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- PDB-9upz: KCMF1 Zn-coordinating domains with RTGG peptide -

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Basic information

Entry
Database: PDB / ID: 9upz
TitleKCMF1 Zn-coordinating domains with RTGG peptide
Components
  • ARG-THR-GLY-GLY
  • E3 ubiquitin-protein ligase KCMF1
KeywordsLIGASE / Complex / ZZ-domain / C2H2 Zn-finger domain / KCMF1 / Arg/N-degron pathway / PEPTIDE BINDING PROTEIN
Function / homology
Function and homology information


negative regulation of HRI-mediated signaling / synaptic signaling / protein K63-linked ubiquitination / protein K48-linked ubiquitination / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / late endosome / response to oxidative stress / ubiquitin-dependent protein catabolic process / ficolin-1-rich granule lumen ...negative regulation of HRI-mediated signaling / synaptic signaling / protein K63-linked ubiquitination / protein K48-linked ubiquitination / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / late endosome / response to oxidative stress / ubiquitin-dependent protein catabolic process / ficolin-1-rich granule lumen / proteasome-mediated ubiquitin-dependent protein catabolic process / lysosome / synapse / Neutrophil degranulation / extracellular region / zinc ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Drought induced 19 protein type, zinc-binding domain / Drought induced 19 protein (Di19), zinc-binding / : / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / zinc finger ...Drought induced 19 protein type, zinc-binding domain / Drought induced 19 protein (Di19), zinc-binding / : / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2-type
Similarity search - Domain/homology
E3 ubiquitin-protein ligase KCMF1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsLee, J.Y. / Shin, J.S. / Song, H.K.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)RS-2020-NR049540 Korea, Republic Of
National Research Foundation (NRF, Korea)RS-2021-NR056577 Korea, Republic Of
National Research Foundation (NRF, Korea)RS-2022-NR067411 Korea, Republic Of
CitationJournal: Science / Year: 2025
Title: Architecture of the UBR4 complex, a giant E4 ligase central to eukaryotic protein quality control.
Authors: Daniel B Grabarczyk / Julian F Ehrmann / Paul Murphy / Woo Seok Yang / Robert Kurzbauer / Lillie E Bell / Luiza Deszcz / Jana Neuhold / Alexander Schleiffer / Alexandra Shulkina / Juyeon Lee ...Authors: Daniel B Grabarczyk / Julian F Ehrmann / Paul Murphy / Woo Seok Yang / Robert Kurzbauer / Lillie E Bell / Luiza Deszcz / Jana Neuhold / Alexander Schleiffer / Alexandra Shulkina / Juyeon Lee / Jin Seok Shin / Anton Meinhart / Gijs A Versteeg / Eszter Zavodszky / Hyun Kyu Song / Ramanujan S Hegde / Tim Clausen /
Abstract: Eukaryotic cells have evolved sophisticated quality control mechanisms to eliminate aggregation-prone proteins that compromise cellular health. Central to this defense is the ubiquitin-proteasome ...Eukaryotic cells have evolved sophisticated quality control mechanisms to eliminate aggregation-prone proteins that compromise cellular health. Central to this defense is the ubiquitin-proteasome system, where UBR4 acts as an essential E4 ubiquitin ligase, amplifying degradation marks on defective proteins. Cryo-electron microscopy analysis of UBR4 in complex with its cofactors KCMF1 and CALM1 reveals a massive 1.3-megadalton ring structure, featuring a central substrate-binding arena and flexibly attached catalytic units. Our structure shows how UBR4 binds substrate and extends lysine-48-specific ubiquitin chains. Efficient substrate targeting depends on both preubiquitination and specific N-degrons, with KCMF1 acting as a key substrate filter. The architecture of the E4 megacomplex is conserved across eukaryotes, but species-specific adaptations allow UBR4 to perform its precisely tuned quality control function in diverse cellular environments.
History
DepositionApr 29, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase KCMF1
D: ARG-THR-GLY-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1646
Polymers13,9032
Non-polymers2624
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area520 Å2
ΔGint3 kcal/mol
Surface area7190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.347, 97.347, 97.347
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number212
Space group name H-MP4332
Space group name HallP4acd2ab3
Components on special symmetry positions
IDModelComponents
11A-311-

HOH

21A-331-

HOH

31A-334-

HOH

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Components

#1: Protein E3 ubiquitin-protein ligase KCMF1 / FGF-induced in gastric cancer / Potassium channel modulatory factor / PCMF / ZZ-type zinc finger- ...FGF-induced in gastric cancer / Potassium channel modulatory factor / PCMF / ZZ-type zinc finger-containing protein 1


Mass: 13569.157 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCMF1, FIGC, ZZZ1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9P0J7, RING-type E3 ubiquitin transferase
#2: Protein/peptide ARG-THR-GLY-GLY


Mass: 333.365 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.4 % / Description: cubic
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.3 M Magnesium chloride hexahydrate, 0.3M Calcium chloride dihydrate, 12.5% MPD, 12.5% PEG1000, 12.5% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.28259 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 8, 2025
RadiationMonochromator: ouble crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28259 Å / Relative weight: 1
ReflectionResolution: 1.71→50 Å / Num. obs: 17490 / % possible obs: 99.53 % / Redundancy: 31.2 % / Biso Wilson estimate: 22.63 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1609 / Rpim(I) all: 0.02888 / Rrim(I) all: 0.1636 / Net I/σ(I): 23.61
Reflection shellResolution: 1.71→1.77 Å / Redundancy: 16.7 % / Rmerge(I) obs: 2.464 / Mean I/σ(I) obs: 1.52 / Num. unique obs: 1687 / CC1/2: 0.69 / CC star: 0.904 / Rpim(I) all: 0.6033 / Rrim(I) all: 2.539 / % possible all: 98.77

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX(1.20.1_4487)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9JNI

9jni


Resolution: 1.71→34.42 Å / SU ML: 0.191 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.003
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2357 1742 10 %
Rwork0.2064 15672 -
obs0.2094 17414 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.36 Å2
Refinement stepCycle: LAST / Resolution: 1.71→34.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms958 0 4 34 996
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0109978
X-RAY DIFFRACTIONf_angle_d1.171322
X-RAY DIFFRACTIONf_chiral_restr0.0571144
X-RAY DIFFRACTIONf_plane_restr0.0152174
X-RAY DIFFRACTIONf_dihedral_angle_d6.062141
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.770.29711420.26331283X-RAY DIFFRACTION98.75
1.77-1.820.28841390.24321241X-RAY DIFFRACTION99.28
1.82-1.890.25881410.24731279X-RAY DIFFRACTION98.82
1.89-1.960.3161420.21481273X-RAY DIFFRACTION99.51
1.96-2.050.21281420.20141280X-RAY DIFFRACTION99.58
2.05-2.160.23431430.19961285X-RAY DIFFRACTION99.65
2.16-2.30.2161440.21081294X-RAY DIFFRACTION99.79
2.3-2.470.24841440.20291297X-RAY DIFFRACTION99.79
2.47-2.720.19451460.20021310X-RAY DIFFRACTION99.86
2.72-3.110.22091460.20141328X-RAY DIFFRACTION99.86
3.12-3.920.24951510.19831346X-RAY DIFFRACTION100
3.93-34.420.22751620.20351456X-RAY DIFFRACTION99.81

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