[English] 日本語
Yorodumi
- EMDB-48505: Cryo-EM structure of p47 bound to VCP N-domain (with D1 domain) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-48505
TitleCryo-EM structure of p47 bound to VCP N-domain (with D1 domain)
Map data
Sample
  • Complex: Complex of valosin containing protein (VCP)/p97 bound to valosin containing protein interacting protein 1 (VCPIP1) and p47
    • Complex: Valosin containing protein (VCP)
      • Protein or peptide: Transitional endoplasmic reticulum ATPase
    • Complex: p47
      • Protein or peptide: NSFL1 cofactor p47
Keywordsdouble-ring hexameric complex / valosin containing protein / ATPase / VCP / mammalian / p97 / p47 / adapter / SHP / UBX / HYDROLASE
Function / homology
Function and homology information


negative regulation of protein localization to centrosome / positive regulation of mitotic centrosome separation / nuclear membrane reassembly / : / 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 ...negative regulation of protein localization to centrosome / positive regulation of mitotic centrosome separation / nuclear membrane reassembly / : / 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 / mitotic spindle disassembly / ubiquitin-modified protein reader activity / 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 / Golgi organization / positive regulation of ATP biosynthetic process / MHC class I protein binding / ubiquitin-like protein ligase binding / establishment of mitotic spindle orientation / RHOH GTPase cycle / polyubiquitin modification-dependent protein binding / autophagosome assembly / autophagosome maturation / negative regulation of hippo signaling / HSF1 activation / endoplasmic reticulum to Golgi vesicle-mediated transport / translesion synthesis / interstrand cross-link repair / ATP metabolic process / endoplasmic reticulum unfolded protein response / proteasomal protein catabolic process / Protein methylation / Attachment and Entry / ERAD pathway / lipid droplet / proteasome complex / viral genome replication / ubiquitin binding / Josephin domain DUBs / negative regulation of smoothened signaling pathway / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / macroautophagy / establishment of protein localization / Hh mutants are degraded by ERAD / positive regulation of protein-containing complex assembly / 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 / Ovarian tumor domain proteases / KEAP1-NFE2L2 pathway / 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 / chromosome / cellular response to heat / site of double-strand break / Neddylation / 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 / membrane fusion / Attachment and Entry / protein ubiquitination / ciliary basal body / protein domain specific binding / DNA repair / intracellular membrane-bounded organelle / DNA damage response
Similarity search - Function
SEP domain / NSFL1 cofactor p47, SEP domain superfamily / SEP domain / SEP domain profile. / Domain present in Saccharomyces cerevisiae Shp1, Drosophila melanogaster eyes closed gene (eyc), and vertebrate p47. / Domain present in ubiquitin-regulatory proteins / UBX domain / UBX domain / UBX domain profile. / UBA-like domain ...SEP domain / NSFL1 cofactor p47, SEP domain superfamily / SEP domain / SEP domain profile. / Domain present in Saccharomyces cerevisiae Shp1, Drosophila melanogaster eyes closed gene (eyc), and vertebrate p47. / Domain present in ubiquitin-regulatory proteins / UBX domain / UBX domain / UBX domain profile. / UBA-like 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 / UBA-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 / NSFL1 cofactor p47
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsShah B / Hunkeler M / Buhrlage SJ / Fischer EF
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

-
Structure visualization

Supplemental images

emd_48505.png

Downloads & links

-
Map

FileDownload / File: emd_48505.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.96 Å/pix.
x 180 pix.
= 353.28 Å		1.96 Å/pix.
x 180 pix.
= 353.28 Å		1.96 Å/pix.
x 180 pix.
= 353.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.96267 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.187
Minimum - Maximum-0.6068542 - 1.0354465
Average (Standard dev.)-0.0011220628 (±0.024708107)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 353.28 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_48505_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Mask #2

Fileemd_48505_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_48505_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half-map B

Fileemd_48505_half_map_1.map
AnnotationHalf-map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half-map A

Fileemd_48505_half_map_2.map
AnnotationHalf-map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Complex of valosin containing protein (VCP)/p97 bound to valosin ...

EntireName: Complex of valosin containing protein (VCP)/p97 bound to valosin containing protein interacting protein 1 (VCPIP1) and p47
Components
  • Complex: Complex of valosin containing protein (VCP)/p97 bound to valosin containing protein interacting protein 1 (VCPIP1) and p47
    • Complex: Valosin containing protein (VCP)
      • Protein or peptide: Transitional endoplasmic reticulum ATPase
    • Complex: p47
      • Protein or peptide: NSFL1 cofactor p47

-
Supramolecule #1: Complex of valosin containing protein (VCP)/p97 bound to valosin ...

SupramoleculeName: Complex of valosin containing protein (VCP)/p97 bound to valosin containing protein interacting protein 1 (VCPIP1) and p47
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) and p47
Source (natural)Organism: Homo sapiens (human)

-
Supramolecule #2: Valosin containing protein (VCP)

SupramoleculeName: Valosin containing protein (VCP) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

-
Supramolecule #3: p47

SupramoleculeName: p47 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1 / Details: Adapter of valosin containing protein (VCP)/p97

-
Macromolecule #1: NSFL1 cofactor p47

MacromoleculeName: NSFL1 cofactor p47 / type: protein_or_peptide / ID: 1 / Details: N-term His tagged p47 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.535906 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHHHH HDLGTENLYF QSMMAAERQE ALREFVAVTG AEEDRARFFL ESAGWDLQIA LASFYEDGGD EDIVTISQAT PSSVSRGTA PSDNRVTSFR DLIHDQDEDE EEEEGQRFYA GGSERSGQQI VGPPRKKSPN ELVDDLFKGA KEHGAVAVER V TKSPGETS ...String:
MHHHHHHHHH HDLGTENLYF QSMMAAERQE ALREFVAVTG AEEDRARFFL ESAGWDLQIA LASFYEDGGD EDIVTISQAT PSSVSRGTA PSDNRVTSFR DLIHDQDEDE EEEEGQRFYA GGSERSGQQI VGPPRKKSPN ELVDDLFKGA KEHGAVAVER V TKSPGETS KPRPFAGGGY RLGAAPEEES AYVAGEKRQH SSQDVHVVLK LWKSGFSLDN GELRSYQDPS NAQFLESIRR GE VPAELRR LAHGGQVNLD MEDHRDEDFV KPKGAFKAFT GEGQKLGSTA PQVLSTSSPA QQAENEAKAS SSILIDESEP TTN IQIRLA DGGRLVQKFN HSHRISDIRL FIVDARPAMA ATSFILMTTF PNKELADESQ TLKEANLLNA VIVQRLT

UniProtKB: NSFL1 cofactor p47

-
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: 1 / 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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2 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
DetailsFinal concentration of 0.2 mM CHAPSO

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 12261 / Average exposure time: 2.87 sec. / Average electron dose: 49.22 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 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

+
Image processing

Particle selectionNumber selected: 2003371
CTF correctionSoftware - Name: cryoSPARC (ver. 4.60) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 54855
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.60)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

5ftk


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

PDB-9mpu:
Cryo-EM structure of p47 bound to VCP N-domain (with D1 domain)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more