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Yorodumi- PDB-8ebm: Structure of KLHDC2 substrate binding domain bound to KLHDC2's C-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ebm | |||||||||
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Title | Structure of KLHDC2 substrate binding domain bound to KLHDC2's C-degron mimic | |||||||||
Components |
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Keywords | LIGASE / E3 ligase | |||||||||
Function / homology | Function and homology information ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Cul2-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / nuclear membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear body / protein ubiquitination / nucleoplasm / nucleus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | |||||||||
Authors | Scott, D.C. / Schulman, B.A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Mol Cell / Year: 2023 Title: E3 ligase autoinhibition by C-degron mimicry maintains C-degron substrate fidelity. Authors: Daniel C Scott / Moeko T King / Kheewoong Baek / Clifford T Gee / Ravi Kalathur / Jerry Li / Nicholas Purser / Amanda Nourse / Sergio C Chai / Sivaraja Vaithiyalingam / Taosheng Chen / ...Authors: Daniel C Scott / Moeko T King / Kheewoong Baek / Clifford T Gee / Ravi Kalathur / Jerry Li / Nicholas Purser / Amanda Nourse / Sergio C Chai / Sivaraja Vaithiyalingam / Taosheng Chen / Richard E Lee / Stephen J Elledge / Gary Kleiger / Brenda A Schulman / Abstract: E3 ligase recruitment of proteins containing terminal destabilizing motifs (degrons) is emerging as a major form of regulation. How those E3s discriminate bona fide substrates from other proteins ...E3 ligase recruitment of proteins containing terminal destabilizing motifs (degrons) is emerging as a major form of regulation. How those E3s discriminate bona fide substrates from other proteins with terminal degron-like sequences remains unclear. Here, we report that human KLHDC2, a CRL2 substrate receptor targeting C-terminal Gly-Gly degrons, is regulated through interconversion between two assemblies. In the self-inactivated homotetramer, KLHDC2's C-terminal Gly-Ser motif mimics a degron and engages the substrate-binding domain of another protomer. True substrates capture the monomeric CRL2, driving E3 activation by neddylation and subsequent substrate ubiquitylation. Non-substrates such as NEDD8 bind KLHDC2 with high affinity, but its slow on rate prevents productive association with CRL2. Without substrate, neddylated CRL2 assemblies are deactivated via distinct mechanisms: the monomer by deneddylation and the tetramer by auto-ubiquitylation. Thus, substrate specificity is amplified by KLHDC2 self-assembly acting like a molecular timer, where only bona fide substrates may bind before E3 ligase inactivation. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ebm.cif.gz | 276.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ebm.ent.gz | 219.2 KB | Display | PDB format |
PDBx/mmJSON format | 8ebm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/8ebm ftp://data.pdbj.org/pub/pdb/validation_reports/eb/8ebm | HTTPS FTP |
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-Related structure data
Related structure data | 8eblC 8ebnC 6do2S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 39764.422 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KLHDC2, HCA33 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y2U9 #2: Protein/peptide | Mass: 1269.261 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.98 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 8-12% PEG3350, 0.2M NaSCN, 0.1 M Bis-Tris Propane, 5 nM Hexamine cobalt (III) chloride, pH = 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 25, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.58→50 Å / Num. obs: 90061 / % possible obs: 97.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 20.89 Å2 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.046 / Rrim(I) all: 0.084 / Χ2: 2.176 / Net I/σ(I): 11.1 / Num. measured all: 296998 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6DO2 Resolution: 1.58→39.41 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 25.7 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 59.28 Å2 / Biso mean: 27.1283 Å2 / Biso min: 11.11 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.58→39.41 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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