signaling pathway / negative regulation of RIG-I signaling pathway / CD95 death-inducing signaling complex / flavin adenine dinucleotide catabolic process / VCP-NSFL1C complex / protein kinase regulator activity / intracellular protein-containing complex / endoplasmic reticulum stress-induced pre-emptive quality control / endosome to lysosome transport via multivesicular body sorting pathway ...UFD1-NPL4 complex / Fas signaling pathway / negative regulation of RIG-I signaling pathway / CD95 death-inducing signaling complex / flavin adenine dinucleotide catabolic process / VCP-NSFL1C complex / protein kinase regulator activity / intracellular protein-containing complex / endoplasmic reticulum stress-induced pre-emptive quality control / endosome to lysosome transport via multivesicular body sorting pathway / BAT3 complex binding / cellular response to arsenite ion / cytoplasmic ubiquitin ligase complex / Derlin-1 retrotranslocation complex / positive regulation of protein K63-linked deubiquitination / protein-DNA covalent cross-linking repair / deubiquitinase activator activity / positive regulation of oxidative phosphorylation / peptidyl-lysine trimethylation / cytoplasm protein quality control / regulation of protein localization to chromatin / ubiquitin-modified protein reader activity / RQC complex / cellular response to misfolded protein / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / mitochondrion transport along microtubule / positive regulation of mitochondrial membrane potential / positive regulation of protein monoubiquitination / regulation of protein catabolic process / vesicle-fusing ATPase / K48-linked polyubiquitin modification-dependent protein binding / nuclear outer membrane-endoplasmic reticulum membrane network / NAD+ metabolic process / regulation of aerobic respiration / K63-linked polyubiquitin modification-dependent protein binding / retrograde protein transport, ER to cytosol / stress granule disassembly / negative regulation of type I interferon production / ubiquitin-specific protease binding / polyubiquitin modification-dependent protein binding / ATPase complex / regulation of synapse organization / Golgi organization / positive regulation of ATP biosynthetic process / ubiquitin-like protein ligase binding / RHOH GTPase cycle / intracellular membrane-bounded organelle / skeletal system development / autophagosome maturation / MHC class I protein binding / HSF1 activation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of hippo signaling / endoplasmic reticulum to Golgi vesicle-mediated transport / NF-kappaB binding / mitophagy / interstrand cross-link repair / ATP metabolic process / protein unfolding / endoplasmic reticulum unfolded protein response / heat shock protein binding / Attachment and Entry / ribosome-associated ubiquitin-dependent protein catabolic process / ERAD pathway / Protein methylation / neuron projection morphogenesis / translesion synthesis / proteasome complex / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / regulation of mitochondrial membrane potential / FLT3 signaling by CBL mutants / regulation of neuron apoptotic process / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Prevention of phagosomal-lysosomal fusion / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / positive regulation of DNA replication / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Constitutive Signaling by NOTCH1 HD Domain Mutants / viral genome replication / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / positive regulation of protein ubiquitination / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / regulation of proteasomal protein catabolic process
Similarity search - Function
Nuclear pore localisation protein Npl4, ubiquitin-like domain / Nuclear pore localisation protein NPL4 / FAS-associated factor 1-like, UBX domain / FAF1, UBA-like domain / : / Fas-associated factor 1 / UAS / UAS / : / Ubiquitin fusion degradation protein Ufd1-like ...Nuclear pore localisation protein Npl4, ubiquitin-like domain / Nuclear pore localisation protein NPL4 / 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 / NPL4, zinc-binding putative / NPL4 family, putative zinc binding region / Nuclear pore localisation protein NPL4, C-terminal / Nuclear protein localization protein 4 / NPL4 family / Domain present in ubiquitin-regulatory proteins / UBX domain / UBX domain profile. / UBX domain / UBA-like domain / 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. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / CDC48 domain 2-like superfamily / Zinc finger, RanBP2-type / 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 domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / 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
Polyubiquitin-B / Transitional endoplasmic reticulum ATPase / Nuclear protein localization protein 4 homolog / 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: 8.0 Å
AuthorsDrakonaki A / van den Boom J / Kroening A / Meyer H / Gatsogiannis C
Funding support Germany, 5 items
OrganizationGrant numberCountry
German Research Foundation (DFG)424228829 Germany
German Research Foundation (DFG)509479817 Germany
German Research Foundation (DFG)496113311 Germany
German Research Foundation (DFG)DFG INST 211/667-1 Germany
German Research Foundation (DFG)INST-208767513-1_FUGG Germany
CitationJournal: Nat Commun / Year: 2026
Title: Structural dynamics of substrate processing by the p97-Ufd1-Npl4-FAF1 machinery.
Authors: Athina Drakonaki / Johannes van den Boom / Alexander Kröning / Hemmo Meyer / Christos Gatsogiannis /
Abstract: The AAA-ATPase VCP/p97 unfolds ubiquitylated proteins in key signaling and cellular homeostasis pathways, yet the mechanisms by which Ufd1-Npl4 and FAF1 adapters handle ubiquitin chains to coordinate ...The AAA-ATPase VCP/p97 unfolds ubiquitylated proteins in key signaling and cellular homeostasis pathways, yet the mechanisms by which Ufd1-Npl4 and FAF1 adapters handle ubiquitin chains to coordinate substrate loading and processing remain unclear. Our cryo-EM study of p97-Ufd1-Npl4 and FAF1 engaging a substrate reveal interactions that drive substrate processing. While Npl4 is capped by distal ubiquitins, and the initiator ubiquitin can be traced from the Npl4 groove to the ATPase channel at near-atomic resolution, we find that the Npl4 tower adaptively responds to the configurational changes in the ATPase motor's spiral staircase. A helix in FAF1 together with the Ufd1-UT3 domain engage proximal ubiquitins while providing the necessary structural plasticity to accommodate this motion and deliver ubiquitins to Npl4's groove. Our study reveals the intricate, dynamic interplay between p97, Ufd1-Npl4, and FAF1 in efficient processing of ubiquitylated substrates.
History
DepositionJun 16, 2026-
Header (metadata) releaseNov 4, 2026-
Map releaseNov 4, 2026-
UpdateNov 4, 2026-
Current statusNov 4, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_58599.png

Downloads & links

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Map

FileDownload / File: emd_58599.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.79 Å/pix.
x 576 pix.
= 453.888 Å		0.79 Å/pix.
x 576 pix.
= 453.888 Å		0.79 Å/pix.
x 576 pix.
= 453.888 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.788 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.18
Minimum - Maximum-14.816863 - 39.257603000000003
Average (Standard dev.)0.021017767 (±1.009485)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions576576576
Spacing576576576
CellA=B=C: 453.888 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Substrate engaged p97 in complex with Ufd1/Npl4 and only-C-term FAF1

EntireName: Substrate engaged p97 in complex with Ufd1/Npl4 and only-C-term FAF1
Components
  • Cell: Substrate engaged p97 in complex with Ufd1/Npl4 and only-C-term FAF1
    • Protein or peptide: Polyubiquitin-B
    • Protein or peptide: Nuclear protein localization protein 4 homolog
    • Protein or peptide: Ubiquitin recognition factor in ER-associated degradation protein 1
    • Protein or peptide: Transitional endoplasmic reticulum ATPase
    • Protein or peptide: FAS-associated factor 1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Substrate engaged p97 in complex with Ufd1/Npl4 and only-C-term FAF1

SupramoleculeName: Substrate engaged p97 in complex with Ufd1/Npl4 and only-C-term FAF1
type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Polyubiquitin-B

MacromoleculeName: Polyubiquitin-B / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.576831 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG

UniProtKB: Polyubiquitin-B

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Macromolecule #2: Nuclear protein localization protein 4 homolog

MacromoleculeName: Nuclear protein localization protein 4 homolog / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 68.202016 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MAESIIIRVQ SPDGVKRITA TKRETAATFL KKVAKEFGFQ NNGFSVYINR NKTGEITASS NKSLNLLKIK HGDLLFLFPS SLAGPSSEM ETSVPPGFKV FGAPNVVEDE IDQYLSKQDG KIYRSRDPQL CRHGPLGKCV HCVPLEPFDE DYLNHLEPPV K HMSFHAYI ...String:
MAESIIIRVQ SPDGVKRITA TKRETAATFL KKVAKEFGFQ NNGFSVYINR NKTGEITASS NKSLNLLKIK HGDLLFLFPS SLAGPSSEM ETSVPPGFKV FGAPNVVEDE IDQYLSKQDG KIYRSRDPQL CRHGPLGKCV HCVPLEPFDE DYLNHLEPPV K HMSFHAYI RKLTGGADKG KFVALENISC KIKSGCEGHL PWPNGICTKC QPSAITLNRQ KYRHVDNIMF ENHTVADRFL DF WRKTGNQ HFGYLYGRYT EHKDIPLGIR AEVAAIYEPP QIGTQNSLEL LEDPKAEVVD EIAAKLGLRK VGWIFTDLVS EDT RKGTVR YSRNKDTYFL SSEECITAGD FQNKHPNMCR LSPDGHFGSK FVTAVATGGP DNQVHFEGYQ VSNQCMALVR DECL LPCKD APELGYAKES SSEQYVPDVF YKDVDKFGNE ITQLARPLPV EYLIIDITTT FPKDPVYTFS ISQNPFPIEN RDVLG ETQD FHSLATYLSQ NTSSVFLDTI SDFHLLLFLV TNEVMPLQDS ISLLLEAVRT RNEELAQTWK RSEQWATIEQ LCSTVG GQL PGLHEYGAVG GSTHTATAAM WACQHCTFMN QPGTGHCEMC SLPRT

UniProtKB: Nuclear protein localization protein 4 homolog

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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: 34.544316 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MFSFNMFDHP IPRVFQNRFS TQYRCFSVSM LAGPNDRSDV EKGGKIIMPP SALDQLSRLN ITYPMLFKLT NKNSDRMTHC GVLEFVADE GICYLPHWMM QNLLLEEGGL VQVESVNLQV ATYSKFQPQS PDFLDITNPK AVLENALRNF ACLTTGDVIA I NYNEKIYE ...String:
MFSFNMFDHP IPRVFQNRFS TQYRCFSVSM LAGPNDRSDV EKGGKIIMPP SALDQLSRLN ITYPMLFKLT NKNSDRMTHC GVLEFVADE GICYLPHWMM QNLLLEEGGL VQVESVNLQV ATYSKFQPQS PDFLDITNPK AVLENALRNF ACLTTGDVIA I NYNEKIYE LRVMETKPDK AVSIIECDMN VDFDAPLGYK EPERQVQHEE STEGEADHSG YAGELGFRAF SGSGNRLDGK KK GVEPSPS PIKPGDIKRG IPNYEFKLGK ITFIRNSRPL VKKVEEDEAG GRFVAFSGEG QSLRKKGRKP

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

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Macromolecule #4: Transitional endoplasmic reticulum ATPase

MacromoleculeName: Transitional endoplasmic reticulum ATPase / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO / EC number: vesicle-fusing ATPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 89.493852 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
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 LFKEIGVKPP 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 LFFDQLDSIA KARGGNIGDG GGAADRVINQ ILTEMDGMST KKNVFIIGAT NRPDIIDPAI LRPGRLD QL IYIPLPDEKS RVAILKANLR KSPVAKDVDL EFLAKMTNGF SGADLTEICQ RACKLAIRES IESEIRRERE RQTNPSAM E VEEDDPVPEI RRDHFEEAMR FARRSVSDND IRKYEMFAQT LQQSRGFGSF RFPSGNQGGA GPSQGSGGGT GGSVYTEDN DDDLYG

UniProtKB: Transitional endoplasmic reticulum ATPase

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Macromolecule #5: FAS-associated factor 1

MacromoleculeName: FAS-associated factor 1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.227676 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MAAMEIFTAQ QQEDIKDEDE REARENVKRE QDEAYRLSLE ADRAKREAHE REMAEQFRLE QIRKEQEEER EAIRLSLEQA LPPEPKEEN AEPVSKLRIR TPSGEFLERR FLASNKLQIV FDFVASKGFP WDEYKLLSTF PRRDVTQLDP NKSLLEVKLF P QETLFLEA KE

UniProtKB: FAS-associated factor 1

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Macromolecule #6: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 12 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

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Macromolecule #7: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 7 / Number of copies: 10 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

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Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 10 / 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

Concentration12 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
20.0 mMHEPES
100.0 mMPotassium chlorideKCl
5.0 mMMagnesium chlorideMgCl2
0.5 mMTCEP
1.0 mMADP
1.0 mMBeryllium sulfateBeSO4
4.0 mMSodium fluorideNaF

Details: pH 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 286.15 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 2 / Number real images: 279701 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination 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: 270000
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: 10568986
CTF correctionSoftware - Name: cryoSPARC (ver. v3.3-v4.6.2) / Type: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v3.3-v4.6.2) / Number images used: 39948
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v3.3-v4.6.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v3.3-v4.6.2)
Final 3D classificationSoftware - Name: cryoSPARC (ver. v3.3-v4.6.2)

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