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- PDB-9mpv: Cryo-EM structure of three VCPIP1 VCPIDs bound to VCP -

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Basic information

Entry
Database: PDB / ID: 9mpv
TitleCryo-EM structure of three VCPIP1 VCPIDs bound to VCP
Components
  • Deubiquitinating protein VCPIP1
  • Transitional endoplasmic reticulum ATPase
KeywordsHYDROLASE / double-ring hexameric complex / valosin containing protein / ATPase / VCP / mammalian / DUB / deubiquitinase / deubiquitinating enzyme / VCIP135 / p97 / VCPIP1 / VCPID / p47 / adapter
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsShah, B. / Hunkeler, M. / Buhrlage, S.J. / Fischer, E.F.
Funding support United States, 3items
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, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Deubiquitinating protein VCPIP1
H: Deubiquitinating protein VCPIP1
I: Deubiquitinating protein VCPIP1
A: Transitional endoplasmic reticulum ATPase
B: Transitional endoplasmic reticulum ATPase
C: Transitional endoplasmic reticulum ATPase
D: Transitional endoplasmic reticulum ATPase
E: Transitional endoplasmic reticulum ATPase
F: Transitional endoplasmic reticulum ATPase


Theoretical massNumber of molelcules
Total (without water)964,1429
Polymers964,1429
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Deubiquitinating protein VCPIP1 / Valosin-containing protein p97/p47 complex-interacting protein 1 / Valosin-containing protein ...Valosin-containing protein p97/p47 complex-interacting protein 1 / Valosin-containing protein p97/p47 complex-interacting protein p135 / VCP/p47 complex-interacting 135-kDa protein


Mass: 137335.422 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: N-term Strep-tagged VCPIP1 / Source: (gene. exp.) Homo sapiens (human) / Gene: VCPIP1, KIAA1850, VCIP135 / Cell (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: Q96JH7, ubiquitinyl hydrolase 1
#2: Protein
Transitional endoplasmic reticulum ATPase / TER ATPase / 15S Mg(2+)-ATPase p97 subunit / Valosin-containing protein / VCP


Mass: 92022.539 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: N-term FLAG-tagged VCP / Source: (gene. exp.) Homo sapiens (human) / Gene: VCP, HEL-220, HEL-S-70 / Cell (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: P55072, vesicle-fusing ATPase
Has protein modificationY

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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

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Complex of valosin containing protein (VCP)/p97 bound to valosin containing protein interacting protein 1 (VCPIP1) and p47COMPLEXFull length valosin containing protein (VCP)/p97 with full length valosin containing protein interacting protein 1 (VCPIP1) and p47all0MULTIPLE SOURCES
2Valosin containing protein (VCP)COMPLEX#21RECOMBINANT
3Valosin containing protein interacting domain (VCPID) with stalk regionCOMPLEX#11RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
22
43
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
53Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
53Escherichia coli (E. coli)562
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
130 mMHEPES1
2150 mMsodium chlorideNaCl1
33 mMTCEP1
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Final concentration of 0.2 mM CHAPSO
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 283.15 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: 2200 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.87 sec. / Electron dose: 49.22 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 12261
EM imaging opticsEnergyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.6particle selection
2EPU3.7image acquisitionData collection in counting mode, using multi-shot scheme (9 holes per stage position, 3 movies per hole)
4cryoSPARC4.6CTF correction
7UCSF ChimeraX1.6model fitting
8ISOLDEmodel fitting
10cryoSPARC4.6initial Euler assignment
11cryoSPARC4.6.0final Euler assignment
13cryoSPARC4.6.03D reconstruction
14PHENIX1.21.1_5286model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2003371
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 77321 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 5FTK

5ftk


Accession code: 5FTK / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 90.93 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002428983
ELECTRON MICROSCOPYf_angle_d0.446439099
ELECTRON MICROSCOPYf_chiral_restr0.03844332
ELECTRON MICROSCOPYf_plane_restr0.00375185
ELECTRON MICROSCOPYf_dihedral_angle_d5.44394003

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