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- EMDB-59990: CryoEM structure of substrate engaged p97 in complex with Ufd1/Np... -

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Basic information

Entry
Database: EMDB / ID: EMD-59990
TitleCryoEM structure of substrate engaged p97 in complex with Ufd1/Npl4 and C-terminal FAF1-State II (non-normalized map)
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: Transitional endoplasmic reticulum ATPase
    • Protein or peptide: Ubiquitin recognition factor in ER-associated degradation protein 1
    • Protein or peptide: FAS-associated factor 1
KeywordsComplex / ATPase / Protein unfolding / Cell cycle / TRANSLOCASE
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
DepositionSep 18, 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_59990.png

Downloads & links

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Map

FileDownload / File: emd_59990.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: 0.0295
Minimum - Maximum-0.25969484 - 0.5825162
Average (Standard dev.)0.0000894185 (±0.010894945)
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: Transitional endoplasmic reticulum ATPase
    • Protein or peptide: Ubiquitin recognition factor in ER-associated degradation protein 1
    • Protein or peptide: FAS-associated factor 1

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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: all
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

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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

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Macromolecule #3: Transitional endoplasmic reticulum ATPase

MacromoleculeName: Transitional endoplasmic reticulum ATPase / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO / EC number: vesicle-fusing ATPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 91.665227 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH MASGADSKGD DLSTAILKQK NRPNRLIVDE AINEDNSVVS LSQPKMDELQ LFRGDTVLLK GKKRREAVC IVLSDDTCSD EKIRMNRVVR NNLRVRLGDV ISIQPCPDVK YGKRIHVLPI DDTVEGITGN LFEVYLKPYF L EAYRPIRK ...String:
MGSSHHHHHH SSGLVPRGSH MASGADSKGD DLSTAILKQK NRPNRLIVDE AINEDNSVVS LSQPKMDELQ LFRGDTVLLK GKKRREAVC IVLSDDTCSD EKIRMNRVVR NNLRVRLGDV ISIQPCPDVK YGKRIHVLPI DDTVEGITGN LFEVYLKPYF L EAYRPIRK GDIFLVRGGM RAVEFKVVET DPSPYCIVAP DTVIHCEGEP IKREDEEESL NEVGYDDIGG CRKQLAQIKE MV ELPLRHP ALFKEIGVKP PRGILLYGPP GTGKTLIARA VANETGAFFF LINGPEIMSK LAGESESNLR KAFEEAEKNA PAI IFIDEL DAIAPKREKT HGEVERRIVS QLLTLMDGLK QRAHVIVMAA TNRPNSIDPA LRRFGRFDRE VDIGIPDATG RLEI LQIHT KNMKLADDVD LEQVANETHG HVGADLAALC SEAALQAIRK KMDLIDLEDE TIDAEVMNSL AVTMDDFRWA LSQSN PSAL RETVVEVPQV TWEDIGGLED VKRELQELVQ YPVEHPDKFL KFGMTPSKGV LFYGPPGCGK TLLAKAIANE CQANFI SIK GPELLTMWFG ESEANVREIF DKARQAAPCV LFFDQLDSIA KARGGNIGDG GGAADRVINQ ILTEMDGMST KKNVFII GA TNRPDIIDPA ILRPGRLDQL IYIPLPDEKS RVAILKANLR KSPVAKDVDL EFLAKMTNGF SGADLTEICQ RACKLAIR E SIESEIRRER ERQTNPSAME VEEDDPVPEI RRDHFEEAMR FARRSVSDND IRKYEMFAQT LQQSRGFGSF RFPSGNQGG AGPSQGSGGG TGGSVYTEDN DDDLYG

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Macromolecule #4: Ubiquitin recognition factor in ER-associated degradation protein 1

MacromoleculeName: Ubiquitin recognition factor in ER-associated degradation protein 1
type: protein_or_peptide / ID: 4 / 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

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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

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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 / 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) / 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

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: 64905
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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