3D biomolecular Structures Determined by Us

Since 2019 the lab established, we have determined >30 protein structures by cryo-EM, X-ray crystallography and/or NMR spectroscopy. The table below lists all the structures we have determined and deposited. Some are not in published papers. Stay tuned for our updated news. Here are the list of structures determined, categorized by the projects.

Ubiquitin, variants, and design

• Machine-learning designed ubiquitin variants R4 and R10
  R4: PDB 8J0A (X-ray, 3.0 Å), 9LQM (X-ray, 1.4 Å)
  R10: PDB 9LQK (X-ray)
  Published in ACS Synthetic Biology(2023)

Enzymes in the ubiquitin-like protein cascades

• CryoEM structure of bovine UBA7 disulfide bonded with UBE2L6 and adenylated ISG15
  PDB: 9JTC (cryoEM)
  EMDB: 61794 (UBA7-UBE2L6-ISG15) and 61979 (MBP-fused UBA7-UBE2L6)
  Published in eLife(2025)

Deubiquitinase (DUB)

• Papain-like protease domain from SARS CoV2 NSP3
  PDB 7D47 8JUX (X-ray)

Protein Filaments and Fibrils

• Filamentous form of Ecoli Glutamine Synthetase
  PDB 7W85, EMDB 32352 (cryoEM)
  Published in Protein Science (2022)
• Fibril structure of alpha-synuclein A53T w/o, w/ Ca²⁺
  PDB 7WNZ (cryoEM) 7WO0 (w/ Ca²⁺, cryoEM)
  EMDB 32636, 32637, EMPIAR 11155, 11156
• A tetra-protofilament form of hamster prion 108-144
  PDB 7YAT, EDMB 33719 (cryoEM)
  Published in JACS (2022)

Biological enzymes

• RNA polymerase in complex with polymyxin resistance PmrA
  PDB 8JO2 (replaced) 7W8C, EMDB 36453 (replaced) 32354 (cryoEM)
  Published in Nucleic Acids Research (2023)
• Cryo-EM and crystal structures of a 723-aa malate synthase G
  PDB 7YQM (cryo-EM), 7YQN (X-ray), EMDB 34029, 34030, EMPIAR 11167 (cryoEM)
  Published in Journal of Structural Biology (2023)

Benchmarks

• 1.5 Å cryo-EM structure of mouse heavy-chain apoferritin in 290 nm gold foil holes (HexAuFoil)
  PDB 9IUY, EMDB 60915, EMPIAR 12240 (or at EMPIAR-PDBj)

Prior to joining IBC, AS

The domain III of the Japanese Encephalitis virus envelope protein, JBC (2003) PDB 1PJW

Ecoli periplasmic dimeric protein YmgD (unpublished) PDB: 2LRM (dimer form), (monomeric subunit: 2LRV)

NEDD4L HECT domain and its cognate ubiquitin variant NL.1, Molecular Cell (2016) PDB: 5HPK

Rsp5 HECT domain and its cognate ubiquitin variant R5.4, Molecular Cell (2016) PDB: 5HPL

WWP1 HECT domain and its cognate ubiquitin variant P1.1, Molecular Cell (2016) PDB: 5HPS

WWP1 HECT domain, UBCH7 and its cognate ubiquitin variant P2.3, Molecular Cell (2016) PDB: 5HPT