[English] 日本語
Yorodumi
- EMDB-35929: Cryo-EM structure of Ufd4 in complex with K29/48 triUb -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-35929
TitleCryo-EM structure of Ufd4 in complex with K29/48 triUb
Map dataUfd4 in complex with K29/K48 TriUb (3.31 angstrom)
Sample
  • Complex: Complex of Ufd4 in complex with K29/48 TriUb
    • Complex: Ufd4
      • Protein or peptide: Ubiquitin fusion degradation protein 4
    • Complex: Ub
      • Protein or peptide: Ubiquitin
      • Protein or peptide: Ubiquitin
KeywordsUfd4 / HECT / E3 / K29/48 / LYASE
Function / homology
Function and homology information


proteasome regulatory particle binding / protein K29-linked ubiquitination / free ubiquitin chain polymerization / Antigen processing: Ubiquitination & Proteasome degradation / HECT-type E3 ubiquitin transferase / Transferases; Acyltransferases; Aminoacyltransferases / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule ...proteasome regulatory particle binding / protein K29-linked ubiquitination / free ubiquitin chain polymerization / Antigen processing: Ubiquitination & Proteasome degradation / HECT-type E3 ubiquitin transferase / Transferases; Acyltransferases; Aminoacyltransferases / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / energy homeostasis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Constitutive Signaling by NOTCH1 HD Domain Mutants / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Pexophagy / InlA-mediated entry of Listeria monocytogenes into host cells / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / NF-kB is activated and signals survival / Regulation of PTEN localization / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Gap-filling DNA repair synthesis and ligation in GG-NER / Downregulation of TGF-beta receptor signaling / Translesion synthesis by POLI / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Regulation of activated PAK-2p34 by proteasome mediated degradation / neuron projection morphogenesis / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / regulation of mitochondrial membrane potential / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / positive regulation of protein ubiquitination / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / NOTCH3 Activation and Transmission of Signal to the Nucleus / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Negative regulators of DDX58/IFIH1 signaling / Degradation of DVL / Deactivation of the beta-catenin transactivating complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Recognition of DNA damage by PCNA-containing replication complex / Fanconi Anemia Pathway
Similarity search - Function
E3 ubiquitin-protein ligase HECTD1/TRIP12-like / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Armadillo-like helical ...E3 ubiquitin-protein ligase HECTD1/TRIP12-like / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Armadillo-like helical / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Armadillo-type fold / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Polyubiquitin-B / Ubiquitin fusion degradation protein 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.31 Å
AuthorsAi HS / Mao JX / Wu XW / Pan M / Liu L
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structural Insights into the Molecular Mechanism of Ufd4-catalyzed Elongation of K48-linked Ubiquitin Chain through Lys29 Linkage
Authors: Mao JX / Ai HS / Wu XW / Pan M / Liu L
History
DepositionApr 13, 2023-
Header (metadata) releaseApr 17, 2024-
Map releaseApr 17, 2024-
UpdateApr 17, 2024-
Current statusApr 17, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_35929.png

Downloads & links

-
Map

FileDownload / File: emd_35929.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUfd4 in complex with K29/K48 TriUb (3.31 angstrom)
Voxel sizeX=Y=Z: 1.074 Å
Density
Contour LevelBy AUTHOR: 0.013
Minimum - Maximum-0.047338333 - 0.07969289
Average (Standard dev.)0.0001258466 (±0.0017035115)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 274.944 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Ufd4 in complex with K29/K48 TriUb (3.60 angstrom)...

Fileemd_35929_additional_1.map
AnnotationUfd4 in complex with K29/K48 TriUb (3.60 angstrom) with a better resolution at donor Ub
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_35929_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_35929_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Complex of Ufd4 in complex with K29/48 TriUb

EntireName: Complex of Ufd4 in complex with K29/48 TriUb
Components
  • Complex: Complex of Ufd4 in complex with K29/48 TriUb
    • Complex: Ufd4
      • Protein or peptide: Ubiquitin fusion degradation protein 4
    • Complex: Ub
      • Protein or peptide: Ubiquitin
      • Protein or peptide: Ubiquitin

-
Supramolecule #1: Complex of Ufd4 in complex with K29/48 TriUb

SupramoleculeName: Complex of Ufd4 in complex with K29/48 TriUb / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

-
Supramolecule #2: Ufd4

SupramoleculeName: Ufd4 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

-
Supramolecule #3: Ub

SupramoleculeName: Ub / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Ubiquitin fusion degradation protein 4

MacromoleculeName: Ubiquitin fusion degradation protein 4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Transferases; Acyltransferases; Aminoacyltransferases
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 168.026031 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae BY4741 (yeast)
SequenceString: MSENNSHNLD EHESHSENSD YMMDTQVEDD YDEDGHVQGE YSYYPDEDED EHMLSSVGSF EADDGEDDDN DYHHEDDSGL LYGYHRTQN GSDEDRNEEE DGLERSHDNN EFGSNPLHLP DILETFAQRL EQRRQTSEGL GQHPVGRTLP EILSMIGGRM E RSAESSAR ...String:
MSENNSHNLD EHESHSENSD YMMDTQVEDD YDEDGHVQGE YSYYPDEDED EHMLSSVGSF EADDGEDDDN DYHHEDDSGL LYGYHRTQN GSDEDRNEEE DGLERSHDNN EFGSNPLHLP DILETFAQRL EQRRQTSEGL GQHPVGRTLP EILSMIGGRM E RSAESSAR NERISKLIEN TGNASEDPYI AMESLKELSE NILMMNQMVV DRIIPMETLI GNIAAILSDK ILREELELQM QA CRCMYNL FEVCPESISI AVDEHVIPIL QGKLVEISYI DLAEQVLETV EYISRVHGRD ILKTGQLSIY VQFFDFLTIH AQR KAIAIV SNACSSIRTD DFKTIVEVLP TLKPIFSNAT DQPILTRLVN AMYGICGALH GVDKFETLFS LDLIERIVQL VSIQ DTPLE NKLKCLDILT VLAMSSDVLS RELREKTDIV DMATRSFQHY SKSPNAGLHE TLIYVPNSLL ISISRFIVVL FPPED ERIL SADKYTGNSD RGVISNQEKF DSLVQCLIPI LVEIYTNAAD FDVRRYVLIA LLRVVSCINN STAKAINDQL IKLIGS ILA QKETASNANG TYSSEAGTLL VGGLSLLDLI CKKFSELFFP SIKREGIFDL VKDLSVDFNN IDLKEDGNEN ISLSDEE GD LHSSIEECDE GDEEYDYEFT DMEIPDSVKP KKISIHIFRT LSLAYIKNKG VNLVNRVLSQ MNVEQEAITE ELHQIEGV V SILENPSTPD KTEEDWKGIW SVLKKCIFHE DFDVSGFEFT STGLASSITK RITSSTVSHF ILAKSFLEVF EDCIDRFLE ILQSALTRLE NFSIVDCGLH DGGGVSSLAK EIKIKLVYDG DASKDNIGTD LSSTIVSVHC IASFTSLNEF LRHRMVRMRF LNSLIPNLT SSSTEADREE EENCLDHMRK KNFDFFYDNE KVDMESTVFG VIFNTFVRRN RDLKTLWDDT HTIKFCKSLE G NNRESEAA EEANEGKKLR DFYKKREFAQ VDTGSSADIL TLLDFLHSCG VKSDSFINSK LSAKLARQLD EPLVVASGAL PD WSLFLTR RFPFLFPFDT RMLFLQCTSF GYGRLIQLWK NKSKGSKDLR NDEALQQLGR ITRRKLRISR KTIFATGLKI LSK YGSSPD VLEIEYQEEA GTGLGPTLEF YSVVSKYFAR KSLNMWRCNS YSYRSEMDVD TTDDYITTLL FPEPLNPFSN NEKV IELFG YLGTFVARSL LDNRILDFRF SKVFFELLHR MSTPNVTTVP SDVETCLLMI ELVDPLLAKS LKYIVANKDD NMTLE SLSL TFTVPGNDDI ELIPGGCNKS LNSSNVEEYI HGVIDQILGK GIEKQLKAFI EGFSKVFSYE RMLILFPDEL VDIFGR VEE DWSMATLYTN LNAEHGYTMD SSIIHDFISI ISAFGKHERR LFLQFLTGSP KLPIGGFKSL NPKFTVVLKH AEDGLTA DE YLPSVMTCAN YLKLPKYTSK DIMRSRLCQA IEEGAGAFLL S

UniProtKB: Ubiquitin fusion degradation protein 4

-
Macromolecule #2: Ubiquitin

MacromoleculeName: Ubiquitin / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.576831 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG

UniProtKB: Polyubiquitin-B

-
Macromolecule #3: Ubiquitin

MacromoleculeName: Ubiquitin / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.550794 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKACI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG

UniProtKB: Polyubiquitin-B

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 43.3 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 172037

+
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