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- PDB-8j1p: Cryo-EM structure of Ufd4 in complex with K29/48 triUb -

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Basic information

Entry
Database: PDB / ID: 8j1p
TitleCryo-EM structure of Ufd4 in complex with K29/48 triUb
Components
  • (Ubiquitin) x 2
  • Ubiquitin fusion degradation protein 4
KeywordsLYASE / Ufd4 / HECT / E3 / K29/48
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.31 Å
AuthorsAi, H.S. / Mao, J.X. / Wu, X.W. / Pan, M. / Liu, L.
Funding support China, 1items
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, J.X. / Ai, H.S. / Wu, X.W. / Pan, M. / Liu, L.
History
DepositionApr 13, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.0Apr 17, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 17, 2024Data content type: Additional map / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 17, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 17, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 17, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 17, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 25, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin fusion degradation protein 4
C: Ubiquitin
D: Ubiquitin
E: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)193,7304
Polymers193,7304
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Ubiquitin fusion degradation protein 4 / UB fusion protein 4 / HECT-type E3 ubiquitin transferase UFD4


Mass: 168026.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: UFD4, YKL010C, YKL162 / Production host: Saccharomyces cerevisiae BY4741 (yeast)
References: UniProt: P33202, Transferases; Acyltransferases; Aminoacyltransferases, HECT-type E3 ubiquitin transferase
#2: Protein Ubiquitin


Mass: 8576.831 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#3: Protein Ubiquitin


Mass: 8550.794 Da / Num. of mol.: 1 / Mutation: K29C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Complex of Ufd4 in complex with K29/48 TriUbCOMPLEXall0RECOMBINANT
2Ufd4COMPLEX#11RECOMBINANT
3UbCOMPLEX#2-#31RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
23Homo sapiens (human)9606
32Saccharomyces cerevisiae (brewer's yeast)4932
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
23Escherichia coli (E. coli)562
32Saccharomyces cerevisiae BY4741 (yeast)1247190BY4741
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 43.3 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 172037 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00311709
ELECTRON MICROSCOPYf_angle_d0.74615817
ELECTRON MICROSCOPYf_dihedral_angle_d5.6331545
ELECTRON MICROSCOPYf_chiral_restr0.0451864
ELECTRON MICROSCOPYf_plane_restr0.0042011

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