[English] 日本語
Yorodumi
- EMDB-7477: Cdc48 in the presence of ADP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-7477
TitleCdc48 in the presence of ADP
Map dataCdc48-Npl4 complex in the presence of ATP-gamma-S
Sample
  • Organelle or cellular component: Cdc48
    • Protein or peptide: Cdc48
Biological speciesChaetomium thermophilum (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.2 Å
AuthorsKim KH / Bodnar NO
CitationJournal: Nat Struct Mol Biol / Year: 2018
Title: Structure of the Cdc48 ATPase with its ubiquitin-binding cofactor Ufd1-Npl4.
Authors: Nicholas O Bodnar / Kelly H Kim / Zhejian Ji / Thomas E Wales / Vladimir Svetlov / Evgeny Nudler / John R Engen / Thomas Walz / Tom A Rapoport /
Abstract: Many polyubiquitinated proteins are extracted from membranes or complexes by the conserved ATPase Cdc48 (in yeast; p97 or VCP in mammals) before proteasomal degradation. Each Cdc48 hexamer contains ...Many polyubiquitinated proteins are extracted from membranes or complexes by the conserved ATPase Cdc48 (in yeast; p97 or VCP in mammals) before proteasomal degradation. Each Cdc48 hexamer contains two stacked ATPase rings (D1 and D2) and six N-terminal (N) domains. Cdc48 binds various cofactors, including the Ufd1-Npl4 heterodimer. Here, we report structures of the Cdc48-Ufd1-Npl4 complex from Chaetomium thermophilum. Npl4 interacts through its UBX-like domain with a Cdc48 N domain, and it uses two Zn-finger domains to anchor the enzymatically inactive Mpr1-Pad1 N-terminal (MPN) domain, homologous to domains found in several isopeptidases, to the top of the D1 ATPase ring. The MPN domain of Npl4 is located above Cdc48's central pore, a position similar to the MPN domain from deubiquitinase Rpn11 in the proteasome. Our results indicate that Npl4 is unique among Cdc48 cofactors and suggest a mechanism for binding and translocation of polyubiquitinated substrates into the ATPase.
History
DepositionFeb 22, 2018-
Header (metadata) releaseMar 14, 2018-
Map releaseJul 4, 2018-
UpdateDec 5, 2018-
Current statusDec 5, 2018Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7477.png

Downloads & links

-
Map

FileDownload / File: emd_7477.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCdc48-Npl4 complex in the presence of ATP-gamma-S
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.24 Å/pix.
x 256 pix.
= 317.44 Å		1.24 Å/pix.
x 256 pix.
= 317.44 Å		1.24 Å/pix.
x 256 pix.
= 317.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.24 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.12085942 - 0.15911137
Average (Standard dev.)0.00046948393 (±0.006046737)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 317.44 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.241.241.24
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z317.440317.440317.440
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1210.1590.000

-
Supplemental data

-
Sample components

-
Entire : Cdc48

EntireName: Cdc48
Components
  • Organelle or cellular component: Cdc48
    • Protein or peptide: Cdc48

-
Supramolecule #1: Cdc48

SupramoleculeName: Cdc48 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Chaetomium thermophilum (fungus)
Recombinant expressionOrganism: Escherichia coli (E. coli)

-
Macromolecule #1: Cdc48

MacromoleculeName: Cdc48 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum (fungus)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAPESKDHKK KVNLTDPSGA EHREENDTAT AILKKKKKPN QLMVTDAVND DNSIIALSNN TMEALQLFRG DTVLVRGKKR RDTVLIVLAD DDLDDGSARI NRVVRHNLRV KHGDMITIHP CPDIKYAKRI AVLPIADTVE GLTGSLFDVF LAPYFREAYR PVRQGDLFTV ...String:
MAPESKDHKK KVNLTDPSGA EHREENDTAT AILKKKKKPN QLMVTDAVND DNSIIALSNN TMEALQLFRG DTVLVRGKKR RDTVLIVLAD DDLDDGSARI NRVVRHNLRV KHGDMITIHP CPDIKYAKRI AVLPIADTVE GLTGSLFDVF LAPYFREAYR PVRQGDLFTV RGGMRQVEFK VVEVDPPEYG IVAQDTIIHC EGEPIPREEE ENNLNEVGYD DIGGCRKQLA QIREMVELPL RHPQLFKSIG IKPPRGVLLY GPPGTGKTLM ARAVANETGA FFFLINGPEI MSKMAGESES NLRKAFEEAE KNSPAIIFID EIDSIAPKRE KTNGEVERRV VSQLLTLMDG MKARSNVVVM AATNRPNSID PALRRFGRFD REVDIGIPDP TGRLEILQIH TKNMKLADDV DLEQIAAETH GYVGSDLAAL CSEAAMQQIR EKMDLIDLDE DTIDAEVLDS LGVTMDNFRY ALGVSNPSAL REVAVVEVPN VRWEDIGGLE QVKQELKEQV QYPVDHPEKF LKFGLSPSRG VLFYGPPGTG KTMLAKAVAN ECAANFISVK GPELLSMWFG ESESNIRDIF DKARAAAPCV VFLDELDSIA KARGGSIGDA GGASDRVVNQ LLTEMDGMTS KKNVFVIGAT NRPEQLDPAL CRPGRLDQLI YVPLPDEAGR LSILKAQLRK TPVSKDVDLA YIASKTHGFS GADLAFITQR AVKLAIKESI AAEIERQKAR EAAGEDVNME DDEDPVPELT KRHFEEAMRD ARRSVSDVEI RRYEAFAQQM KNAGPGAFFK FPDSTTDNSA SNAAGNSFGD AGNDDDLYT

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
50.0 mMHEPES
150.0 mMsodium chlorideNaCl
5.0 mMmagnesium chlorideMgCl2
0.5 mMTCEP
100.0 uMADP
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Instrument: GATAN CRYOPLUNGE 3

-
Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 1628 / Average exposure time: 6.0 sec. / Average electron dose: 1.04 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: 3.0 µm / Nominal defocus min: 1.6 µm / Nominal magnification: 31000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 52348
CTF correctionSoftware - Name: CTFFIND
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 7.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 9751
Initial angle assignmentType: COMMON LINE / Software - Name: SPARX
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION
FSC plot (resolution estimation)

+
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