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- EMDB-48501: Cryo-EM structure of VCPIP1 VCPID bound to VCP D2 domain dimer (w... -

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Basic information

Entry
Database: EMDB / ID: EMD-48501
TitleCryo-EM structure of VCPIP1 VCPID bound to VCP D2 domain dimer (with extra D2 domain)
Map data
Sample
  • Complex: Complex of valosin containing protein (VCP)/p97 and valosin containing protein interacting protein 1 (VCPIP1)
    • Complex: Valosin containing protein interacting domain (VCPID) with connecting residues of VCPIP1 stalk region
      • Protein or peptide: Deubiquitinating protein VCPIP1
    • Complex: Valosin containing protein (VCP) D2 Domain
      • Protein or peptide: Transitional endoplasmic reticulum ATPase
Keywordsdouble-ring hexameric complex / valosin containing protein / ATPase / VCP / mammalian / DUB / deubiquitinase / deubiquitinating enzyme / VCIP135 / p97 / VCPIP1 / hydrolase / VCPID
Function / homology
Function and homology information


protein K11-linked deubiquitination / endoplasmic reticulum membrane fusion / Golgi reassembly / protein K48-linked deubiquitination / : / flavin adenine dinucleotide catabolic process / VCP-NSFL1C complex / endosome to lysosome transport via multivesicular body sorting pathway / endoplasmic reticulum stress-induced pre-emptive quality control / BAT3 complex binding ...protein K11-linked deubiquitination / endoplasmic reticulum membrane fusion / Golgi reassembly / protein K48-linked deubiquitination / : / flavin adenine dinucleotide catabolic process / VCP-NSFL1C complex / endosome to lysosome transport via multivesicular body sorting pathway / endoplasmic reticulum stress-induced pre-emptive quality control / 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 / cytoplasm protein quality control / positive regulation of oxidative phosphorylation / : / Golgi stack / aggresome assembly / deubiquitinase activator activity / ubiquitin-modified protein reader activity / mitotic spindle disassembly / regulation of protein localization to chromatin / VCP-NPL4-UFD1 AAA ATPase complex / cellular response to misfolded protein / negative regulation of protein localization to chromatin / positive regulation of mitochondrial membrane potential / vesicle-fusing ATPase / K48-linked polyubiquitin modification-dependent protein binding / regulation of aerobic respiration / retrograde protein transport, ER to cytosol / stress granule disassembly / ATPase complex / regulation of synapse organization / ubiquitin-specific protease binding / MHC class I protein binding / positive regulation of ATP biosynthetic process / ubiquitin-like protein ligase binding / RHOH GTPase cycle / polyubiquitin modification-dependent protein binding / protein deubiquitination / autophagosome maturation / negative regulation of hippo signaling / endoplasmic reticulum to Golgi vesicle-mediated transport / HSF1 activation / translesion synthesis / interstrand cross-link repair / ATP metabolic process / proteasomal protein catabolic process / endoplasmic reticulum unfolded protein response / Protein methylation / Attachment and Entry / ERAD pathway / lipid droplet / proteasome complex / viral genome replication / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / negative regulation of smoothened signaling pathway / macroautophagy / positive regulation of protein-containing complex assembly / Hh mutants are degraded by ERAD / establishment of protein localization / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / positive regulation of non-canonical NF-kappaB signal transduction / Translesion Synthesis by POLH / ADP binding / ABC-family proteins mediated transport / autophagy / cytoplasmic stress granule / Aggrephagy / positive regulation of protein catabolic process / azurophil granule lumen / KEAP1-NFE2L2 pathway / Ovarian tumor domain proteases / positive regulation of canonical Wnt signaling pathway / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / double-strand break repair / E3 ubiquitin ligases ubiquitinate target proteins / site of double-strand break / Neddylation / cellular response to heat / ubiquitin-dependent protein catabolic process / secretory granule lumen / protein phosphatase binding / regulation of apoptotic process / ficolin-1-rich granule lumen / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Attachment and Entry / protein ubiquitination / ciliary basal body / endoplasmic reticulum lumen / protein domain specific binding / DNA repair / intracellular membrane-bounded organelle / lipid binding / DNA damage response
Similarity search - Function
Deubiquitinating protein VCPIP1 / Deubiquitinating protein VCPIP1, N-terminal / VCIP135 N-terminal / : / OTU1, UBXL domain / OTU-like cysteine protease / OTU domain / OTU domain profile. / AAA ATPase, CDC48 family / Cell division protein 48 (CDC48), N-terminal domain ...Deubiquitinating protein VCPIP1 / Deubiquitinating protein VCPIP1, N-terminal / VCIP135 N-terminal / : / OTU1, UBXL domain / OTU-like cysteine protease / OTU domain / OTU domain profile. / 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 / Aspartate decarboxylase-like 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 / 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
Transitional endoplasmic reticulum ATPase / Deubiquitinating protein VCPIP1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsShah B / Hunkeler M / Buhrlage SJ / Fischer ES
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA262188 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA233800 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)5F31 CA281197 United States
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis of VCP-VCPIP1-p47 ternary complex in Golgi maintenance.
Authors: Binita Shah / Moritz Hunkeler / Ariana Bratt / Hong Yue / Isabella Jaen Maisonet / Eric S Fischer / Sara J Buhrlage /
Abstract: VCP/p97 regulates a wide range of cellular processes, including post-mitotic Golgi reassembly. In this context, VCP is assisted by p47, an adapter protein, and VCPIP1, a deubiquitylase (DUB). ...VCP/p97 regulates a wide range of cellular processes, including post-mitotic Golgi reassembly. In this context, VCP is assisted by p47, an adapter protein, and VCPIP1, a deubiquitylase (DUB). However, how they organize into a functional ternary complex to promote Golgi assembly remains unknown. Here, we use cryo-EM to characterize both VCP-VCPIP1 and VCP-VCPIP1-p47 complexes. We show that VCPIP1 engages VCP through two interfaces: one involving the N-domain of VCP and the UBX domain of VCPIP1, and the other involving the VCP D2 domains and a region of VCPIP1 we refer to as VCPID. The p47 UBX domain competitively binds to the VCP N-domain, while not affecting VCPID binding. We show that VCPID is critical for VCP-mediated enhancement of DUB activity and proper Golgi assembly. The ternary structure along with biochemical and cellular data provides new insights into the complex interplay of VCP with its co-factors.
History
DepositionDec 31, 2024-
Header (metadata) releaseOct 15, 2025-
Map releaseOct 15, 2025-
UpdateOct 15, 2025-
Current statusOct 15, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48501.png

Downloads & links

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Map

FileDownload / File: emd_48501.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 440 pix.
= 363. Å		0.83 Å/pix.
x 440 pix.
= 363. Å		0.83 Å/pix.
x 440 pix.
= 363. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
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Contour LevelBy AUTHOR: 0.0471
Minimum - Maximum-0.107563965 - 0.27595043
Average (Standard dev.)-0.00014855295 (±0.004103565)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 363.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48501_msk_1.map
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Mask #2

Fileemd_48501_msk_2.map
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Additional map: #1

Fileemd_48501_additional_1.map
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Additional map: Main map post-processed using deepEMhancer

Fileemd_48501_additional_2.map
AnnotationMain map post-processed using deepEMhancer
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Half map: Half-map A

Fileemd_48501_half_map_1.map
AnnotationHalf-map A
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Half map: Half-map B

Fileemd_48501_half_map_2.map
AnnotationHalf-map B
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Sample components

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Entire : Complex of valosin containing protein (VCP)/p97 and valosin conta...

EntireName: Complex of valosin containing protein (VCP)/p97 and valosin containing protein interacting protein 1 (VCPIP1)
Components
  • Complex: Complex of valosin containing protein (VCP)/p97 and valosin containing protein interacting protein 1 (VCPIP1)
    • Complex: Valosin containing protein interacting domain (VCPID) with connecting residues of VCPIP1 stalk region
      • Protein or peptide: Deubiquitinating protein VCPIP1
    • Complex: Valosin containing protein (VCP) D2 Domain
      • Protein or peptide: Transitional endoplasmic reticulum ATPase

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Supramolecule #1: Complex of valosin containing protein (VCP)/p97 and valosin conta...

SupramoleculeName: Complex of valosin containing protein (VCP)/p97 and valosin containing protein interacting protein 1 (VCPIP1)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Full length valosin containing protein (VCP)/p97 with full length valosin containing protein interacting protein 1 (VCPIP1)
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Valosin containing protein interacting domain (VCPID) with connec...

SupramoleculeName: Valosin containing protein interacting domain (VCPID) with connecting residues of VCPIP1 stalk region
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Valosin containing protein (VCP) D2 Domain

SupramoleculeName: Valosin containing protein (VCP) D2 Domain / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Details: Valosin containing protein (VCP) D2 domain with extra density of VCP (not modeled)
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Deubiquitinating protein VCPIP1

MacromoleculeName: Deubiquitinating protein VCPIP1 / type: protein_or_peptide / ID: 1 / Details: N-term Strep-tagged VCPIP1 / Number of copies: 1 / Enantiomer: LEVO / EC number: ubiquitinyl hydrolase 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 137.335422 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGDWSHPQFE KSGGGSGGLE VLFQGPGSMS QPPPPPPPLP PPPPPPEAPQ TPSSLASAAA SGGLLKRRDR RILSGSCPDP KCQARLFFP ASGSVSIECT ECGQRHEQQQ LLGVEEVTDP DVVLHNLLRN ALLGVTGAPK KNTELVKVMG LSNYHCKLLS P ILARYGMD ...String:
MGDWSHPQFE KSGGGSGGLE VLFQGPGSMS QPPPPPPPLP PPPPPPEAPQ TPSSLASAAA SGGLLKRRDR RILSGSCPDP KCQARLFFP ASGSVSIECT ECGQRHEQQQ LLGVEEVTDP DVVLHNLLRN ALLGVTGAPK KNTELVKVMG LSNYHCKLLS P ILARYGMD KQTGRAKLLR DMNQGELFDC ALLGDRAFLI EPEHVNTVGY GKDRSGSLLY LHDTLEDIKR ANKSQECLIP VH VDGDGHC LVHAVSRALV GRELFWHALR ENLKQHFQQH LARYQALFHD FIDAAEWEDI INECDPLFVP PEGVPLGLRN IHI FGLANV LHRPIILLDS LSGMRSSGDY SATFLPGLIP AEKCTGKDGH LNKPICIAWS SSGRNHYIPL VGIKGAALPK LPMN LLPKA WGVPQDLIKK YIKLEEDGGC VIGGDRSLQD KYLLRLVAAM EEVFMDKHGI HPSLVADVHQ YFYRRTGVIG VQPEE VTAA AKKAVMDNRL HKCLLCGALS ELHVPPEWLA PGGKLYNLAK STHGQLRTDK NYSFPLNNLV CSYDSVKDVL VPDYGM SNL TACNWCHGTS VRKVRGDGSI VYLDGDRTNS RSTGGKCGCG FKHFWDGKEY DNLPEAFPIT LEWGGRVVRE TVYWFQY ES DSSLNSNVYD VAMKLVTKHF PGEFGSEILV QKVVHTILHQ TAKKNPDDYT PVNIDGAHAQ RVGDVQGQES ESQLPTKI I LTGQKTKTLH KEELNMSKTE RTIQQNITEQ ASVMQKRKTE KLKQEQKGQP RTVSPSTIRD GPSSAPATPT KAPYSPTTS KEKKIRITTN DGRQSMVTLK SSTTFFELQE SIAREFNIPP YLQCIRYGFP PKELMPPQAG MEKEPVPLQH GDRITIEILK SKAEGGQSA AAHSAHTVKQ EDIAVTGKLS SKELQEQAEK EMYSLCLLAT LMGEDVWSYA KGLPHMFQQG GVFYSIMKKT M GMADGKHC TFPHLPGKTF VYNASEDRLE LCVDAAGHFP IGPDVEDLVK EAVSQVRAEA TTRSRESSPS HGLLKLGSGG VV KKKSEQL HNVTAFQGKG HSLGTASGNP HLDPRARETS VVRKHNTGTD FSNSSTKTEP SVFTASSSNS ELIRIAPGVV TMR DGRQLD PDLVEAQRKK LQEMVSSIQA SMDRHLRDQS TEQSPSDLPQ RKTEVVSSSA KSGSLQTGLP ESFPLTGGTE NLNT ETTDG CVADALGAAF ATRSKAQRGN SVEELEEMDS QDAEMTNTTE PMDHS

UniProtKB: Deubiquitinating protein VCPIP1

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Macromolecule #2: Transitional endoplasmic reticulum ATPase

MacromoleculeName: Transitional endoplasmic reticulum ATPase / type: protein_or_peptide / ID: 2 / Details: N-term FLAG-tagged VCP / Number of copies: 3 / Enantiomer: LEVO / EC number: vesicle-fusing ATPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 92.022539 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGDYKDDDDK GGGSGGLEVL FQGPGSMASG ADSKGDDLST AILKQKNRPN RLIVDEAINE DNSVVSLSQP KMDELQLFRG DTVLLKGKK RREAVCIVLS DDTCSDEKIR MNRVVRNNLR VRLGDVISIQ PCPDVKYGKR IHVLPIDDTV EGITGNLFEV Y LKPYFLEA ...String:
MGDYKDDDDK GGGSGGLEVL FQGPGSMASG ADSKGDDLST AILKQKNRPN RLIVDEAINE DNSVVSLSQP KMDELQLFRG DTVLLKGKK RREAVCIVLS DDTCSDEKIR MNRVVRNNLR VRLGDVISIQ PCPDVKYGKR IHVLPIDDTV EGITGNLFEV Y LKPYFLEA YRPIRKGDIF LVRGGMRAVE FKVVETDPSP YCIVAPDTVI HCEGEPIKRE DEEESLNEVG YDDIGGCRKQ LA QIKEMVE LPLRHPALFK AIGVKPPRGI LLYGPPGTGK TLIARAVANE TGAFFFLING PEIMSKLAGE SESNLRKAFE EAE KNAPAI IFIDELDAIA PKREKTHGEV ERRIVSQLLT LMDGLKQRAH VIVMAATNRP NSIDPALRRF GRFDREVDIG IPDA TGRLE ILQIHTKNMK LADDVDLEQV ANETHGHVGA DLAALCSEAA LQAIRKKMDL IDLEDETIDA EVMNSLAVTM DDFRW ALSQ SNPSALRETV VEVPQVTWED IGGLEDVKRE LQELVQYPVE HPDKFLKFGM TPSKGVLFYG PPGCGKTLLA KAIANE CQA NFISIKGPEL LTMWFGESEA NVREIFDKAR QAAPCVLFFD ELDSIAKARG GNIGDGGGAA DRVINQILTE MDGMSTK KN VFIIGATNRP DIIDPAILRP GRLDQLIYIP LPDEKSRVAI LKANLRKSPV AKDVDLEFLA KMTNGFSGAD LTEICQRA C KLAIRESIES EIRRERERQT NPSAMEVEED DPVPEIRRDH FEEAMRFARR SVSDNDIRKY EMFAQTLQQS RGFGSFRFP SGNQGGAGPS QGSGGGTGGS VYTEDNDDDL YG

UniProtKB: Transitional endoplasmic reticulum ATPase

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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

Concentration1.8 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
30.0 mMHEPES
150.0 mMsodium chlorideNaCl
3.0 mMTCEP
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 283.15 K / Instrument: LEICA EM GP
DetailsThis sample was crosslinked with 400x molar excess of BS3 and plunged with 0.2 mM CHAPSO (final concentration).

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 11580 / Average exposure time: 2.83 sec. / Average electron dose: 53.69 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: 2.2 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 105000
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: 2050250
CTF correctionSoftware - Name: cryoSPARC (ver. 3.3.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 592034
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5ftk


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL
Output model

PDB-9mps:
Cryo-EM structure of VCPIP1 VCPID bound to VCP D2 domain dimer (with extra D2 domain)

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