+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35929 | |||||||||
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Title | Cryo-EM structure of Ufd4 in complex with K29/48 triUb | |||||||||
Map data | Ufd4 in complex with K29/K48 TriUb (3.31 angstrom) | |||||||||
Sample |
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Keywords | Ufd4 / HECT / E3 / K29/48 / LYASE | |||||||||
Function / homology | Function and homology information proteasome regulatory particle binding / free ubiquitin chain polymerization / protein K29-linked ubiquitination / 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 ...proteasome regulatory particle binding / free ubiquitin chain polymerization / protein K29-linked ubiquitination / 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 / Antigen processing: Ubiquitination & Proteasome degradation / regulation of neuron apoptotic process / energy homeostasis / Regulation of pyruvate metabolism / regulation of proteasomal protein catabolic process / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / 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 / Endosomal Sorting Complex Required For Transport (ESCRT) / 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 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / PINK1-PRKN Mediated Mitophagy / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Josephin domain DUBs / neuron projection morphogenesis / Gap-filling DNA repair synthesis and ligation in GG-NER / Regulation of activated PAK-2p34 by proteasome mediated degradation / 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 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / regulation of mitochondrial membrane potential / 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 / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.31 Å | |||||||||
Authors | Ai HS / Mao JX / Wu XW / Pan M / Liu L | |||||||||
Funding support | China, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_35929.map.gz | 4.5 MB | EMDB map data format | |
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Header (meta data) | emd-35929-v30.xml emd-35929.xml | 19.2 KB 19.2 KB | Display Display | EMDB header |
Images | emd_35929.png | 69.5 KB | ||
Filedesc metadata | emd-35929.cif.gz | 6.2 KB | ||
Others | emd_35929_additional_1.map.gz emd_35929_half_map_1.map.gz emd_35929_half_map_2.map.gz | 1.7 MB 49.7 MB 49.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35929 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35929 | HTTPS FTP |
-Validation report
Summary document | emd_35929_validation.pdf.gz | 732.3 KB | Display | EMDB validaton report |
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Full document | emd_35929_full_validation.pdf.gz | 731.9 KB | Display | |
Data in XML | emd_35929_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | emd_35929_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35929 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35929 | HTTPS FTP |
-Related structure data
Related structure data | 8j1pMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_35929.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Ufd4 in complex with K29/K48 TriUb (3.31 angstrom) | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.074 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Ufd4 in complex with K29/K48 TriUb (3.60 angstrom)...
File | emd_35929_additional_1.map | ||||||||||||
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Annotation | Ufd4 in complex with K29/K48 TriUb (3.60 angstrom) with a better resolution at donor Ub | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_35929_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_35929_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of Ufd4 in complex with K29/48 TriUb
Entire | Name: Complex of Ufd4 in complex with K29/48 TriUb |
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Components |
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-Supramolecule #1: Complex of Ufd4 in complex with K29/48 TriUb
Supramolecule | Name: Complex of Ufd4 in complex with K29/48 TriUb / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: Ufd4
Supramolecule | Name: Ufd4 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Supramolecule #3: Ub
Supramolecule | Name: Ub / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Ubiquitin fusion degradation protein 4
Macromolecule | Name: Ubiquitin fusion degradation protein 4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO EC number: Transferases; Acyltransferases; Aminoacyltransferases |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 168.026031 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae BY4741 (yeast) |
Sequence | String: 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
Macromolecule | Name: Ubiquitin / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 8.576831 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG UniProtKB: Polyubiquitin-B |
-Macromolecule #3: Ubiquitin
Macromolecule | Name: Ubiquitin / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 8.550794 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MQIFVKTLTG KTITLEVEPS DTIENVKACI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG UniProtKB: Polyubiquitin-B |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 43.3 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 172037 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |