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- PDB-9wbv: Cryo-EM structure of the human UBR2 N-domain in complex with tryp... -

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Basic information

Entry
Database: PDB / ID: 9wbv
TitleCryo-EM structure of the human UBR2 N-domain in complex with tryptophan
ComponentsE3 ubiquitin-protein ligase UBR2
KeywordsMETAL BINDING PROTEIN / Ubiquitinalytion
Function / homology
Function and homology information


histone H2A ubiquitin ligase activity / L-leucine binding / ubiquitin-dependent protein catabolic process via the N-end rule pathway / male meiotic nuclear division / transposable element silencing / cellular response to L-leucine / positive regulation of T cell receptor signaling pathway / negative regulation of TOR signaling / reciprocal meiotic recombination / ubiquitin ligase complex ...histone H2A ubiquitin ligase activity / L-leucine binding / ubiquitin-dependent protein catabolic process via the N-end rule pathway / male meiotic nuclear division / transposable element silencing / cellular response to L-leucine / positive regulation of T cell receptor signaling pathway / negative regulation of TOR signaling / reciprocal meiotic recombination / ubiquitin ligase complex / protein K63-linked ubiquitination / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / heterochromatin formation / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / chromatin / zinc ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / E3 ubiquitin-protein ligase ELL-like / E3 ubiquitin-protein ligase UBR-like, C-terminal / : / Proteolysis_6 C-terminal / E3 ubiquitin-protein ligase UBR1-like, winged-helix domain / E3 ubiquitin-protein ligase UBR1-like / Adaptor protein ClpS, core / ATP-dependent Clp protease adaptor protein ClpS / Putative zinc finger in N-recognin (UBR box) ...: / E3 ubiquitin-protein ligase ELL-like / E3 ubiquitin-protein ligase UBR-like, C-terminal / : / Proteolysis_6 C-terminal / E3 ubiquitin-protein ligase UBR1-like, winged-helix domain / E3 ubiquitin-protein ligase UBR1-like / Adaptor protein ClpS, core / ATP-dependent Clp protease adaptor protein ClpS / Putative zinc finger in N-recognin (UBR box) / Zinc finger, UBR-type / Zinc finger UBR-type profile. / Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / Winged helix DNA-binding domain superfamily
Similarity search - Domain/homology
TRYPTOPHAN / E3 ubiquitin-protein ligase UBR2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.13 Å
AuthorsYan, R. / Hu, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of the human UBR2 N-domain in complex with tryptophan
Authors: Yan, R. / Hu, Z.
History
DepositionAug 15, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase UBR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,9852
Polymers200,7811
Non-polymers2041
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein E3 ubiquitin-protein ligase UBR2 / N-recognin-2 / Ubiquitin-protein ligase E3-alpha-2 / Ubiquitin-protein ligase E3-alpha-II


Mass: 200781.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBR2, C6orf133, KIAA0349 / Production host: Eukaryota (eukaryotes)
References: UniProt: Q8IWV8, RING-type E3 ubiquitin transferase
#2: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2O2
Has ligand of interestN
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

ComponentName: Cryo-EM structure of the human UBR2 N-domain in complex with tryptophan
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Eukaryota (eukaryotes)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1400 nm
Image recordingElectron dose: 1.5625 e/Å2 / Film or detector model: DIRECT ELECTRON APOLLO (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 416289 / Symmetry type: POINT

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