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- PDB-9jni: KCMF1 Zn-coordinating domains with RCKG peptide (Sulfonic Cysteine) -

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Basic information

Entry
Database: PDB / ID: 9jni
TitleKCMF1 Zn-coordinating domains with RCKG peptide (Sulfonic Cysteine)
Components
  • ARG-OCS-LYS-GLY
  • E3 ubiquitin-protein ligase KCMF1
KeywordsPEPTIDE BINDING PROTEIN / Complex / ZZ-domain / C2H2 Zn-finger domain / KCMF1 / Arg/N-degon pathway
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsYang, W.S. / Shin, J.S. / Song, H.K.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2020R1A2C3008285 Korea, Republic Of
National Research Foundation (NRF, Korea)2021M3A9I4030068 Korea, Republic Of
National Research Foundation (NRF, Korea)2022M3A9G8082638 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
DepositionSep 23, 2024Deposition 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
B: ARG-OCS-LYS-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3136
Polymers14,0522
Non-polymers2624
Water59433
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.592, 97.592, 97.592
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number212
Space group name H-MP4332
Space group name HallP4acd2ab3
Symmetry operation#1: x,y,z
#2: x+3/4,-z+3/4,y+1/4
#3: x+1/4,z+3/4,-y+3/4
#4: z+1/4,y+3/4,-x+3/4
#5: -z+3/4,y+1/4,x+3/4
#6: -y+3/4,x+1/4,z+3/4
#7: y+3/4,-x+3/4,z+1/4
#8: z,x,y
#9: y,z,x
#10: -y+1/2,-z,x+1/2
#11: z+1/2,-x+1/2,-y
#12: -y,z+1/2,-x+1/2
#13: -z+1/2,-x,y+1/2
#14: -z,x+1/2,-y+1/2
#15: y+1/2,-z+1/2,-x
#16: x+1/2,-y+1/2,-z
#17: -x,y+1/2,-z+1/2
#18: -x+1/2,-y,z+1/2
#19: y+1/4,x+3/4,-z+3/4
#20: -y+1/4,-x+1/4,-z+1/4
#21: z+3/4,-y+3/4,x+1/4
#22: -z+1/4,-y+1/4,-x+1/4
#23: -x+3/4,z+1/4,y+3/4
#24: -x+1/4,-z+1/4,-y+1/4
Components on special symmetry positions
IDModelComponents
11A-514-

HOH

21A-533-

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: 13539.088 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-OCS-LYS-GLY


Mass: 512.581 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#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.: 33 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 55.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES, pH 7.0 1 M Magnesium chloride hexahydrate 20 % w/v PEG 6000 10 % v/v Ethylene glycol

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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 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28259 Å / Relative weight: 1
ReflectionResolution: 1.92→29.43 Å / Num. obs: 12643 / % possible obs: 99.69 % / Redundancy: 75.9 % / Biso Wilson estimate: 39.61 Å2 / CC1/2: 1 / Net I/σ(I): 38.1
Reflection shellResolution: 1.92→1.989 Å / Num. unique obs: 1204 / CC1/2: 0.733

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Processing

Software
NameVersionClassification
PHENIX1.18rc7_3834refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→29.43 Å / SU ML: 0.2052 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.7166
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2293 2298 10.04 %
Rwork0.1974 20587 -
obs0.2005 12642 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.11 Å2
Refinement stepCycle: LAST / Resolution: 1.92→29.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms938 0 4 33 975
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0129958
X-RAY DIFFRACTIONf_angle_d1.43541296
X-RAY DIFFRACTIONf_chiral_restr0.0669139
X-RAY DIFFRACTIONf_plane_restr0.0094170
X-RAY DIFFRACTIONf_dihedral_angle_d25.5835342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.960.32771380.30061266X-RAY DIFFRACTION95.84
1.96-2.010.3121370.26141270X-RAY DIFFRACTION100
2.01-2.060.26241500.24011302X-RAY DIFFRACTION100
2.06-2.110.23211420.23841277X-RAY DIFFRACTION100
2.11-2.180.28651450.23261274X-RAY DIFFRACTION100
2.18-2.250.23291450.20531302X-RAY DIFFRACTION100
2.25-2.330.21611420.20611300X-RAY DIFFRACTION100
2.33-2.420.22771430.20781281X-RAY DIFFRACTION100
2.42-2.530.25741390.20491295X-RAY DIFFRACTION100
2.53-2.660.27271480.19971279X-RAY DIFFRACTION100
2.66-2.830.21261440.20751290X-RAY DIFFRACTION100
2.83-3.050.20951460.19941284X-RAY DIFFRACTION100
3.05-3.350.26991410.20521288X-RAY DIFFRACTION100
3.36-3.830.23531420.17851295X-RAY DIFFRACTION100
3.84-4.830.17461470.17031291X-RAY DIFFRACTION100
4.84-29.430.23531490.19861293X-RAY DIFFRACTION100

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