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Open data
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Basic information
| Entry | Database: PDB / ID: 9d1i | ||||||
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| Title | Structure of Ubiquitin bound to KLHDC3-EloB/C | ||||||
Components |
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Keywords | LIGASE / KLHDC3 / Ubiquitin / C-degron / Cullin-RING / E3 | ||||||
| Function / homology | Function and homology informationXBP1(S) activates chaperone genes / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / target-directed miRNA degradation / elongin complex / hypothalamus gonadotrophin-releasing hormone neuron development / reciprocal meiotic recombination / female meiosis I / VCB complex / positive regulation of protein monoubiquitination / Cul5-RING ubiquitin ligase complex ...XBP1(S) activates chaperone genes / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / target-directed miRNA degradation / elongin complex / hypothalamus gonadotrophin-releasing hormone neuron development / reciprocal meiotic recombination / female meiosis I / VCB complex / positive regulation of protein monoubiquitination / Cul5-RING ubiquitin ligase complex / fat pad development / mitochondrion transport along microtubule / Cul2-RING ubiquitin ligase complex / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / ubiquitin-like ligase-substrate adaptor activity / Formation of HIV elongation complex in the absence of HIV Tat / energy homeostasis / RNA Polymerase II Transcription Elongation / regulation of neuron apoptotic process / Formation of RNA Pol II elongation complex / neuron projection morphogenesis / regulation of proteasomal protein catabolic process / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / RNA Polymerase II Pre-transcription Events / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Pexophagy / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / positive regulation of protein ubiquitination / transcription corepressor binding / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / TCF dependent signaling in response to WNT / APC/C:Cdc20 mediated degradation of Securin / regulation of mitochondrial membrane potential / Regulation of NF-kappa B signaling / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Asymmetric localization of PCP proteins / activated TAK1 mediates p38 MAPK activation / Ubiquitin-dependent degradation of Cyclin D Similarity search - Function | ||||||
| Biological species | Homo sapiens (human) | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Schulman, B.A. / Scott, D.C. | ||||||
| Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2024Title: Structural basis for C-degron selectivity across KLHDCX family E3 ubiquitin ligases. Authors: Daniel C Scott / Sagar Chittori / Nicholas Purser / Moeko T King / Samuel A Maiwald / Kelly Churion / Amanda Nourse / Chan Lee / Joao A Paulo / Darcie J Miller / Stephen J Elledge / J Wade ...Authors: Daniel C Scott / Sagar Chittori / Nicholas Purser / Moeko T King / Samuel A Maiwald / Kelly Churion / Amanda Nourse / Chan Lee / Joao A Paulo / Darcie J Miller / Stephen J Elledge / J Wade Harper / Gary Kleiger / Brenda A Schulman / ![]() Abstract: Specificity of the ubiquitin-proteasome system depends on E3 ligase-substrate interactions. Many such pairings depend on E3 ligases binding to peptide-like sequences - termed N- or C-degrons - at the ...Specificity of the ubiquitin-proteasome system depends on E3 ligase-substrate interactions. Many such pairings depend on E3 ligases binding to peptide-like sequences - termed N- or C-degrons - at the termini of substrates. However, our knowledge of structural features distinguishing closely related C-degron substrate-E3 pairings is limited. Here, by systematically comparing ubiquitylation activities towards a suite of common model substrates, and defining interactions by biochemistry, crystallography, and cryo-EM, we reveal principles of C-degron recognition across the KLHDCX family of Cullin-RING ligases (CRLs). First, a motif common across these E3 ligases anchors a substrate's C-terminus. However, distinct locations of this C-terminus anchor motif in different blades of the KLHDC2, KLHDC3, and KLHDC10 β-propellers establishes distinct relative positioning and molecular environments for substrate C-termini. Second, our structural data show KLHDC3 has a pre-formed pocket establishing preference for an Arg or Gln preceding a C-terminal Gly, whereas conformational malleability contributes to KLHDC10's recognition of varying features adjacent to substrate C-termini. Finally, additional non-consensus interactions, mediated by C-degron binding grooves and/or by distal propeller surfaces and substrate globular domains, can substantially impact substrate binding and ubiquitylatability. Overall, the data reveal combinatorial mechanisms determining specificity and plasticity of substrate recognition by KLDCX-family C-degron E3 ligases. | ||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 9d1i.cif.gz | 280 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb9d1i.ent.gz | 222.4 KB | Display | PDB format |
| PDBx/mmJSON format | 9d1i.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/9d1i ftp://data.pdbj.org/pub/pdb/validation_reports/d1/9d1i | HTTPS FTP |
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-Related structure data
| Related structure data | ![]() 9d1yC ![]() 9d1zC ![]() 9d8pC C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
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Assembly
| Deposited unit | ![]()
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| Unit cell |
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| Components on special symmetry positions |
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Components
-Protein , 4 types, 4 molecules ABCD
| #1: Protein | Mass: 43245.082 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KLHDC3, PEAS / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9BQ90 |
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| #2: Protein | Mass: 11748.406 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ELOB, TCEB2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q15370 |
| #3: Protein | Mass: 13855.611 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ELOC, TCEB1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q15369 |
| #4: Protein | Mass: 8576.831 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: ![]() |
-Non-polymers , 2 types, 614 molecules 


| #5: Chemical | ChemComp-GOL / |
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| #6: Water | ChemComp-HOH / |
-Details
| Has ligand of interest | Y |
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| Has protein modification | Y |
-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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Sample preparation
| Crystal | Density Matthews: 3.45 Å3/Da / Density % sol: 64.37 % |
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| Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 10%PEG5KMME, 0.1M HEPES pH=7.0, 5% Tascsimate pH=7.0 |
-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: 0.97872 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Apr 27, 2022 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Reflection | Resolution: 2→50 Å / Num. obs: 72013 / % possible obs: 99.8 % / Redundancy: 8.8 % / CC1/2: 0.984 / CC star: 0.996 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.035 / Rrim(I) all: 0.107 / Χ2: 1.786 / Net I/σ(I): 4.5 / Num. measured all: 632350 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Reflection shell | Diffraction-ID: 1
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→38.29 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 18.07 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refinement step | Cycle: LAST / Resolution: 2→38.29 Å
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| Refine LS restraints |
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| LS refinement shell |
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| Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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| Refinement TLS group |
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Movie
Controller
About Yorodumi




Homo sapiens (human)
X-RAY DIFFRACTION
United States, 1items
Citation





PDBj
























Trichoplusia ni (cabbage looper)