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- EMDB-35929: Cryo-EM structure of Ufd4 in complex with K29/48 triUb -

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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 / HECT-type E3 ubiquitin transferase / Transferases; Acyltransferases; Aminoacyltransferases / symbiont entry into host cell via disruption of host cell glycocalyx / symbiont entry into host cell via disruption of host cell envelope / virus tail / Antigen processing: Ubiquitination & Proteasome degradation / protein polyubiquitination ...proteasome regulatory particle binding / protein K29-linked ubiquitination / free ubiquitin chain polymerization / HECT-type E3 ubiquitin transferase / Transferases; Acyltransferases; Aminoacyltransferases / symbiont entry into host cell via disruption of host cell glycocalyx / symbiont entry into host cell via disruption of host cell envelope / virus tail / Antigen processing: Ubiquitination & Proteasome degradation / protein polyubiquitination / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear speck / mitochondrion / nucleus / cytoplasm
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 / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Pectin lyase fold / Pectin lyase fold/virulence factor ...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 / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Pectin lyase fold / Pectin lyase fold/virulence factor / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Tail fiber / 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-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35929.png

Downloads & links

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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)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 274.944 Å		1.07 Å/pix.
x 256 pix.
= 274.944 Å		1.07 Å/pix.
x 256 pix.
= 274.944 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.074 Å
Density

Histogram

Histogram (log scale)
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 °

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Supplemental data

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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)

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Half map: #1

Fileemd_35929_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_35929_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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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

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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

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Supramolecule #2: Ufd4

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

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Supramolecule #3: Ub

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

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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

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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: Tail fiber

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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: Tail fiber

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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: 7.5
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: 43.3 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: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 172037
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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