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- PDB-29ui: FAM72A-UNG2 bound to the discoidin domain of substrate receptor MKLN1 -

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Basic information

Entry
Database: PDB / ID: 29ui
TitleFAM72A-UNG2 bound to the discoidin domain of substrate receptor MKLN1
Components
  • Muskelin
  • Protein FAM72A
  • Uracil-DNA glycosylase
KeywordsLIGASE / complex
Function / homology
Function and homology information


postsynaptic specialization membrane of symmetric synapse / postsynaptic endosome membrane / neurotransmitter receptor transport postsynaptic membrane to endosome / GID complex / base-excision repair, AP site formation via deaminated base removal / regulation of receptor internalization / uracil-DNA glycosylase / depyrimidination / Displacement of DNA glycosylase by APEX1 / uracil DNA N-glycosylase activity ...postsynaptic specialization membrane of symmetric synapse / postsynaptic endosome membrane / neurotransmitter receptor transport postsynaptic membrane to endosome / GID complex / base-excision repair, AP site formation via deaminated base removal / regulation of receptor internalization / uracil-DNA glycosylase / depyrimidination / Displacement of DNA glycosylase by APEX1 / uracil DNA N-glycosylase activity / single strand break repair / ribosomal small subunit binding / cell-matrix adhesion / ruffle / ubiquitin ligase complex / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Regulation of pyruvate metabolism / Chromatin modifications during the maternal to zygotic transition (MZT) / regulation of cell shape / GABA-ergic synapse / base-excision repair / actin cytoskeleton organization / cell cortex / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / postsynapse / negative regulation of apoptotic process / synapse / signal transduction / protein homodimerization activity / mitochondrion / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Protein FAM72 / Yippee homolog 2 zinc finger protein / Muskelin, N-terminal / : / Muskelin N-terminus / : / Attractin/LZTR1 beta-propeller / CTLH, C-terminal LisH motif / C-terminal to LisH (CTLH) motif profile. / Uracil-DNA glycosylase family 1 ...Protein FAM72 / Yippee homolog 2 zinc finger protein / Muskelin, N-terminal / : / Muskelin N-terminus / : / Attractin/LZTR1 beta-propeller / CTLH, C-terminal LisH motif / C-terminal to LisH (CTLH) motif profile. / Uracil-DNA glycosylase family 1 / Uracil DNA glycosylase superfamily / UreE urease accessory protein, C-terminal domain / Galactose oxidase/kelch, beta-propeller / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Lissencephaly type-1-like homology motif / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Kelch motif / Kelch repeat type 1 / Kelch-type beta propeller / Galactose-binding-like domain superfamily
Similarity search - Domain/homology
Uracil-DNA glycosylase / Protein FAM72A / Muskelin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsSepic, S. / Du, J. / Prabu, J.R. / Schulman, B.A.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nat Commun / Year: 2026
Title: Multimodal substrate recruitment enables CTLH E3 ligase to target acetylated N-, C-, and internal degrons.
Authors: Sara Sepic / Karthik V Gottemukkala / Jiale Du / Samuel A Maiwald / Jakub Chrustowicz / Eleftheria C Papadopoulou / Luca J Stier / Susanne von Gronau / Brenda A Schulman /
Abstract: The GID/CTLH family of E3 ubiquitin ligases employs several substrate receptor subunits that recruit distinct degrons, but the substrate recognition mechanisms of the CTLH assembly have largely ...The GID/CTLH family of E3 ubiquitin ligases employs several substrate receptor subunits that recruit distinct degrons, but the substrate recognition mechanisms of the CTLH assembly have largely remained elusive. Here, we reconstitute CTLH-dependent ubiquitylation of three biochemically distinct substrates - MKLN1 itself, ZMYND19, and FAM72A-recruited UNG2, and determine cryo-EM structures of each substrate bound to MKLN1. The structures reveal how MKLN1's discoidin and Kelch β-propeller domains engage substrates through multivalent contacts. MKLN1 recruits itself through discoidin-Kelch interactions between MKLN1 dimers, forming an assembly that competes with other substrates. ZMYND19 and FAM72A each bind to MKLN1 through loops engaging the discoidin trench domain while their C-terminal Arg residues engage the MKLN1 Kelch central channel, identifying MKLN1 as an Arg/C-degron receptor. The acetylated N-terminus of UNG2 is positioned within a Y-shaped tunnel of FAM72A, defining an adaptor-mediated Ac/N-degron recognition mechanism. Thus, our data reveal how combinatorial deployment of MKLN1 discoidin and Kelch domains enable a single receptor subunit to recognize a diverse substrate repertoire, adding to a complex picture of degron recognition across the GID/CTLH family.
History
DepositionApr 8, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 28, 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

Downloads & links

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Assembly

Deposited unit
B: Protein FAM72A
D: Uracil-DNA glycosylase
C: Uracil-DNA glycosylase
F: Muskelin
E: Muskelin
A: Protein FAM72A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)272,30610
Polymers272,0456
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Protein FAM72A / Latent membrane protein 1-induced protein / LMP1-induced protein / LMPIP


Mass: 16636.326 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAM72A, UGENE / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5TYM5
#2: Protein Uracil-DNA glycosylase / UDG


Mass: 34722.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UNG, DGU, UNG1, UNG15 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P13051, uracil-DNA glycosylase
#3: Protein Muskelin


Mass: 84663.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MKLN1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9UL63
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: Structure of FAM72A-UNG2 bound to MKLN1 discoidin domain
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2600 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX2.0_5936model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1117642 / Symmetry type: POINT
RefinementHighest resolution: 3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0036881
ELECTRON MICROSCOPYf_angle_d0.4959312
ELECTRON MICROSCOPYf_dihedral_angle_d3.696890
ELECTRON MICROSCOPYf_chiral_restr0.041024
ELECTRON MICROSCOPYf_plane_restr0.0041176

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