[English] 日本語
Yorodumi
- EMDB-2319: Cryo-EM of full-length p97-FAF1 protein complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2319
TitleCryo-EM of full-length p97-FAF1 protein complex
Map dataReconstruction of full-length p97-FAF1 protein complex
Sample
  • Sample: Full-length p97-FAF1
  • Protein or peptide: p97
  • Protein or peptide: Fas-associated factor 1
Function / homology
Function and homology information


positive regulation of protein catabolic process => GO:0045732 / RHOH GTPase cycle / HSF1 activation / : / Protein methylation / Translesion Synthesis by POLH / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / Ovarian tumor domain proteases ...positive regulation of protein catabolic process => GO:0045732 / RHOH GTPase cycle / HSF1 activation / : / Protein methylation / Translesion Synthesis by POLH / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / Ovarian tumor domain proteases / Hedgehog ligand biogenesis / cytoplasmic sequestering of NF-kappaB / cell death / KEAP1-NFE2L2 pathway / ABC-family proteins mediated transport / Neddylation / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / protein-DNA covalent cross-linking repair / endosome to lysosome transport via multivesicular body sorting pathway / positive regulation of ubiquitin-dependent protein catabolic process / endoplasmic reticulum stress-induced pre-emptive quality control / cellular response to arsenite ion / BAT3 complex binding / Derlin-1 retrotranslocation complex / positive regulation of protein K63-linked deubiquitination / deubiquitinase activator activity / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / aggresome assembly / regulation of protein localization to chromatin / NADH metabolic process / vesicle-fusing ATPase / : / positive regulation of mitochondrial membrane potential / stress granule disassembly / K48-linked polyubiquitin modification-dependent protein binding / negative regulation of protein localization to chromatin / ERAD pathway / ubiquitin-modified protein reader activity / retrograde protein transport, ER to cytosol / regulation of aerobic respiration / ATPase complex / regulation of synapse organization / positive regulation of ATP biosynthetic process / ubiquitin-specific protease binding / regulation of protein catabolic process / ubiquitin-like protein ligase binding / autophagosome maturation / polyubiquitin modification-dependent protein binding / NF-kappaB binding / translesion synthesis / endoplasmic reticulum to Golgi vesicle-mediated transport / MHC class I protein binding / positive regulation of DNA replication / interstrand cross-link repair / negative regulation of smoothened signaling pathway / regulation of cell adhesion / ATP metabolic process / : / heat shock protein binding / Neutrophil degranulation / proteasome complex / lipid droplet / viral genome replication / ubiquitin binding / ADP binding / proteasomal protein catabolic process / positive regulation of protein-containing complex assembly / macroautophagy / autophagy / cytoplasmic stress granule / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of canonical Wnt signaling pathway / positive regulation of protein catabolic process / double-strand break repair / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / site of double-strand break / myelin sheath / cellular response to heat / nuclear envelope / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein phosphatase binding / protein ubiquitination / protein domain specific binding / DNA repair / lipid binding / glutamatergic synapse / synapse / apoptotic process / DNA damage response / ubiquitin protein ligase binding / protein-containing complex binding / endoplasmic reticulum membrane / protein kinase binding / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity
Similarity search - Function
FAS-associated factor 1-like, UBX domain / FAF1, UBA-like domain / UAS / UAS / Domain present in ubiquitin-regulatory proteins / UBX domain / UBX domain / UBX domain profile. / AAA ATPase, CDC48 family / Cell division protein 48 (CDC48), N-terminal domain ...FAS-associated factor 1-like, UBX domain / FAF1, UBA-like domain / UAS / UAS / Domain present in ubiquitin-regulatory proteins / UBX domain / UBX domain / UBX 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 / Thioredoxin-like superfamily / 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
FAS-associated factor 1 / Transitional endoplasmic reticulum ATPase
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 17.0 Å
AuthorsEwens CA / Kloppsteck P / McKeown C / Ebong I-O / Robinson C / Zhang X / Freemont P
CitationJournal: J Biol Chem / Year: 2014
Title: The p97-FAF1 protein complex reveals a common mode of p97 adaptor binding.
Authors: Caroline A Ewens / Silvia Panico / Patrik Kloppsteck / Ciaran McKeown / Ima-Obong Ebong / Carol Robinson / Xiaodong Zhang / Paul S Freemont /
Abstract: p97, also known as valosin-containing protein, is a versatile participant in the ubiquitin-proteasome system. p97 interacts with a large network of adaptor proteins to process ubiquitylated ...p97, also known as valosin-containing protein, is a versatile participant in the ubiquitin-proteasome system. p97 interacts with a large network of adaptor proteins to process ubiquitylated substrates in different cellular pathways, including endoplasmic reticulum-associated degradation and transcription factor activation. p97 and its adaptor Fas-associated factor-1 (FAF1) both have roles in the ubiquitin-proteasome system during NF-κB activation, although the mechanisms are unknown. FAF1 itself also has emerging roles in other cell-cycle pathways and displays altered expression levels in various cancer cell lines. We have performed a detailed study the p97-FAF1 interaction. We show that FAF1 binds p97 stably and in a stoichiometry of 3 to 6. Cryo-EM analysis of p97-FAF1 yielded a 17 Å reconstruction of the complex with FAF1 above the p97 ring. Characteristics of p97-FAF1 uncovered in this study reveal common features in the interactions of p97, providing mechanistic insight into how p97 mediates diverse functionalities.
History
DepositionFeb 23, 2013-
Header (metadata) releaseMar 13, 2013-
Map releaseMar 12, 2014-
UpdateMay 7, 2014-
Current statusMay 7, 2014Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0296
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0296
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

2319-for-emd...

Downloads & links

-
Map

FileDownload / File: emd_2319.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of full-length p97-FAF1 protein complex
Voxel sizeX=Y=Z: 3.52 Å
Density
Contour LevelBy AUTHOR: 0.0296 / Movie #1: 0.0296
Minimum - Maximum-0.18447417 - 0.68788624
Average (Standard dev.)0.00144989 (±0.02399133)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-64-64-64
Dimensions128128128
Spacing128128128
CellA=B=C: 450.56 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.523.523.52
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z450.560450.560450.560
α/β/γ90.00090.00090.000
start NX/NY/NZ-36-12-40
NX/NY/NZ732581
MAP C/R/S123
start NC/NR/NS-64-64-64
NC/NR/NS128128128
D min/max/mean-0.1840.6880.001

-
Supplemental data

-
Sample components

-
Entire : Full-length p97-FAF1

EntireName: Full-length p97-FAF1
Components
  • Sample: Full-length p97-FAF1
  • Protein or peptide: p97
  • Protein or peptide: Fas-associated factor 1

-
Supramolecule #1000: Full-length p97-FAF1

SupramoleculeName: Full-length p97-FAF1 / type: sample / ID: 1000
Oligomeric state: One hexamer of p97 bound to one trimer of FAF1
Number unique components: 2
Molecular weightTheoretical: 780 KDa / Method: Theoretical

-
Macromolecule #1: p97

MacromoleculeName: p97 / type: protein_or_peptide / ID: 1 / Name.synonym: VCP / Details: full-length, wild-type / Number of copies: 1 / Oligomeric state: hexamer / Recombinant expression: Yes
Source (natural)Organism: Mus musculus (house mouse) / synonym: House Mouse
Molecular weightExperimental: 550 KDa / Theoretical: 550 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: Rosetta 2 / Recombinant plasmid: PET28b
SequenceUniProtKB: Transitional endoplasmic reticulum ATPase

-
Macromolecule #2: Fas-associated factor 1

MacromoleculeName: Fas-associated factor 1 / type: protein_or_peptide / ID: 2 / Details: N-terminally His6-tagged, full-length, wild-type / Number of copies: 1 / Oligomeric state: trimer / Recombinant expression: Yes
Source (natural)Organism: Mus musculus (house mouse) / synonym: House Mouse
Molecular weightTheoretical: 230 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: Rosetta2 / Recombinant plasmid: pProEx
SequenceUniProtKB: FAS-associated factor 1

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.3 mg/mL
BufferpH: 7.4 / Details: 20mM HEPES, 150mM KCl
GridDetails: holey carbon, quantifoil, glow discharged
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK IV / Method: 3sec blot, 0sec drain

-
Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.1 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Nitrogen cooled / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureMin: 94 K / Max: 104 K / Average: 94 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification
DateDec 20, 2011
Image recordingCategory: CCD / Film or detector model: GENERIC TVIPS / Digitization - Sampling interval: 1.76 µm / Number real images: 281 / Average electron dose: 10 e/Å2 / Bits/pixel: 16

-
Image processing

CTF correctionDetails: each micrograph
Final two d classificationNumber classes: 457
Final angle assignmentDetails: Imagic
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: OTHER / Software - Name: Imagic / Number images used: 4500

-
Atomic model buiding 1

Initial modelPDB ID:

3cf2


Chain - Chain ID: a
SoftwareName: chimera, WEDA
Detailsdomains were separately fitted and taking account of symmetry
RefinementSpace: REAL / Protocol: RIGID BODY FIT

-
Atomic model buiding 2

Initial modelPDB ID:

3qq8


Chain - #0 - Chain ID: a / Chain - #1 - Chain ID: b
SoftwareName: chimera, WEDA
Detailsdomains were separately fitted and taking account of symmetry
RefinementSpace: REAL / Protocol: RIGID BODY FIT

+
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