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- EMDB-39360: Cryo-EM structure of P97-VCPIP1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-39360
TitleCryo-EM structure of P97-VCPIP1 complex
Map data
Sample
  • Complex: P97-VCPIP1 complex
    • Protein or peptide: Transitional endoplasmic reticulum ATPase
    • Protein or peptide: Deubiquitinating protein VCPIP1
KeywordsP97/VCP ATPase / Golgi apparatus / membrane fusion / VCPIP1 / HYDROLASE
Function / homology
Function and homology information


endoplasmic reticulum membrane fusion / protein K11-linked deubiquitination / Golgi reassembly / protein K48-linked deubiquitination / Golgi stack / positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / cytoplasm protein quality control ...endoplasmic reticulum membrane fusion / protein K11-linked deubiquitination / Golgi reassembly / protein K48-linked deubiquitination / Golgi stack / positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / cytoplasm protein quality control / endosome to lysosome transport via multivesicular body sorting pathway / endoplasmic reticulum stress-induced pre-emptive quality control / cellular response to arsenite ion / Derlin-1 retrotranslocation complex / BAT3 complex binding / protein-DNA covalent cross-linking repair / positive regulation of protein K63-linked deubiquitination / deubiquitinase activator activity / ubiquitin-modified protein reader activity / regulation of protein localization to chromatin / aggresome assembly / NADH metabolic process / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / vesicle-fusing ATPase / cellular response to misfolded protein / stress granule disassembly / negative regulation of protein localization to chromatin / positive regulation of mitochondrial membrane potential / retrograde protein transport, ER to cytosol / K48-linked polyubiquitin modification-dependent protein binding / regulation of aerobic respiration / regulation of synapse organization / positive regulation of ATP biosynthetic process / ATPase complex / ubiquitin-specific protease binding / MHC class I protein binding / ubiquitin-like protein ligase binding / RHOH GTPase cycle / polyubiquitin modification-dependent protein binding / autophagosome maturation / protein deubiquitination / HSF1 activation / negative regulation of hippo signaling / endoplasmic reticulum to Golgi vesicle-mediated transport / translesion synthesis / proteasomal protein catabolic process / Protein methylation / interstrand cross-link repair / ATP metabolic process / negative regulation of smoothened signaling pathway / endoplasmic reticulum unfolded protein response / ERAD pathway / Attachment and Entry / proteasome complex / viral genome replication / lipid droplet / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Hh mutants are degraded by ERAD / macroautophagy / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / positive regulation of protein-containing complex assembly / ADP binding / Translesion Synthesis by POLH / establishment of protein localization / ABC-family proteins mediated transport / : / autophagy / Aggrephagy / cytoplasmic stress granule / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of protein catabolic process / azurophil granule lumen / KEAP1-NFE2L2 pathway / positive regulation of canonical Wnt signaling pathway / Ovarian tumor domain proteases / double-strand break repair / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / E3 ubiquitin ligases ubiquitinate target proteins / site of double-strand break / Neddylation / cellular response to heat / ubiquitin-dependent protein catabolic process / protein phosphatase binding / secretory granule lumen / regulation of apoptotic process / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / ficolin-1-rich granule lumen / cysteine-type deubiquitinase activity / Attachment and Entry / protein ubiquitination / protein domain specific binding / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / DNA repair / 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: 3.45 Å
AuthorsLiu Y / Lu P / Gao H / Li F
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32370742 China
National Natural Science Foundation of China (NSFC)32271258 China
CitationJournal: Adv Sci (Weinh) / Year: 2024
Title: Molecular Basis of VCPIP1 and P97/VCP Interaction Reveals Its Functions in Post-Mitotic Golgi Reassembly.
Authors: Tianzhui Liao / Ruotong Li / Ping Lu / Yusong Liu / Rong Yang / Hao Guo / Zhuoxi Wu / Ruiwen Wang / Ling Yuan / Zhengmao Hu / Haishan Gao / Faxiang Li /
Abstract: The VCPIP1-P97/VCP (Valosin-Containing Protein) complex is required for post-mitotic Golgi cisternae reassembly and maintenance in interphase. However, the organization and mechanism of this complex ...The VCPIP1-P97/VCP (Valosin-Containing Protein) complex is required for post-mitotic Golgi cisternae reassembly and maintenance in interphase. However, the organization and mechanism of this complex in regulating Golgi membrane fusion is still elusive. Here, the cryo-electron microscopy (cryo-EM) structures of the human VCPIP1-P97/VCP complex are presented. These studies reveal that three independent VCPIP1 molecules sit over the C-terminal substrate exit tunnel formed by P97/VCP homo-hexamer, resulting in an unusual C3 to C6 symmetric barrel architecture. The UFD1 (unknown function domain 1) from VCPIP1, but not the N-terminal OTU domain and the C-terminal UBL domain, docks to the two adjacent D2 domains of P97/VCP, allosterically causing the cofactors binding domain-NTDs (N-terminal domains) of P97/VCP in a "UP" and D1 domain in an ATPase competent conformation. Conversely, VCPIP1 bound P97/VCP hexamer favors the binding of P47, and thus the intact SNARE complex, promoting Golgi membrane fusion. These studies not only reveal the unexpected organization of humanVCPIP1-P97/VCP complex, but also provide new insights into the mechanism of VCPIP1-P97/VCP mediated Golgi apparatus reassembly, which is a fundamental cellular event for protein and lipid processing.
History
DepositionMar 4, 2024-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateOct 2, 2024-
Current statusOct 2, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39360.png

Downloads & links

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Map

FileDownload / File: emd_39360.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 360 pix.
= 387.828 Å		1.08 Å/pix.
x 360 pix.
= 387.828 Å		1.08 Å/pix.
x 360 pix.
= 387.828 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0773 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.217
Minimum - Maximum-1.7458504 - 3.1606972
Average (Standard dev.)0.002306596 (±0.075422116)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 387.82797 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_39360_half_map_1.map
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Half map: #2

Fileemd_39360_half_map_2.map
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Sample components

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Entire : P97-VCPIP1 complex

EntireName: P97-VCPIP1 complex
Components
  • Complex: P97-VCPIP1 complex
    • Protein or peptide: Transitional endoplasmic reticulum ATPase
    • Protein or peptide: Deubiquitinating protein VCPIP1

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Supramolecule #1: P97-VCPIP1 complex

SupramoleculeName: P97-VCPIP1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Transitional endoplasmic reticulum ATPase

MacromoleculeName: Transitional endoplasmic reticulum ATPase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: vesicle-fusing ATPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 85.528961 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: LSTAILKQKN RPNRLIVDEA INEDNSVVSL SQPKMDELQL FRGDTVLLKG KKRREAVCIV LSDDTCSDEK IRMNRVVRNN LRVRLGDVI SIQPCPDVKY GKRIHVLPID DTVEGITGNL FEVYLKPYFL EAYRPIRKGD IFLVRGGMRA VEFKVVETDP S PYCIVAPD ...String:
LSTAILKQKN RPNRLIVDEA INEDNSVVSL SQPKMDELQL FRGDTVLLKG KKRREAVCIV LSDDTCSDEK IRMNRVVRNN LRVRLGDVI SIQPCPDVKY GKRIHVLPID DTVEGITGNL FEVYLKPYFL EAYRPIRKGD IFLVRGGMRA VEFKVVETDP S PYCIVAPD TVIHCEGEPI KREDEEESLN EVGYDDIGGC RKQLAQIKEM VELPLRHPAL FKAIGVKPPR GILLYGPPGT GK TLIARAV ANETGAFFFL INGPEIMSKL AGESESNLRK AFEEAEKNAP AIIFIDELDA IAPKREKTHG EVERRIVSQL LTL MDGLKQ RAHVIVMAAT NRPNSIDPAL RRFGRFDREV DIGIPDATGR LEILQIHTKN MKLADDVDLE QVANETHGHV GADL AALCS EAALQAIRKK MDLIDLEDET IDAEVMNSLA VTMDDFRWAL SQSNPSALRE TVVEVPQVTW EDIGGLEDVK RELQE LVQY PVEHPDKFLK FGMTPSKGVL FYGPPGCGKT LLAKAIANEC QANFISIKGP ELLTMWFGES EANVREIFDK ARQAAP CVL FFDELDSIAK ARGGNIGDGG GAADRVINQI LTEMDGMSTK KNVFIIGATN RPDIIDPAIL RPGRLDQLIY IPLPDEK SR VAILKANLRK SPVAKDVDLE FLAKMTNGFS GADLTEICQR ACKLAIRESI ESEIRRERER QTNPSAMEVE EDDPVPEI R RDHFEEAMRF ARRSVSDNDI RKYEMFAQTL QQSRGFGSFR FPS

UniProtKB: Transitional endoplasmic reticulum ATPase

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Macromolecule #2: Deubiquitinating protein VCPIP1

MacromoleculeName: Deubiquitinating protein VCPIP1 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: ubiquitinyl hydrolase 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 63.416523 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GVTGAPKKNT ELVKVMGLSN YHCKLLSPIL ARYGMDKQTG RAKLLRDMNQ GELFDCALLG DRAFLIEPEH VNTVGYGKDR SGSLLYLHD TLEDIKRANK SQECLIPVHV DGDGHCLVHA VSRALVGREL FWHALRENLK QHFQQHLARY QALFHDFIDA A EWEDIINE ...String:
GVTGAPKKNT ELVKVMGLSN YHCKLLSPIL ARYGMDKQTG RAKLLRDMNQ GELFDCALLG DRAFLIEPEH VNTVGYGKDR SGSLLYLHD TLEDIKRANK SQECLIPVHV DGDGHCLVHA VSRALVGREL FWHALRENLK QHFQQHLARY QALFHDFIDA A EWEDIINE CDPLFVPPEG VPLGLRNIHI FGLANVLHRP IILLDSLSGM RSSGDYSATF LPGLIPAEKC TGKDGHLNKP IC IAWSSSG RNHYIPLVGI KGAALPKLPM NLLPKAWGVP QDLIKKYIKL EEDGGCVIGG DRSLQDKYLL RLVAAMEEVF MDK HGIHPS LVADVHQYFY RRTGVIGVQP EEVTAAAKKA VMDNRLHKCL LCGALSELHV PPEWLAPGGK LYNLAKSTHG QLRT DKNYS FPLNNLVCSY DSVKDVLVPD YGMSNLTACN WCHGTSVRKV RGDGSIVYLD GDRTNSRSTG GKCGCGFKHF WDGKE YDNL PEAFPITLEW GGRVVRETVY WFQYESDSSL NSNVYDVAMK LVTKHFPGEF GSEILVQKVV HTILHQTAKK NPDDYT PVN IDGAHA

UniProtKB: Deubiquitinating protein VCPIP1

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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

BufferpH: 7.9
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 168188
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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